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Difficulty fully reproducing example.sh #33

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mmore500 opened this issue Dec 31, 2023 · 9 comments
Closed

Difficulty fully reproducing example.sh #33

mmore500 opened this issue Dec 31, 2023 · 9 comments

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@mmore500
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Working to reproduce example.sh. I've gotten part way but seem to be running into some kind of server error. I've made some minor modifications along the way to allow example.sh to be run without hardcoding and to provide specific troubleshooting instructions where I've been able to figure them out. I've opened the work I've done on example.sh so far as PR #32.

Here is my log when trying to run example.sh, with private information redacted.


----------------------------------------------------------------------------------------------
Check server status:
----------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as XXXXXXXXXXXXXXXX

----------------------------------------------------------------------------------------------
List all users:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
* processing: http://localhost:8080/users?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 

  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:46:52 GMT
< Connection: close
< 
{ [36 bytes data]

100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all taxa
----------------------------------------------------------------------------------------------
Taxa:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}

----------------------------------------------------------------------------------------------
Create taxon:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
} [68 bytes data]

100    68    0     0  100    68      0     56  0:00:01  0:00:01 --:--:--    56
100    68    0     0  100    68      0     30  0:00:02  0:00:02 --:--:--    30< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:46:57 GMT
< Connection: close
< 
{ [36 bytes data]

100    98    0    30  100    68     12     28  0:00:02  0:00:02 --:--:--    41
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all loci:
----------------------------------------------------------------------------------------------
Loci:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}

----------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/loci/ftsZ?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:02 GMT
< Connection: close
< 
{ [36 bytes data]

100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Create locus:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus1?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    55
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:04 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     27  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus2?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    54
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:07 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     27  0:00:02  0:00:02 --:--:--    40
100    96    0    30  100    66     12     27  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus3?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    54
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:09 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     27  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus4?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    54
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     28  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus5?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    54
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:14 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     28  0:00:02  0:00:02 --:--:--    40
100    96    0    30  100    66     12     28  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus6?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    54
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:16 GMT
< Connection: close
< 
{ [41 bytes data]

100    96    0    30  100    66     12     27  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus7?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]

100    66    0     0  100    66      0     54  0:00:01  0:00:01 --:--:--    55
100    66    0     0  100    66      0     29  0:00:02  0:00:02 --:--:--    29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:18 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66     12     28  0:00:02  0:00:02 --:--:--    40
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Load alleles:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus1/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------c738321f324ad367
> 
} [234 bytes data]
* We are completely uploaded and fine

100   234    0     0  100   234      0   1166 --:--:-- --:--:-- --:--:--  1164
100   234    0     0  100   234      0    194  0:00:01  0:00:01 --:--:--   194
100   234    0     0  100   234      0    106  0:00:02  0:00:02 --:--:--   106< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:21 GMT
< Connection: close
< 
{ [36 bytes data]

100   264    0    30  100   234     12     99  0:00:02  0:00:02 --:--:--   111
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus2/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------70b2c8ef1cf50a56
> 
} [276 bytes data]
* We are completely uploaded and fine

100   276    0     0  100   276      0    229  0:00:01  0:00:01 --:--:--   229
100   276    0     0  100   276      0    125  0:00:02  0:00:02 --:--:--   125< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:23 GMT
< Connection: close
< 
{ [36 bytes data]

100   306    0    30  100   276     12    117  0:00:02  0:00:02 --:--:--   129
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus3/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------c86ed064a617e4e0
> 
} [318 bytes data]
* We are completely uploaded and fine

100   318    0     0  100   318      0    264  0:00:01  0:00:01 --:--:--   264
100   318    0     0  100   318      0    144  0:00:02  0:00:02 --:--:--   144< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:26 GMT
< Connection: close
< 
{ [36 bytes data]

100   348    0    30  100   318     12    134  0:00:02  0:00:02 --:--:--   147
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus4/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------bf0637ad20dc1fcc
> 
} [404 bytes data]
* We are completely uploaded and fine

100   404    0     0  100   404      0   2013 --:--:-- --:--:-- --:--:--  2009
100   404    0     0  100   404      0    336  0:00:01  0:00:01 --:--:--   336
100   404    0     0  100   404      0    183  0:00:02  0:00:02 --:--:--   183< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:28 GMT
< Connection: close
< 
{ [36 bytes data]

100   434    0    30  100   404     12    170  0:00:02  0:00:02 --:--:--   183
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus5/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------7a9201d078966e11
> 
} [447 bytes data]
* We are completely uploaded and fine

