Start to make components easier to deploy (See #64).

ielab · Aug 26, 2020 · e61a0ac · e61a0ac
1 parent 5bef34d
commit e61a0ac
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Showing 11 changed files with 128 additions and 60 deletions.
diff --git a/.gitignore b/.gitignore
@@ -21,4 +21,6 @@ document_frequency/None/
 objective_qf/params/None/
 top_subheadings/None/
 None/
-statistics/None/
+statistics/None/
+
+resources/quickrank
diff --git a/Makefile b/Makefile
@@ -1,22 +1,33 @@
 plugin_dirs := $(wildcard plugin/*/)
 plugin_obs := $(foreach plugin,$(plugin_dirs),$(plugin)plugin.so)
 plugin_src := $(patsubst %plugin.so,%*.go,$(plugin_obs))
+quicklearn_bin := resources/quickrank/bin/quicklearn
 go_source = *.go cmd/searchrefiner/*.go
-
 SERVER = server
 
 plugin: $(plugin_obs)
-PHONEY: run all plugin clean
+PHONEY: run all plugin clean quicklearn
+
+# These compile the quicklearn binary, which are required for the QueryLens plugin.
+$(quicklearn_bin):
+	@git clone --recursive https://github.com/hpclab/quickrank.git
+	@cd quickrank && mkdir build_ && cd build_ && cmake .. -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_BUILD_TYPE=Release && make
+	@mv quickrank quickrank/resources
+
+quicklearn: $(quicklearn_bin)
 
+# The main server compilation step. It depends on the compilation of any plugins that exist.
 $(SERVER): $(plugin_obs) $(go_source)
 	go build -o server cmd/searchrefiner/server.go
 
+# The plugins are just shared object files that should only need to be recompiled if changed.
 .SECONDEXPANSION:
 $(plugin_obs): $$(patsubst %plugin.so,%*.go,$$@)
 	go build -buildmode=plugin -o $@ $^
 
-run: clean $(SERVER)
+# Running the server may optionally depend on quicklearn.
+run: quicklearn $(SERVER)
 	@./server
 
 clean:
-	@[ -f server ] && rm $(foreach plugin,$(plugin_obs),$(plugin)) server] || true
+	@[ -f server ] && rm $(foreach plugin,$(plugin_obs),$(plugin)) server || true
diff --git a/api.go b/api.go
@@ -28,8 +28,9 @@ import (
 type searchResponse struct {
 	Start            int
 	TotalHits        int64
+	RelRet           float64
 	TookInMillis     float64
-	OriginalQuery    string
+	QueryString      string
 	TransformedQuery string
 	PreviousQueries  []Query
 	Documents        []guru.MedlineDocument
@@ -41,6 +42,9 @@ type searchResponse struct {
 	MeshExploded     float64
 	MeshAvgDepth     float64
 	MeshMaxDepth     float64
+
+	Plugins     []InternalPluginDetails
+	PluginTitle string
 }
 
 type suggestion struct {

diff --git a/cmd/searchrefiner/server.go b/cmd/searchrefiner/server.go
@@ -35,17 +35,17 @@ func main() {
 	}
 
 	fmt.Println("loading quiche...")
-	quicheCache, err := quiche.Load(c.Options.Quiche)
+	quicheCache, err := quiche.Load(c.Resources.Quiche)
 	if err != nil {
 		panic(err)
 	}
 	fmt.Println("loading cui2vec mapping...")
-	cuiMapping, err := cui2vec.LoadCUIMapping(c.Options.Cui2VecMappings)
+	cuiMapping, err := cui2vec.LoadCUIMapping(c.Resources.Cui2VecMappings)
 	if err != nil {
 		panic(err)
 	}
 	fmt.Println("loading cui2vec model...")
-	cui2vecf, err := os.Open(c.Options.Cui2VecEmbeddings)
+	cui2vecf, err := os.Open(c.Resources.Cui2VecEmbeddings)
 	if err != nil {
 		panic(err)
 	}

diff --git a/components/util.tmpl.html b/components/util.tmpl.html
@@ -1,5 +1,5 @@
 {{define "version"}}
-    30.June.2020
+    25.Aug.2020
 {{end}}
 
