Skip to content

Commit

Permalink
Fixed #322
Browse files Browse the repository at this point in the history
  • Loading branch information
@IgorRodchenkov
IgorRodchenkov committed Jul 12, 2024
1 parent 5a601d8 commit 47a5c03
Show file tree
Hide file tree
Showing 3 changed files with 18 additions and 18 deletions.
16 changes: 8 additions & 8 deletions src/main/java/cpath/web/ApiControllerV1.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ public class ApiControllerV1 extends BasicController {
@Operation(
summary = "Fetch a BioPAX sub-model by URIs/IDs and optionally convert to another output format (query parameters must be URL-encoded and not too many)",
description = "Retrieve BioPAX pathways, interactions, physical entities from the db by URIs; " +
"optionally, convert the result to other <a href='/#formats'>output formats</a>."
"optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void fetchQueryGet(@Valid Fetch args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response) {
Expand All @@ -50,7 +50,7 @@ public void fetchQueryGet(@Valid Fetch args, BindingResult bindingResult,
@Operation(
summary = "Fetch a BioPAX sub-model by URIs/IDs and optionally convert to another output format",
description = "Retrieve pathways/interactions/entities by their BioPAX URIs; " +
"optionally, convert the result to other <a href='/#formats'>output formats</a>."
"optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void fetchQuery(@Valid Fetch args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -76,7 +76,7 @@ public void fetchQuery(@Valid Fetch args, BindingResult bindingResult,
summary = "Search for top-level bio pathways",
description = "Find root/parent Pathway objects, i.e, ones that are neither 'controlled' " +
"nor a 'pathwayComponent' of another biological process; trivial pathways are excluded from the results;" +
" can filter by <a href='/datasources'>datasource</a> and organism."
" can filter by <a href='../datasources'>datasource</a> and organism."
)
public SearchResponse topPathwaysQueryGet(@Valid TopPathways args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -91,7 +91,7 @@ public SearchResponse topPathwaysQueryGet(@Valid TopPathways args, BindingResult
summary = "Search for top-level bio pathways",
description = "Find root/parent Pathway objects that are neither <code>controlled</code> " +
"nor a <code>pathwayComponent</code> of another biological process; trivial pathways are excluded from the results;" +
" can filter by <a href='/datasources'>datasource</a> and organism."
" can filter by <a href='../datasources'>datasource</a> and organism."
)
public SearchResponse topPathwaysQuery(@Valid TopPathways args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand Down Expand Up @@ -180,7 +180,7 @@ public TraverseResponse traverseQuery(@Valid Traverse args, BindingResult bindin
summary = "A BioPAX graph query and optional converter to another output formats (parameters must be URL-encoded and not too many)",
description = "Find connections of bio network elements, such as the shortest path between " +
"two proteins or the neighborhood for a particular protein state or all states. " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>." +
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>." +
"Graph searches consider detailed BioPAX semantics, such as generics, nested complexes, " +
"and traverse the graph accordingly."
)
Expand All @@ -198,7 +198,7 @@ public void graphQueryGet(@Valid Graph args, BindingResult bindingResult,
summary = "A BioPAX graph query and optional converter to another output formats",
description = "Find connections of bio network elements, such as the shortest path between " +
"two proteins or the neighborhood for a particular protein state or all states. " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>." +
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>." +
"Graph searches consider detailed BioPAX semantics, such as generics, nested complexes, " +
"and traverse the graph accordingly."
)
Expand Down Expand Up @@ -260,7 +260,7 @@ and nested properties (e.g. a Complex can be found by one of its member's names
</p>
<p>
Returns an ordered list of hits (<var>maxHitsPerPage</var> is configured on the server) as JSON or
<a href="/help/schema">XML</a> depending on 'Accept: application/json' or
<a href="../help/schema">XML</a> depending on 'Accept: application/json' or
'Accept: application/xml' request header.
</p>
"""
Expand All @@ -286,7 +286,7 @@ and nested properties (e.g. a Complex can be found by one of its member's names
</p>
<p>
Returns an ordered list of hits (<var>maxHitsPerPage</var> is configured on the server) as JSON or
<a href="/help/schema">XML</a> depending on 'Accept: application/json' or
<a href="../help/schema">XML</a> depending on 'Accept: application/json' or
'Accept: application/xml' request header.
</p>
"""
Expand Down
14 changes: 7 additions & 7 deletions src/main/java/cpath/web/ApiControllerV2.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ public class ApiControllerV2 extends BasicController {
@Operation(
summary = "Fetch a BioPAX sub-model by URIs/IDs and optionally convert to another output format",
description = "Retrieve pathways/interactions/entities by their BioPAX URIs; " +
"optionally, convert the result to other <a href='/#formats'>output formats</a>."
"optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void fetchQuery(@Valid @RequestBody Fetch args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -66,7 +66,7 @@ public void fetchQuery(@Valid @RequestBody Fetch args, BindingResult bindingResu
summary = "Search for top-level bio pathways",
description = "Find root/parent Pathway objects that are neither <code>controlled</code> " +
"nor a <code>pathwayComponent</code> of another biological process; trivial pathways are excluded from the results;" +
" can filter by <a href='/datasources'>datasource</a> and organism."
" can filter by <a href='../datasources'>datasource</a> and organism."
)
public SearchResponse topPathwaysQuery(@Valid @RequestBody TopPathways args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand Down Expand Up @@ -139,7 +139,7 @@ and nested properties (e.g. a Complex can be found by one of its member's names
</p>
<p>
Returns an ordered list of hits (<var>maxHitsPerPage</var> is configured on the server) as JSON or
<a href="/help/schema">XML</a> depending on 'Accept: application/json' or
<a href="../help/schema">XML</a> depending on 'Accept: application/json' or
'Accept: application/xml' request header.
</p>
"""
Expand Down Expand Up @@ -175,7 +175,7 @@ public SearchResponse searchQuery(@Valid @RequestBody Search args, BindingResult
@Operation(
summary = "BioPAX Neighborhood graph query and optional converter to another output format",
description = "Find the neighborhood network given the source bio entity URIs/IDs. " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>."
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void neighborhoodQuery(@Valid @RequestBody Neighborhood args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -200,7 +200,7 @@ public void neighborhoodQuery(@Valid @RequestBody Neighborhood args, BindingResu
@Operation(
summary = "BioPAX PathsBetween graph query and optional converter to another output format",
description = "Find the BioPAX subnetwork that includes all paths between given source bio entities (URIs/IDs). " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>."
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void pathsbetweenQuery(@Valid @RequestBody PathsBetween args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -226,7 +226,7 @@ public void pathsbetweenQuery(@Valid @RequestBody PathsBetween args, BindingResu
summary = "BioPAX PathsFromTo graph query and optional converter to another output format",
description = "Find a subnetwork that includes entities on the paths from the source bio " +
"entities (URIs/IDs) to the targets (if empty array, then PathsBetween algorithm is used). " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>."
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void pathsfromtoQuery(@Valid @RequestBody PathsFromTo args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand All @@ -251,7 +251,7 @@ public void pathsfromtoQuery(@Valid @RequestBody PathsFromTo args, BindingResult
@Operation(
summary = "BioPAX CommonStream graph query and optional converter to another output format",
description = "Find a BioPAX common stream subnetwork from the source bio entities (URIs/IDs). " +
"Optionally, convert the result to other <a href='/#formats'>output formats</a>."
"Optionally, convert the result to other <a href='../home#formats'>output formats</a>."
)
public void commonstreamQuery(@Valid @RequestBody CommonStream args, BindingResult bindingResult,
HttpServletRequest request, HttpServletResponse response)
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/cpath/web/args/Search.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ and nested properties (e.g. a Complex can be found by one of its member's names