100   447    0     0  100   447      0    372  0:00:01  0:00:01 --:--:--   372
100   447    0     0  100   447      0    202  0:00:02  0:00:02 --:--:--   202< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:30 GMT
< Connection: close
< 
{ [36 bytes data]

100   477    0    30  100   447     12    189  0:00:02  0:00:02 --:--:--   202
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus6/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------8b536850a85edf27
> 
} [362 bytes data]
* We are completely uploaded and fine

100   362    0     0  100   362      0    301  0:00:01  0:00:01 --:--:--   301
100   362    0     0  100   362      0    164  0:00:02  0:00:02 --:--:--   164< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:33 GMT
< Connection: close
< 
{ [41 bytes data]

100   392    0    30  100   362     12    153  0:00:02  0:00:02 --:--:--   166
100   392    0    30  100   362     12    153  0:00:02  0:00:02 --:--:--   166
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus7/alleles/files?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------b3ffd1349a1ccd95
> 
} [491 bytes data]
* We are completely uploaded and fine

100   491    0     0  100   491      0    408  0:00:01  0:00:01 --:--:--   408
100   491    0     0  100   491      0    222  0:00:02  0:00:02 --:--:--   222< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:35 GMT
< Connection: close
< 
{ [36 bytes data]

100   521    0    30  100   491     12    208  0:00:02  0:00:02 --:--:--   221
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List alleles:
----------------------------------------------------------------------------------------------
Alleles[locus1]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus2]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus3]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus4]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus5]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus6]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Alleles[locus7]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
An allele:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}

----------------------------------------------------------------------------------------------
List all schemas:
----------------------------------------------------------------------------------------------
Schemas:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}
Schema:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}

----------------------------------------------------------------------------------------------
Create schema:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/schemas/mlst7?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
} [199 bytes data]

100   199    0     0  100   199      0    165  0:00:01  0:00:01 --:--:--   165
100   199    0     0  100   199      0     90  0:00:02  0:00:02 --:--:--    90< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:48:01 GMT
< Connection: close
< 
{ [36 bytes data]

100   229    0    30  100   199     12     84  0:00:02  0:00:02 --:--:--    96
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all projects:
----------------------------------------------------------------------------------------------
Projects:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100    30    0    30    0     0     12      0 --:--:--  0:00:02 --:--:--    12
{"message":"/problems/server"}

----------------------------------------------------------------------------------------------
Create project:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/projects?provider=google
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
} [152 bytes data]

100   152    0     0  100   152      0    757 --:--:-- --:--:-- --:--:--   756
100   152    0     0  100   152      0    126  0:00:01  0:00:01 --:--:--   126
100   152    0     0  100   152      0     69  0:00:02  0:00:02 --:--:--    68< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:48:06 GMT
< Connection: close
< 
{ [36 bytes data]

100   182    0    30  100   152     12     64  0:00:02  0:00:02 --:--:--    77
* Closing connection
{"message":"/problems/server"}Error: PROJECT is not defined. Please follow these steps:

# TODO
#
# Then, execute
#
# > export PROJECT="YOUR_PROJECT_ID"
#
# and run this script again.
@mmore500
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Contributor Author

The issue seems to be related to the {"message":"/problems/server"} coming through on most of the curl requests. I'm not sure quite what the issue is, because the curl requests seem to be otherwise succeeding.

To set up, I went to https://developers.google.com/oauthplayground/ to receive a token and then performed

export TOKEN="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
export USER_ID="XXXXXXXXXXXXXXX"
./configure.sh
./docker/build-docker.sh
./docker/start-docker.sh
./scripts/example/examples.sh

Here is my environment configuration.

mmore500@fedora 
--------------- 
OS: Fedora Linux 39 (Workstation Edition) x86_64 
Host: 20U9005MUS ThinkPad X1 Carbon Gen 8 
Kernel: 6.6.6-200.fc39.x86_64 
Uptime: 5 days, 1 hour, 48 mins 
Packages: 6989 (rpm), 19 (flatpak) 
Shell: zsh 5.9 
Resolution: 1920x1080 
DE: GNOME 45.2 
WM: Mutter 
WM Theme: Nordic 
Theme: Nordic [GTK2/3] 
Icons: Adwaita [GTK2/3] 
Terminal: tmux 
CPU: Intel i7-10510U (8) @ 4.900GHz 
GPU: Intel CometLake-U GT2 [UHD Graphics] 
Memory: 11597MiB / 15649MiB

I have buildx v0.12.0, docker version 24.0.5, and Java version

openjdk 17.0.9 2023-10-17
OpenJDK Runtime Environment (Red_Hat-17.0.9.0.9-2) (build 17.0.9+9)
OpenJDK 64-Bit Server VM (Red_Hat-17.0.9.0.9-2) (build 17.0.9+9, mixed mode, sharing)

@mmore500
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Contributor Author

Note that I have not defined PROJECT or DATASET environment variables, because I am not able to get those keys out of the current output.