 {{define "footer"}}
@@ -22,4 +22,36 @@
     <div class="hero-lg bg-primary  " style="width: 100%;position:fixed;bottom: 0;padding: 1%;z-index: 10000">
         {{template "footer"}}
     </div>
+{{ end }}
+
+
+{{ define "send_query" }}
+    {{ $query := .QueryString }}
+    {{ $lang := .Language }}
+    {{ $title := .PluginTitle }}
+    {{ range $plugin := .Plugins }}
+        {{ if $plugin.AcceptsQueryPosts }}
+            {{ if ne $title $plugin.Title }}
+                <form action="/{{ $plugin.URL }}" method="post">
+                    <input type="hidden" name="query" v-bind:value="textQuery" value="{{ $query }}">
+                    <input type="hidden" name="lang" value="{{ $lang }}">
+                    <button class="btn btn-link">{{ $plugin.Title }} <i class="icon icon-arrow-right"></i></button>
+                </form>
+            {{ end }}
+        {{ end }}
+    {{ end }}
+    <button class="btn btn-link" v-on:click="sendToPolyglot()" onclick="sendToPolyglot()">Polyglot (external tool)<i class="icon icon-arrow-right"></i></button>
+    <script>
+        sendToPolyglot = function () {
+            var request = new XMLHttpRequest();
+            request.addEventListener("load", function (ev) {
+                if (ev.currentTarget.status === 200) {
+                    window.open("https://sr-accelerator.com/#/polyglot?token=" + ev.target.responseText, target = "_blank");
+                }
+            });
+            request.open("POST", "https://ielab-sysrev3.uqcloud.net/exchange", true);
+            request.setRequestHeader('Content-Type', 'application/json');
+            request.send(JSON.stringify({data: {query: {{ $query }}}, referrer: "searchrefiner"}));
+        }
+    </script>
 {{ end }}
diff --git a/configuration.go b/configuration.go
@@ -57,19 +57,19 @@ type OtherServiceAddresses struct {
 }
 
 type Config struct {
-	Host       string
-	AdminEmail string
-	Admins     []string
-	Entrez     EntrezConfig
-	Options    Options // TODO: This should be merged into the Services struct.
-	Mode       string
-	EnableAll  bool
-	Services   Services
+	Host                  string
+	AdminEmail            string
+	Admins                []string
+	Entrez                EntrezConfig
+	Resources             Resources // TODO: This should be merged into the Services struct.
+	Mode                  string
+	EnableAll             bool
+	Services              Services
 	ExchangeServerAddress string
 	OtherServiceAddresses OtherServiceAddresses
 }
 
-type Options struct {
+type Resources struct {
 	Cui2VecEmbeddings string
 	Cui2VecMappings   string
 	Quiche            string
@@ -83,6 +83,9 @@ type Query struct {
 	NumRet      int64     `csv:"num_ret"`
 	NumRelRet   int64     `csv:"num_rel_ret"`
 	Relevant    []string  `csv:"relevant"`
+
+	Plugins     []InternalPluginDetails
+	PluginTitle string
 }
 
 type ErrorPage struct {
@@ -124,6 +127,8 @@ type PluginDetails struct {
 	Author      string
 	Version     string
 	ProjectURL  string
+
+	AcceptsQueryPosts bool
 }
 
 // InternalPluginDetails contains details about a plugin which are vital in rendering the plugin page.

diff --git a/plugin/queryvis/index.html b/plugin/queryvis/index.html
@@ -170,9 +170,10 @@
                         <button class="btn btn nav-height" id="btn-update-tree" v-on:click="updateTree('none')">
                             <i class="icon icon-refresh"></i> Visualise
                         </button>
-                        <button class="btn btn-link" v-on:click="sendToPolyglot()" type="button">
-                            Open Query in Polyglot <i class="icon icon-arrow-right"></i>
-                        </button>
+                        {{ template "send_query" .}}
+                        {{/*                        <button class="btn btn-link" v-on:click="sendToPolyglot()" type="button">*/}}
+                        {{/*                            Open Query in Polyglot <i class="icon icon-arrow-right"></i>*/}}
+                        {{/*                        </button>*/}}
                     </div>
                 </div>
                 <div class="form-group p-2">
@@ -926,6 +927,8 @@
         document.body.appendChild(form);
         form.submit();
     };
+    sendToPolyglot = function () {
+    }
 </script>
 </body>
 </html>
diff --git a/plugin/queryvis/main.go b/plugin/queryvis/main.go
@@ -62,7 +62,7 @@ func handleTree(s searchrefiner.Server, c *gin.Context, relevant ...combinator.D
 	if len(relevant) == 0 {
 		relevant = s.Settings[username].Relevant
 	}
-	
+
 	var root combinator.LogicalTree
 	root, err = combinator.NewShallowLogicalTree(gpipeline.NewQuery("searchrefiner", "0", repr.(cqr.CommonQueryRepresentation)), s.Entrez, relevant)
 	if err != nil {
@@ -147,7 +147,7 @@ func (QueryVisPlugin) Serve(s searchrefiner.Server, c *gin.Context) {
 	c.Render(http.StatusOK, searchrefiner.RenderPlugin(searchrefiner.TemplatePlugin("plugin/queryvis/index.html"), struct {
 		searchrefiner.Query
 		View string
-	}{searchrefiner.Query{QueryString: rawQuery, Language: lang}, c.Query("view")}))
+	}{searchrefiner.Query{QueryString: rawQuery, Language: lang, Plugins: s.Plugins, PluginTitle: "QueryVis"}, c.Query("view")}))
 	return
 }
 