@Schema(
description = """
BioPAX class filter (<a href="/home#biopax_types">values</a>; case-insensitive).
BioPAX class filter (<a href="../home#biopax_types">values</a>; case-insensitive).
Note that some query filters, such as <code>&amp;type=biosource</code>
(for most BioPAX UtilityClass, such as Score, Evidence), will not return any hits.
So, use Entity (e.g., Pathway, Control, Protein) or EntityReference types
Expand All @@ -54,7 +54,7 @@ public void setType(String type) {
<var>homo sapiens</var> or NCBI Taxon IDs, <var>9606</var>. If multiple values
are provided, then the union of hits is returned; e.g.,
<code>organism=9606&amp;organism=10016</code> results in both human and mouse related hits.
See also: <a href="/home#organisms">supported species</a> (other organisms data,
See also: <a href="../home#organisms">supported species</a> (other organisms data,
such as viruses and model organisms, can go together with e.g. human models that we integrated).
""",
example = "[\"9606\"]"
Expand All @@ -64,7 +64,7 @@ public void setType(String type) {
@Schema(
description = """
filter by data source (an array of names, URIs
of the <a href="/datasources">data sources</a> or any <var>Provenance</var>).
of the <a href="../datasources">data sources</a> or any <var>Provenance</var>).
If multiple data source values are specified, a union of hits from specified sources is returned;
e.g., <code>datasource=reactome&amp;datasource=pid</code>.
""",
Expand Down

0 comments on commit 47a5c03

Please sign in to comment.