@cvaz
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Collaborator

cvaz commented Dec 31, 2023 •
edited
Loading

Thank you for your feedback and analysis. The script example.sh was not intended to run in a single shot. I improved it so that it can be ran that way, namely PROJECT and DATASET are now defined automatically. I also changed the initialisation of the docker containers to allow them to stabilize before loading initial data and schema.

After looking to your log, it seems to me that the connection to neo4j database in your environment is not at localhost. Containers are named in our scripts, and hence in some environments the connection string must be adapted. Just take a look at application.properties, namely at the first commented line.

@cvaz cvaz closed this as completed Dec 31, 2023
@mmore500
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Contributor Author

mmore500 commented Feb 15, 2024 •
edited
Loading

Hi --

Could I get some more guidance on resolving the {"message":"/problems/server"}? I am still running into this issue locally. I was able to reproduce it on <shell.cloud.google.com>. (This service is free, so you should hopefully be able to access the same environment.) Here are the sequence of commands and outputs I ran on Google CloudShell.

  • export TOKEN=XXXXXXXXXX
  • export USER_ID=XXXXXXXXX
  • git clone https://github.com/phyloviz/phyloDB
  • cd phyloDB
  • ./scripts/init/make_init_data.cypher.sh
  • cat scripts/init/init_data.cypher
    • this file is initialized as expected
  • ./configure.sh
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:c6ec5ebf3afb07af0fc037cd2f3000f6b596f1b2c2b9441e532a055499acc0a2
  • ./docker/start_docker.sh
./docker/start-docker.sh 
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
  • ./scripts/example/example.sh

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as [email protected]

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    30    0    30    0     0    697      0 --:--:-- --:--:-- --:--:--   697
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    714      0 --:--:-- --:--:-- --:--:--   731
{"message":"/problems/server"}

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
} [68 bytes data]
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    98    0    30  100    68    576   1307 --:--:-- --:--:-- --:--:--  1884
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    600      0 --:--:-- --:--:-- --:--:--   588
100    30    0    30    0     0    600      0 --:--:-- --:--:-- --:--:--   588
{"message":"/problems/server"}

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    30    0    30    0     0    545      0 --:--:-- --:--:-- --:--:--   545
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    555   1222 --:--:-- --:--:-- --:--:--  1811
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    576   1269 --:--:-- --:--:-- --:--:--  1882
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    588   1294 --:--:-- --:--:-- --:--:--  1882
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    666   1466 --:--:-- --:--:-- --:--:--  2181
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    535   1178 --:--:-- --:--:-- --:--:--  1714
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    483   1064 --:--:-- --:--:-- --:--:--  1548
* Closing connection 0
{"message":"/problems/server"}  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
} [66 bytes data]
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100    96    0    30  100    66    434    956 --:--:-- --:--:-- --:--:--  1391
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------40aa8ffe2c21863d
> 
} [234 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:11 GMT
< Connection: close
< 
{ [36 bytes data]

100   264    0    30  100   234    500   3900 --:--:-- --:--:-- --:--:--  4400
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------9f343471fdf7f29f
> 
} [276 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   306    0    30  100   276    600   5520 --:--:-- --:--:-- --:--:--  6120
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------1361358bcca40fc1
> 
} [318 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   348    0    30  100   318    526   5578 --:--:-- --:--:-- --:--:--  6105
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------a7aa69bb2f07e781
> 
} [404 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   434    0    30  100   404    588   7921 --:--:-- --:--:-- --:--:--  8509
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------bc99496694300aee
> 
} [447 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   477    0    30  100   447    588   8764 --:--:-- --:--:-- --:--:--  9540
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------40388839e44ca508
> 
} [362 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   392    0    30  100   362    638   7702 --:--:-- --:--:-- --:--:--  8166
100   392    0    30  100   362    638   7702 --:--:-- --:--:-- --:--:--  8166
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------ac89aee04c035d77
> 
} [491 bytes data]
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:12 GMT
< Connection: close
< 
{ [36 bytes data]