@@ -157,11 +157,12 @@ func (QueryVisPlugin) PermissionType() searchrefiner.PluginPermission {
 
 func (QueryVisPlugin) Details() searchrefiner.PluginDetails {
 	return searchrefiner.PluginDetails{
-		Title:       "QueryVis",
-		Description: "Visualise queries as a syntax tree overlaid with retrieval statistics and other understandability visualisations.",
-		Author:      "ielab",
-		Version:     "12.Feb.2019",
-		ProjectURL:  "ielab.io/searchrefiner",
+		Title:             "QueryVis",
+		Description:       "Visualise queries as a syntax tree overlaid with retrieval statistics and other understandability visualisations.",
+		Author:            "ielab",
+		Version:           "26.Aug.2020",
+		ProjectURL:        "ielab.io/searchrefiner",
+		AcceptsQueryPosts: true,
 	}
 }
 

diff --git a/sample.config.json b/sample.config.json
@@ -8,13 +8,13 @@
     "Email": "[email protected]",
     "APIKey": "1234abcde"
   },
-  "Mode": "",
   "EnableAll": true,
-  "Options": {
-    "Cui2VecEmbeddings": "path/to/cui2vec_precomputed.bin",
-    "Cui2VecMappings": "path/to/cuis.csv",
-    "Quiche": "path/to/quiche.cache",
-    "QuickRank": "path/to/quicklearn"
+  "Mode": "",
+  "Resources": {
+    "Cui2VecEmbeddings": "resources/cui2vec_precomputed.bin",
+    "Cui2VecMappings": "resources/cuis.csv",
+    "Quiche": "resources/quiche.cache",
+    "QuickRank": "resources/quickrank/bin/quicklearn"
   },
   "Services": {
     "MetaMapURL": "ielab-metamap",
@@ -32,8 +32,5 @@
     "Merged": false,
     "Sources": "cui,es"
   },
-  "ExchangeServerAddress": "https://abc.com/exchange",
-  "OtherServiceAddresses": {
-    "SRA": ""
-  }
+  "ExchangeServerAddress": "https://ielab-sysrev3.uqcloud.net/exchange"
 }
diff --git a/views.go b/views.go
@@ -85,7 +85,7 @@ func (s Server) HandleResults(c *gin.Context) {
 		Start:            len(docs),
 		TotalHits:        int64(size),
 		TookInMillis:     float64(time.Since(start).Nanoseconds()) / 1e-6,
-		OriginalQuery:    rawQuery,
+		QueryString:      rawQuery,
 		TransformedQuery: q,
 		Documents:        docs,
 		Language:         lang,
@@ -143,32 +143,45 @@ func (s Server) HandleQuery(c *gin.Context) {
 	sr := searchResponse{
 		TotalHits:        int64(size),
 		TookInMillis:     float64(time.Since(start).Nanoseconds()) / 1e-6,
-		OriginalQuery:    rawQuery,
+		QueryString:      rawQuery,
 		TransformedQuery: transformed,
 		Language:         lang,
+
+		PluginTitle: "searchrefiner",
 	}
 
