Rip visualisation out of core into plugin.

api.go

@@ -2,9 +2,6 @@ package searchrefiner
 
 import (
 	"github.com/gin-gonic/gin"
-	"github.com/hscells/cqr"
-	"github.com/hscells/groove/combinator"
-	gpipeline "github.com/hscells/groove/pipeline"
 	"github.com/hscells/groove/stats"
 	"github.com/hscells/transmute"
 	tpipeline "github.com/hscells/transmute/pipeline"
@@ -30,76 +27,6 @@ type searchResponse struct {
 	MeshMaxDepth     float64
 }
 
-type node struct {
-	ID    int    `json:"id"`
-	Value int    `json:"value"`
-	Level int    `json:"level"`
-	Label string `json:"label"`
-	Shape string `json:"shape"`
-}
-
-type edge struct {
-	From  int    `json:"from"`
-	To    int    `json:"to"`
-	Value int    `json:"value"`
-	Label string `json:"label"`
-}
-
-type tree struct {
-	Nodes     []node `json:"nodes"`
-	Edges     []edge `json:"edges"`
-	relevant  map[combinator.Document]struct{}
-	NumRelRet int
-	NumRel    int
-}
-
-func (s Server) ApiTree(c *gin.Context) {
-	rawQuery := c.PostForm("query")
-	lang := c.PostForm("lang")
-
-	p := make(map[string]tpipeline.TransmutePipeline)
-	p["medline"] = transmute.Medline2Cqr
-	p["pubmed"] = transmute.Pubmed2Cqr
-
-	compiler := p["medline"]
-	if v, ok := p[lang]; ok {
-		compiler = v
-	} else {
-		lang = "medline"
-	}
-
-	cq, err := compiler.Execute(rawQuery)
-	if err != nil {
-		c.AbortWithError(500, err)
-		return
-	}
-
-	if err != nil {
-		c.AbortWithError(500, err)
-		return
-	}
-	repr, err := cq.Representation()
-	if err != nil {
-		c.AbortWithError(500, err)
-		return
-	}
-
-	var root combinator.LogicalTree
-	root, _, err = combinator.NewLogicalTree(gpipeline.NewQuery("searchrefiner", "0", repr.(cqr.CommonQueryRepresentation)), s.Entrez, QueryCacher)
-	if err != nil {
-		c.AbortWithError(500, err)
-		return
-	}
-
-	t := buildTree(root.Root, s.Entrez, getSettings(s, c).Relevant...)
-
-	username := s.Perm.UserState().Username(c.Request)
-	t.NumRel = len(s.Settings[username].Relevant)
-	t.NumRelRet = len(t.relevant)
-
-	c.JSON(200, t)
-}
-
 func (s Server) ApiScroll(c *gin.Context) {
 	rawQuery := c.PostForm("query")
 	lang := c.PostForm("lang")
@@ -116,7 +43,7 @@ func (s Server) ApiScroll(c *gin.Context) {
 	startString := c.PostForm("start")
 	scroll, err := strconv.ParseInt(startString, 10, 64)
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
@@ -135,37 +62,37 @@ func (s Server) ApiScroll(c *gin.Context) {
 
 	cq, err := compiler.Execute(rawQuery)
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	cqString, err := cq.String()
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	pubmedQuery, err := transmute.Cqr2Pubmed.Execute(cqString)
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	q, err := pubmedQuery.String()
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	pmids, err := s.Entrez.Search(q, s.Entrez.SearchStart(int(scroll)), s.Entrez.SearchSize(10))
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	docs, err := s.Entrez.Fetch(pmids)
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
@@ -194,16 +121,16 @@ func ApiTransform(c *gin.Context) {
 
 	cq, err := compiler.Execute(rawQuery)
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	q, err := cq.StringPretty()
 	if err != nil {
-		c.AbortWithError(http.StatusInternalServerError, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
-	c.Data(200, "text/plain", []byte(q))
+	c.Data(http.StatusOK, "text/plain", []byte(q))
 }
 
 func ApiCQR2Query(c *gin.Context) {
@@ -223,17 +150,17 @@ func ApiCQR2Query(c *gin.Context) {
 
 	cq, err := compiler.Execute(rawQuery)
 	if err != nil {
-		c.AbortWithError(500, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	s, err := cq.StringPretty()
 	if err != nil {
-		c.AbortWithError(500, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
-	c.Data(200, "application/json", []byte(s))
+	c.Data(http.StatusOK, "application/json", []byte(s))
 }
 
 func ApiQuery2CQR(c *gin.Context) {
@@ -253,15 +180,15 @@ func ApiQuery2CQR(c *gin.Context) {
 
 	cq, err := compiler.Execute(rawQuery)
 	if err != nil {
-		c.AbortWithError(500, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
 	s, err := cq.StringPretty()
 	if err != nil {
-		c.AbortWithError(500, err)
+		c.String(http.StatusInternalServerError, err.Error())
 		return
 	}
 