100   521    0    30  100   491    625  10229 --:--:-- --:--:-- --:--:-- 10854
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    555      0 --:--:-- --:--:-- --:--:--   555
{"message":"/problems/server"}
Alleles[locus2]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    491      0 --:--:-- --:--:-- --:--:--   491
{"message":"/problems/server"}
Alleles[locus3]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    612      0 --:--:-- --:--:-- --:--:--   612
{"message":"/problems/server"}
Alleles[locus4]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    652      0 --:--:-- --:--:-- --:--:--   666
{"message":"/problems/server"}
Alleles[locus5]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    491      0 --:--:-- --:--:-- --:--:--   491
{"message":"/problems/server"}
Alleles[locus6]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    566      0 --:--:-- --:--:-- --:--:--   566
{"message":"/problems/server"}
Alleles[locus7]:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    612      0 --:--:-- --:--:-- --:--:--   625
{"message":"/problems/server"}
An allele:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    517      0 --:--:-- --:--:-- --:--:--   517
{"message":"/problems/server"}

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    508      0 --:--:-- --:--:-- --:--:--   517
{"message":"/problems/server"}
Schema:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    555      0 --:--:-- --:--:-- --:--:--   555
{"message":"/problems/server"}

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
} [199 bytes data]
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:13 GMT
< Connection: close
< 
{ [36 bytes data]

100   229    0    30  100   199    535   3553 --:--:-- --:--:-- --:--:--  4089
* Closing connection 0
{"message":"/problems/server"}
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    30    0    30    0     0    576      0 --:--:-- --:--:-- --:--:--   588
{"message":"/problems/server"}

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
} [152 bytes data]
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Thu, 15 Feb 2024 22:44:13 GMT
< Connection: close
< 
{ [41 bytes data]

100   182    0    30  100   152    625   3166 --:--:-- --:--:-- --:--:--  3791
100   182    0    30  100   152    625   3166 --:--:-- --:--:-- --:--:--  3714
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):
  File "<string>", line 1, in <module>
KeyError: 0

Here is some diagnostic information:

  • sudo apt-get install -y iptables && sudo iptables -L -n
Chain INPUT (policy ACCEPT)
target     prot opt source               destination         

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination         
DOCKER-USER  all  --  0.0.0.0/0            0.0.0.0/0           
DOCKER-ISOLATION-STAGE-1  all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0            ctstate RELATED,ESTABLISHED
DOCKER     all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0            ctstate RELATED,ESTABLISHED
DOCKER     all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           
ACCEPT     all  --  0.0.0.0/0            0.0.0.0/0           

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination         

Chain DOCKER (2 references)
target     prot opt source               destination         
ACCEPT     tcp  --  0.0.0.0/0            172.18.0.2           tcp dpt:8080
ACCEPT     tcp  --  0.0.0.0/0            172.18.0.3           tcp dpt:7687
ACCEPT     tcp  --  0.0.0.0/0            172.18.0.3           tcp dpt:7474

Chain DOCKER-ISOLATION-STAGE-1 (1 references)
target     prot opt source               destination         
DOCKER-ISOLATION-STAGE-2  all  --  0.0.0.0/0            0.0.0.0/0           
DOCKER-ISOLATION-STAGE-2  all  --  0.0.0.0/0            0.0.0.0/0           
RETURN     all  --  0.0.0.0/0            0.0.0.0/0           

Chain DOCKER-ISOLATION-STAGE-2 (2 references)
target     prot opt source               destination         
DROP       all  --  0.0.0.0/0            0.0.0.0/0           
DROP       all  --  0.0.0.0/0            0.0.0.0/0           
RETURN     all  --  0.0.0.0/0            0.0.0.0/0           