 	gq := gpipeline.NewQuery("searchrefiner", "0", repr.(cqr.CommonQueryRepresentation))
 	sr.BooleanClauses, err = analysis.BooleanClauses.Execute(gq, s.Entrez)
 	sr.BooleanFields, _ = analysis.BooleanFields.Execute(gq, s.Entrez)
 	sr.BooleanKeywords, _ = analysis.BooleanKeywords.Execute(gq, s.Entrez)
 	sr.MeshKeywords, _ = analysis.MeshKeywordCount.Execute(gq, s.Entrez)
-	sr.MeshExploded, _ = analysis.MeshExplodedCount.Execute(gq, s.Entrez)
-	sr.MeshAvgDepth, _ = analysis.MeshAvgDepth.Execute(gq, s.Entrez)
-	sr.MeshMaxDepth, _ = analysis.MeshMaxDepth.Execute(gq, s.Entrez)
-
-	username := s.Perm.UserState().Username(c.Request)
 
-	// Reverse the list of previous queries.
-	rev := make([]Query, len(s.Queries[username]))
-	j := 0
-	for i := len(s.Queries[username]) - 1; i >= 0; i-- {
-		rev[j] = s.Queries[username][i]
-		j++
+	if s.Perm.UserState().UserRights(c.Request) {
+		username := s.Perm.UserState().Username(c.Request)
+		t, err := combinator.NewShallowLogicalTree(gq, s.Entrez, s.Settings[username].Relevant)
+		if err != nil {
+			c.HTML(http.StatusInternalServerError, "error.html", ErrorPage{Error: err.Error(), BackLink: "/"})
+			return
+		}
+		switch q := t.Root.(type) {
+		case combinator.Combinator:
+			sr.RelRet = q.R
+		case combinator.Atom:
+			sr.RelRet = q.R
+		}
+
+		// Reverse the list of previous queries.
+		rev := make([]Query, len(s.Queries[username]))
+		j := 0
+		for i := len(s.Queries[username]) - 1; i >= 0; i-- {
+			rev[j] = s.Queries[username][i]
+			j++
+		}
+		sr.PreviousQueries = rev
+
+		s.Queries[username] = append(s.Queries[username], Query{QueryString: rawQuery, Language: lang, NumRet: sr.TotalHits})
 	}
-	sr.PreviousQueries = rev
-
-	s.Queries[username] = append(s.Queries[username], Query{QueryString: rawQuery, Language: lang, NumRet: sr.TotalHits})
+	sr.Plugins = s.Plugins
 	c.HTML(http.StatusOK, "query.html", sr)
 }
 

diff --git a/web/query.html b/web/query.html
@@ -36,7 +36,7 @@
                     <h3>Query Analysis</h3>
                     <form action="/query" method="post" accept-charset="UTF-8">
                         <div class="form-group">
-                            <textarea name="query" id="query" class="form-input" placeholder="Enter query here." rows="10" required>{{ .OriginalQuery }}</textarea>
+                            <textarea name="query" id="query" class="form-input" placeholder="Enter query here." rows="10" required>{{ .QueryString }}</textarea>
                         </div>
                         <div class="form-group">
                             <label>Query Language
@@ -66,13 +66,13 @@ <h3>Query Analysis</h3>
                     <h4>Statistics</h4>
                     <ul>
                         <li><b>{{ .TotalHits }}</b> results.</li>
+                        <li><b>{{ .RelRet }}</b> seed studies retrieved.</li>
                         <li><b>{{ .BooleanClauses }}</b> clauses.</li>
                         <li><b>{{ .BooleanKeywords }}</b> keywords.</li>
                         <li><b>{{ .MeshKeywords }}</b> MeSH Term keywords.</li>
-                        <li><b>{{ .MeshExploded }}</b> MeSH Term keywords (exploded).</li>
-                        <li><b>{{ .MeshAvgDepth }}</b> MeSH Term average depth.</li>
-                        <li><b>{{ .MeshMaxDepth }}</b> MeSH Term maximum depth.</li>
                     </ul>
+                    <h4>Send this query to...</h4>
+                    {{ template "send_query" .}}
                 </div>
             </div>
             <div class="divider"></div>
@@ -121,7 +121,7 @@ <h4>Statistics</h4>
                     Query Analysis
                 </label>
                 <div class="accordion-body">
-                    <pre id="original" class="code" data-lang="Original">{{ .OriginalQuery }}</pre>
+                    <pre id="original" class="code" data-lang="Original">{{ .QueryString }}</pre>
                     <pre id="transformed" class="code" data-lang="Transformed">{{ .TransformedQuery }}</pre>
                 </div>
             </div>