-	c.Data(200, "application/json", []byte(s))
+	c.Data(http.StatusOK, "application/json", []byte(s))
 }

auth.go

@@ -19,23 +19,20 @@ func (s Server) ApiAccountLogin(c *gin.Context) {
 		username = v
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "no username supplied", BackLink: "/account/login"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if v, ok := c.GetPostForm("password"); ok {
 		password = v
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "no password supplied", BackLink: "/account/login"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if s.Perm.UserState().CorrectPassword(username, password) {
 		err := s.Perm.UserState().Login(c.Writer, username)
 		if err != nil {
 			c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: err.Error(), BackLink: "/account/login"})
-			c.AbortWithError(http.StatusUnauthorized, err)
 			return
 		}
 		c.Redirect(http.StatusFound, "/")
@@ -52,35 +49,30 @@ func (s Server) ApiAccountCreate(c *gin.Context) {
 		username = v
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "no username supplied", BackLink: "/account/create"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if v, ok := c.GetPostForm("password"); ok {
 		password = v
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "passwords do not match", BackLink: "/account/create"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if v, ok := c.GetPostForm("password2"); ok {
 		password2 = v
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "passwords do not match", BackLink: "/account/create"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if password != password2 {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "passwords do not match", BackLink: "/account/create"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
 	if s.Perm.UserState().HasUser(username) {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "a user with that name already exists", BackLink: "/account/create"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 
@@ -103,7 +95,6 @@ func (s Server) ApiAccountCreate(c *gin.Context) {
 	err := s.Perm.UserState().Login(c.Writer, username)
 	if err != nil {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: err.Error(), BackLink: "/account/create"})
-		c.AbortWithError(http.StatusUnauthorized, err)
 		return
 	}
 	c.Redirect(http.StatusFound, "/")
@@ -134,7 +125,6 @@ func (s Server) HandleAdmin(c *gin.Context) {
 	u, err := s.Perm.UserState().AllUnconfirmedUsernames()
 	if err != nil {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: err.Error(), BackLink: "/"})
-		c.AbortWithError(http.StatusInternalServerError, err)
 		return
 	}
 
@@ -150,7 +140,6 @@ func (s Server) ApiAdminConfirm(c *gin.Context) {
 		s.Perm.UserState().Confirm(v)
 	} else {
 		c.HTML(http.StatusUnauthorized, "error.html", ErrorPage{Error: "invalid credentials", BackLink: "/"})
-		c.AbortWithStatus(http.StatusUnauthorized)
 		return
 	}
 

cmd/searchrefiner/server.go

@@ -70,11 +70,11 @@ func main() {
 	}
 
 	s := searchrefiner.Server{
-		Perm:      perm,
-		Config:    c,
-		Queries:   make(map[string][]searchrefiner.Query),
-		Settings:  make(map[string]searchrefiner.Settings),
-		Entrez:    ss,
+		Perm:     perm,
+		Config:   c,
+		Queries:  make(map[string][]searchrefiner.Query),
+		Settings: make(map[string]searchrefiner.Settings),
+		Entrez:   ss,
 	}
 
 	permissionHandler := func(c *gin.Context) {
@@ -97,7 +97,7 @@ func main() {
 
 	g.LoadHTMLFiles(append([]string{
 		// Views.
-		"web/query.html", "web/index.html", "web/transform.html", "web/tree.html",
+		"web/query.html", "web/index.html", "web/transform.html",
 		"web/account_create.html", "web/account_login.html", "web/admin.html",
 		"web/help.html", "web/error.html", "web/results.html", "web/settings.html", "web/plugins.html",
 	}, searchrefiner.Components...)...)
@@ -189,11 +189,6 @@ func main() {
 	g.POST("/api/cqr2query", searchrefiner.ApiCQR2Query)
 	g.POST("/api/query2cqr", searchrefiner.ApiQuery2CQR)
 
-	// Visualisation interface.
-	g.GET("/tree", searchrefiner.HandleTree)
-	g.POST("/tree", searchrefiner.HandleTree)
-	g.POST("/api/tree", s.ApiTree)
-
 	// Settings page.
 	g.GET("/settings", s.HandleSettings)
 	g.POST("/api/settings/relevant", s.ApiSettingsRelevantSet)

components/sidebar.tmpl.html

@@ -4,7 +4,7 @@
         <i class="icon icon-menu"></i> searchrefiner
     </a>
     <div class="off-canvas">
-        <ul class="menu off-canvas-sidebar text-center" id="sidebar">
+        <ul class="menu off-canvas-sidebar" id="sidebar">
             <li class="menu-item">
                 <div class="tile tile-centered">
                     <div class="tile-icon"><img src="/static/favicon.png" class="avatar" width="32px"></div>
@@ -13,8 +13,6 @@
             </li>
             <li class="divider"></li>
             <li class="menu-item"><a href="/">Home</a></li>
-            <li class="menu-item"><a href="/tree">QueryVis</a></li>
-            <li class="menu-item"><a href="/transform">Transform</a></li>
             <li class="menu-item"><a href="/settings">Settings</a></li>
             <li class="menu-item"><a href="/plugins">Plugins</a></li>
         </ul>

components/util.tmpl.html

@@ -3,7 +3,7 @@
 {{end}}
 
 {{define "footer"}}
-<footer>
+<footer class="pt-2">
     Version {{template "version"}} |
     <a href="https://ielab.io/searchrefiner/">about</a> |
     <a href="/help">help</a> |

config.json

@@ -1,11 +1,17 @@
 {
-  "Host": "http://localhost:4853",
-  "AdminEmail": "[email protected]",
+  "Host": "localhost:4853",
+  "AdminEmail": "[email protected]",
   "Admins": [
-    "admin"
+    "hscells"
   ],
   "Entrez": {
-    "Email": "[email protected]",
-    "APIKey": "1234"
+    "Email": "[email protected]",
+    "APIKey": "22a11de46af145ce59bb288e0ede66721f09"
+  },
+  "Options": {
+    "Cui2VecEmbeddings": "/Users/s4558151/Repositories/cui2vec/testdata/cui2vec_precomputed.bin",
+    "Cui2VecMappings": "/Users/s4558151/Repositories/cui2vec/cuis.csv",
+    "Quiche": "/Users/s4558151/Repositories/cui2vec/quiche.cache",
+    "QuickRank": "/Users/s4558151/quickrank/bin/quicklearn"
   }
 }