Chain DOCKER-USER (1 references)
target     prot opt source               destination         
RETURN     all  --  0.0.0.0/0            0.0.0.0/0
  • before running ./docker/stop-docker.sh: sudo apt-get install -y lsof && sudo lsof -i -P -n
COMMAND    PID     USER   FD   TYPE DEVICE SIZE/OFF NODE NAME
sshd        61     root    3u  IPv4  21000      0t0  TCP *:22 (LISTEN)
sshd        61     root    4u  IPv6  21002      0t0  TCP *:22 (LISTEN)
sshd       295     root    4u  IPv4  22673      0t0  TCP 127.0.0.1:22->127.0.0.1:42504 (ESTABLISHED)
editor-pr  296     root    6u  IPv6  20088      0t0  TCP *:970 (LISTEN)
editor-pr  296     root   11u  IPv6  40557      0t0  TCP 127.0.0.1:970->127.0.0.1:57614 (ESTABLISHED)
editor-pr  296     root   13u  IPv4  40561      0t0  TCP 127.0.0.1:38242->127.0.0.1:3000 (ESTABLISHED)
editor-pr  296     root   15u  IPv6  40565      0t0  TCP 127.0.0.1:970->127.0.0.1:57630 (ESTABLISHED)
editor-pr  296     root   16u  IPv4  40569      0t0  TCP 127.0.0.1:38260->127.0.0.1:3000 (ESTABLISHED)
sshd       313     root    4u  IPv4  20100      0t0  TCP 127.0.0.1:22->127.0.0.1:42518 (ESTABLISHED)
node       326 mmore500   18u  IPv4  21262      0t0  TCP *:3000 (LISTEN)
node       326 mmore500   22u  IPv4  39582      0t0  TCP 127.0.0.1:3000->127.0.0.1:38242 (ESTABLISHED)
sshd       327 mmore500    4u  IPv4  22673      0t0  TCP 127.0.0.1:22->127.0.0.1:42504 (ESTABLISHED)
sshd       327 mmore500    9u  IPv4  21098      0t0  TCP 127.0.0.1:44953 (LISTEN)
sshd       341 mmore500    4u  IPv4  20100      0t0  TCP 127.0.0.1:22->127.0.0.1:42518 (ESTABLISHED)
java      1717 mmore500  237u  IPv4  28514      0t0  TCP 127.0.0.1:43029 (LISTEN)
java      1717 mmore500  239u  IPv4  28520      0t0  UDP *:38310 
java      1717 mmore500  283u  IPv4  26601      0t0  TCP 10.88.0.3:43440->151.101.0.215:443 (CLOSE_WAIT)
java      1717 mmore500  284u  IPv4  26602      0t0  TCP 10.88.0.3:43454->151.101.0.215:443 (CLOSE_WAIT)
java      1717 mmore500  285u  IPv4  28557      0t0  TCP 10.88.0.3:43456->151.101.0.215:443 (CLOSE_WAIT)
docker-pr 2120     root    4u  IPv4  32924      0t0  TCP *:8080 (LISTEN)
docker-pr 2135     root    4u  IPv4  31091      0t0  TCP *:7687 (LISTEN)
docker-pr 2150     root    4u  IPv4  30214      0t0  TCP *:7474 (LISTEN)
node      4125 mmore500   20u  IPv4  42117      0t0  TCP 127.0.0.1:3000->127.0.0.1:38260 (ESTABLISHED)
  • after running ./docker/stop-docker.sh: sudo lsof -i -P -n
COMMAND    PID     USER   FD   TYPE DEVICE SIZE/OFF NODE NAME
sshd        61     root    3u  IPv4  21000      0t0  TCP *:22 (LISTEN)
sshd        61     root    4u  IPv6  21002      0t0  TCP *:22 (LISTEN)
sshd       295     root    4u  IPv4  22673      0t0  TCP 127.0.0.1:22->127.0.0.1:42504 (ESTABLISHED)
editor-pr  296     root    6u  IPv6  20088      0t0  TCP *:970 (LISTEN)
editor-pr  296     root   11u  IPv6  40557      0t0  TCP 127.0.0.1:970->127.0.0.1:57614 (ESTABLISHED)
editor-pr  296     root   13u  IPv4  40561      0t0  TCP 127.0.0.1:38242->127.0.0.1:3000 (ESTABLISHED)
editor-pr  296     root   15u  IPv6  40565      0t0  TCP 127.0.0.1:970->127.0.0.1:57630 (ESTABLISHED)
editor-pr  296     root   16u  IPv4  40569      0t0  TCP 127.0.0.1:38260->127.0.0.1:3000 (ESTABLISHED)
sshd       313     root    4u  IPv4  20100      0t0  TCP 127.0.0.1:22->127.0.0.1:42518 (ESTABLISHED)
node       326 mmore500   18u  IPv4  21262      0t0  TCP *:3000 (LISTEN)
node       326 mmore500   22u  IPv4  39582      0t0  TCP 127.0.0.1:3000->127.0.0.1:38242 (ESTABLISHED)
sshd       327 mmore500    4u  IPv4  22673      0t0  TCP 127.0.0.1:22->127.0.0.1:42504 (ESTABLISHED)
sshd       327 mmore500    9u  IPv4  21098      0t0  TCP 127.0.0.1:44953 (LISTEN)
sshd       341 mmore500    4u  IPv4  20100      0t0  TCP 127.0.0.1:22->127.0.0.1:42518 (ESTABLISHED)
java      1717 mmore500  237u  IPv4  28514      0t0  TCP 127.0.0.1:43029 (LISTEN)
java      1717 mmore500  239u  IPv4  28520      0t0  UDP *:38310 
java      1717 mmore500  283u  IPv4  26601      0t0  TCP 10.88.0.3:43440->151.101.0.215:443 (CLOSE_WAIT)
java      1717 mmore500  284u  IPv4  26602      0t0  TCP 10.88.0.3:43454->151.101.0.215:443 (CLOSE_WAIT)
java      1717 mmore500  285u  IPv4  28557      0t0  TCP 10.88.0.3:43456->151.101.0.215:443 (CLOSE_WAIT)
node      4125 mmore500   20u  IPv4  42117      0t0  TCP 127.0.0.1:3000->127.0.0.1:38260 (ESTABLISHED)

I noticed there were some recent changes in application.properties (be09a2e). I tried repeating with the new line bolt://phylodb-neo4j:7687 instead of bolt://localhost:7687 after rm -rf'ing docker/instances/*, but got the same {"message":"/problems/server"} errors.

@aplf
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aplf commented Feb 16, 2024

Hi,

I just tried and I was able to successfully run the example in shell.cloud.google.com. As you noted, and as stated in the main README, we might have to adjust the file application.properties, in particular the Neo4j bolt connection. But then we need to rebuild the jar file and the docker container.

In shell.cloud.google.com, we can successfully reproduce the example by cloning the repository and changing the neo4j connection in application.properties. In this case we should use spring.data.neo4j.uri=bolt://phylodb-neo4j:7687. And then following the instructions for building and deploying.

While running the example, we need also to either load the admin user manually in database or remove the comment in the last line in scripts/init/make_init_data.cypher.sh.

Thanks.

@mmore500
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mmore500 commented Feb 16, 2024 •
edited
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Would it be possible to get some more specifc, step by step instructions? Unfortunately, I'm still running into the /problems/server issue. Thanks!

Here are the steps I am following, including uncommenting the mentioned lines. I used cat to double-check that the edits were being properly saved to disk.

mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

mmore500@cloudshell:~$ export USER_ID=XXXXXXXX

mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.

mmore500@cloudshell:~$ cd phyloDB

at this point, uncomment the following lines

  • spring.data.neo4j.uri=bolt://phylodb-neo4j:7687 in phyloDB/phylodb/bin/main/application.properties
  • cat init_data.cypher | docker exec --interactive phylodb-neo4j sh -c "cypher-shell -u neo4j -p password" in phyloDB/scripts/init/make_init_data.cypher.sh

and comment out

  • # spring.data.neo4j.uri=bolt://localhost:7687 in phyloDB/phylodb/bin/main/application.properties
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j

mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b

mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b

mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.

mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

----------------------------------------mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessa```
mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
mmore500@cloudshell:~$ export USER_ID=XXXXXXXX
mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.
mmore500@cloudshell:~$ cd phyloDB
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j
mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_```
mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
mmore500@cloudshell:~$ export USER_ID=XXXXXXXX
mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.
mmore500@cloudshell:~$ cd phyloDB
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j
mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse```
mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
mmore500@cloudshell:~$ export USER_ID=XXXXXXXX
mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.
mmore500@cloudshell:~$ cd phyloDB
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j
mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse```
mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
mmore500@cloudshell:~$ export USER_ID=XXXXXXXX
mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.
mmore500@cloudshell:~$ cd phyloDB
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j
mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer ya29.a0AfB_byB02ERFYWxjL2o_v8YY2A_gbFTrxO26ENUU_tNhCLk8D1jQDepYPqGpvBgyXG-sckjwX4FPzpv9ixgCiZ_BAlF8PX67Fs4jUp5C3zDG0Nk9taLU-Ia-GktXK9VK_fWq0GPw-pWQ1sPcM6zuZesvc9Jtr0j6HQzgaCgYKAYASA```
mmore500@cloudshell:~$ export TOKEN=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
mmore500@cloudshell:~$ export USER_ID=XXXXXXXX
mmore500@cloudshell:~$ git clone https://github.com/phyloviz/phyloDB
Cloning into 'phyloDB'...
remote: Enumerating objects: 5554, done.
remote: Counting objects: 100% (860/860), done.
remote: Compressing objects: 100% (422/422), done.
remote: Total 5554 (delta 396), reused 802 (delta 359), pack-reused 4694
Receiving objects: 100% (5554/5554), 20.46 MiB | 29.46 MiB/s, done.
Resolving deltas: 100% (2913/2913), done.
mmore500@cloudshell:~$ cd phyloDB
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
Error response from daemon: No such container: phylodb-neo4j
mmore500@cloudshell:~/phyloDB$ ./configure.sh 
[configure.sh][INFO] - Java version: 170 (found in $PATH).
[configure.sh][INFO] - JAVA_HOME (used by Maven and Gradle in this repository):
        /usr/lib/jvm/java-17-openjdk-amd64
        Java version: 170
[configure.sh][INFO] - Maven version: 3.9.5 (57804ffe001d7215b5e7bcb531cf83df38f93546).
[configure.sh][INFO] - Gradle version ('gradlew' from repository): to
7.4.2.
[configure.sh][INFO] - Calling algorithms/configure.sh
[configure.sh][INFO] - Building algorithms:
        /home/mmore500/phyloDB/algorithms/target/algorithms-1.0.jar
[configure.sh][INFO] - Calling phylodb/configure.sh
[configure.sh][INFO] - gradle:
        /home/mmore500/phyloDB/phylodb/gradlew
        Version: to
7.4.2
[configure.sh][INFO] - Building phylodb: /home/mmore500/phyloDB/phylodb/build/libs/phylodb-1.2.1.jar.
[configure.sh][INFO] - Docker version: 25.0.2, build 29cf629.
[configure.sh][INFO] - Docker daemon is running.
[configure.sh][INFO] - User 'mmore500' is in group 'docker'.
[configure.sh][INFO] - Calling docker/build-docker.sh
[configure.sh][INFO] - Preparing Docker image files.
[configure.sh][INFO] - Copying algorithms-1.0.jar.
[configure.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar.
        https://github.com/neo4j/apoc/releases/download/5.13.0/apoc-5.13.0-core.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-core.jar: success.
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar.
        https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.13.0/apoc-5.13.0-extended.jar
[configure.sh][INFO] - Downloading apoc-5.13.0-extended.jar: success.
[configure.sh][INFO] - Building Docker image 'phylodb'.
[configure.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/build-docker.sh 
[build-docker.sh][INFO] - Preparing Docker image files.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../docker/instance/db/plugins/algorithms-1.0.jar exists.
[build-docker.sh][INFO] - /home/mmore500/phyloDB/docker/../phylodb/build/libs/phylodb-1.2.1.jar already exists.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-core.jar.
[build-docker.sh][INFO] - No need to download apoc-5.13.0-extended.jar.
[build-docker.sh][INFO] - Building Docker image 'phylodb'.
[build-docker.sh][INFO] - Docker build command: 'buildx'.
sha256:728dee20416dd85314b9bd979868b461f6012c13d7a0c5a469d408d9bab2301b
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/
build-docker.sh  instance/        start-docker.sh  stop-docker.sh   
mmore500@cloudshell:~/phyloDB$ ./docker/start-docker.sh
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for app_1
WARNING: The NEO4J_VERSION variable is not set. Defaulting to a blank string.
WARNING: The DB_PATH variable is not set. Defaulting to a blank string.
WARNING: The APP_PATH variable is not set. Defaulting to a blank string.
ERROR: No container found for db_1
[start-docker.sh][INFO] - Launching 'phylodb' and 'db' containers with 'docker-compose'.
Creating network "docker_default" with the default driver
Pulling db (neo4j:5.13.0-community)...
5.13.0-community: Pulling from library/neo4j
b7f91549542c: Pull complete
dbb2ec605bdd: Pull complete
6dcf18532b0b: Pull complete
3024503fd6dc: Pull complete
0c79e7641645: Pull complete
Digest: sha256:6c6003e890c75c9136df06b9061afbbf9a70673711d2d9abc5937ca7f01abb16
Status: Downloaded newer image for neo4j:5.13.0-community
Creating phylodb-app   ... done
Creating phylodb-neo4j ... done
[start-docker.sh][INFO] - 'phylodb' and 'db' containers started.
[start-docker.sh][INFO] - waiting for containers...
[start-docker.sh][INFO] - initializing data...
[start-docker.sh][INFO] - done.
mmore500@cloudshell:~/phyloDB$ ./scripts/init/make_init_data.cypher.sh 
ok USER_ID defined as XXXXXXXX
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/
example/ init/    tests/   
mmore500@cloudshell:~/phyloDB$ ./scripts/example/example.sh 

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Check server status:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as mmore50./scripts/init/make_init_data.cypher.sh [email protected]
row, result
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 0, rows: 0, propertiesSet: 0, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 1, nodesDeleted: 2, indexesAdded: 0, labelsAdded: 0, relationshipsCreated: 0, time: 0}
-1, {constraintsRemoved: 0, indexesRemoved: 0, nodesCreated: 2, rows: 0, propertiesSet: 6, constraintsAdded: 0, labelsRemoved: 0, relationshipsDeleted: 0, nodesDeleted: 0, indexesAdded: 0, labelsAdded: 2, relationshipsCreated: 1, time: 0}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all users:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all taxa
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Taxa: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create taxon:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
> 
* upload completely sent off: 68 out of 68 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all loci:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Loci: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create locus:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127../scripts/init/make_init_data.cypher.sh 0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:24 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
> 
* upload completely sent off: 66 out of 66 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Load alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------aadab446f079502f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------b1c2e332fb5ec4ae
> ./scripts/init/make_init_data.cypher.sh 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------ddd84baf7429a131
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------564a5c4664915b0f
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------6b68345863de34ba
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------e38a8cf45f71133c
> 
* We are completely uploaded and fine
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):
```RASFQHGX2MiGOHLOqLt_cUaCutLFhzYgA0171
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):

< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
<

  • Closing connection 0
    {"message":"/problems/server"}Traceback (most recent call last):
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):
```init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):
```ry use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------5ec2a489213e2baa
> 
* We are completely uploaded and fine
* Mark bundle as not supporti./scripts/init/make_init_data.cypher.sh ng multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:25 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List alleles:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Alleles[locus1]: {"message":"/problems/server"}
Alleles[locus2]: {"message":"/problems/server"}
Alleles[locus3]: {"message":"/problems/server"}
Alleles[locus4]: {"message":"/problems/server"}
Alleles[locus5]: {"message":"/problems/server"}
Alleles[locus6]: {"message":"/problems/server"}
Alleles[locus7]: {"message":"/problems/server"}
An allele: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all schemas:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Schemas: {"message":"/problems/server"}
Schema: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create schema:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
> 
* upload completely sent off: 199 out of 199 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List all projects:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Projects: {"message":"/problems/server"}

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Create project:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
*   Trying 127.0.0.1:8080...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/7.74.0
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
> 
* upload completely sent off: 152 out of 152 bytes
* Mark bundle as not supporting multiuse
< HTTP/1.1 500 
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Fri, 16 Feb 2024 19:22:26 GMT
< Connection: close
< 
* Closing connection 0
{"message":"/problems/server"}Traceback (most recent call last):

@aplf
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aplf commented Feb 16, 2024

Hi,

Sure, here are the step by step instructions/commands:

git clone https://github.com/phyloviz/phyloDB.git phyloDB.git
cd phyloDB.git/
vim phylodb/src/main/resources/application.properties   # to comment de 2nd line and uncomment the 1st line
vim scripts/init/make_init_data.cypher.sh               # to uncomment the last line
./configure.sh
cd docker
./build-docker.sh
./start-docker.sh
cd ../scripts/example
export TOKEN="YOUR_TOKEN"
export USER_ID="YOUR_USER_ID"
./example.sh

The end of the output should be:

....
Inferences: [{"id":"8ea5ee4c-c328-4758-9515-6b26054e7791"}]
Inference: {"project_id":"d6ee6d07-e4ef-4b8a-b121-daa1736d96bd","dataset_id":"367ab3e5-22a2-420a-8510-157f44cdb5bc","id":"8ea5ee4c-c328-4758-9515-6b26054e7791","deprecated":false,"algorithm":"goeburst","tree":"((7:1,8:1)9:2)10;(5:2)6;(4:3)1;"}

Thanks.

@mmore500
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mmore500 commented Feb 16, 2024 •
edited
Loading

It works! I think the difference might have been cd'ing into the directories with the scripts.

If you would like, I'd be happy to contribute a pull request adding these more direct step by step instructions.

Out of curiosity, what is the rationale of having the lines in application.properties and make_init_data.cypher.sh commented out? Would it make sense to have the default state in the repository with those arranged so they work with the example? I'd be happy to contribute those changes too.

@aplf
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aplf commented Feb 16, 2024 •
edited
Loading

Hi,

If you would like, I'd be happy to contribute a pull request adding these more direct step by step instructions.

Sure, your pull request is welcome, thanks.

Out of curiosity, what is the rationale of having the lines in application.properties and make_init_data.cypher.sh commented out? Would it make sense to have the default state in the repository with those arranged so they work with the example? I'd be happy to contribute those changes too.

The line commented in file application.properties is given as an example. But the default uncommented line is the default configuration used in the integration tests. In other environments we need to change the neo4j connection string, as is the case in some docker environments where containers are resolved by their names. The last line in file make_init_data.cypher.sh is commented out because the initialization command includes a full delete operation. We believe that it is safer this way.

Thanks for your analysis.

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@aplf @cvaz @mmore500