Merge commit '908dd1' (new db.json spec + templates + updated settings) into with_tina_1.2

00.DOCUMENTATION/A-Introduction/project_structure.md

+Résumé de la structure globale
+----------------------------------
+
+Après commits de la semaine 26-30 juin 2017, une structure plus facile pour les déploiements
+  - les settings sont le seul élément à part
+  - les sous-dossiers respectent la "separation of concerns"
+  - une valeur dans les settings et un script bash à lancer 1 fois (adapt_html_paths.sh) suffisent à reconfigurer toute l'appli pour des routes de déploiement spécifiques (par exemple ajouter un prefixe comme 'static/tinawebJS' à tous les liens internes)
+  - un nouveau dossier twpresets contient des configurations toutes faites pour les cas de déploiement les plus fréquents
+  - les librairies tierces-parties ont été groupées permettant de les substituer avec plus de facilité lors de factorisation avec les mêmes libs déjà déployées autrement, ou lors de màj de ces librairies
+
+```
+├── 00.DOCUMENTATION
+│   └── (fusionné avec ./doc)
+├── data
+│   └── (graphes par sous-projets)
+├── db.json
+├── explorerjs.html         <= point d'entrée lancement
+├── settings_explorerjs.js  <= point d'entrée config
+├── favicon.ico
+├── LICENSE
+├── README.md
+├── twbackends              <= APIS externes
+│   ├── phpAPI              <= api CSV et CortextDB
+│   └── twitterAPI2
+├── twlibs                  <= librairies développées chez nous
+│   ├── css
+│   ├── fonts
+│   ├── img
+│   └── README.md
+├── twlibs3                 <= librairies tierces-parties
+│   ├── bootstrap-3
+│   ├── bootstrap-native
+│   ├── freshslider
+│   ├── jquery-3
+│   ├── readmore.js
+│   ├── sigma_v1.2
+│   ├── sigma_v1.5
+│   └── tweets
+|
+├── twmain                  <=   ancien dossier tinawebJS
+│   ├── main.js
+│   ├── extras_explorerjs.js  <= ajouté à l'intérieur
+│   ├── (etc)
+│   └── Tinaweb.js
+|
+├── twmodules              <= modules internes
+│   ├── crowdsourcingModule
+│   └── histogramModule
+├── twpresets               <= variantes de settings
+│   ├── README.md
+│   └── settings_explorerjs.comex.js
+└── twtools
+    |
+    └── adapt_html_paths.sh  <= "compile" un nouvel explorerjs.prod.html
+                                avec les routes utilisées au déploiement
+```

00.DOCUMENTATION/A-Introduction/servermenu_config.md

+## Servermenu Configuration
+
+The servermenu file associates some metadata to each graph file.
+
+It is used if `sourcemode="servermenu"` is found in the url params or the settings file.
+
+By default, the file is called `./db.json` (this can be modified in settings under `TW.conf.paths.sourceMenu`)
+
+The `db.json` file of this distribution contains many examples.
+
+------------------------------------------------------
+#### Minimal Config
+
+One minimal servermenu entry contains:
+  - a data dir path (**the project**)
+  - for each project: a list of graph files subpaths (**the graph source**)
+  - for each graph file: a list of expected node types starting by 'node0' (**the nodetypes**)
+
+```json
+  "$$data/yourprojectdir": {
+    "graphs": {
+      "$$graph_source.gexf":{
+        "node0": {"name": "$$a_typename_of_nodes"}
+      },
+      "$$another_graph_source.json":{
+        "node0": {"name": "$$a_typename_of_nodes"}
+      }
+    }
+  }
+```
+The value **typename_of_nodes** should match the `type` or `category` attribute value of your nodes in the source gexf or json. It acts as a filter specifying the nodes that will be displayed in the ProjectExplorer GUI.
+
+##### For a bipartite graph
+If the source file has 2 types of nodes, the config should look like this:
+```json
+  "$$data/yourprojectdir": {
+    "graphs": {
+      "$$source_file.ext":{
+        "node0": {"name": "$$typename_of_term_nodes"},
+        "node1": {"name": "$$typename_of_context_nodes"}
+      }
+    }
+  }
+```
+
+NB: giving an empty string value to `node1.name` property will group all other found types in an "other" category.
+
+Having a node0.name entry and optionally a node1.name is enough to display the graph.
+
+###### Real life example
+```json
+"data/comexjsons": {
+  "graphs": {
+    "graph_example.json": {
+      "node0": { "name": "NGram" },
+      "node1": { "name": "Document" }
+    }
+  }
+}
+```
+
+------------------------------------------------------
+#### Activating relatedDocs LocalDB queries
+
+The servermenu file also allows configuration of associated queries for selected node(s): **relatedDocs**
+
+To enable it, you need to add to your node entry the `reldbfile` key:
+
+```json
+  "node0": {
+    "name": "$$blabla",
+    "reldbfile": "$$relpath/to/csv/or/sqlite"
+  }
+```
+
+The presence of this property `reldbfile` makes the API usable in db.json.
+
+##### More relatedDocs settings
+In addition, for full configuration, the following entries can be set under node0 or node1.
+
+###### => for a CSV doc-by-doc table
+Expected type is `"csv"` and you should fill the columns to search in.
+```json
+"reldbtype": "csv",
+"reldbqcols": ["list", "of", "columns", "to", "search", "in", "for", "node0"]
+```
+
+###### Real life example
+```json
+"data/gargistex": {
+    "first": "shale_and_ice.gexf",
+    "graphs": {
+      "shale_and_ice.gexf": {
+        "node0": {
+          "name": "terms",
+          "reldbtype": "csv",
+          "reldbfile": "shale_and_ice.csv",
+          "reldbqcols": ["title", "abstract"]
+        }
+      },
+      "model_calibration.gexf": {
+        "node0": {
+          "name": "terms",
+          "reldbtype": "csv",
+          "reldbfile": "model_calibration.csv",
+          "reldbqcols": ["title", "abstract"]
+        }
+      }
+    }
+}
+```
+
+###### => for CortextDB SQL tables
+Expected type is `"CortextDB"` and you should fill the table to search in.
+```json
+"reldbtype": "CortextDB",
+"reldbqtable": []
+```

data/test/mini_for_csv.csv

+"title"	"pubdate"	"author"	"journal"	"keywords"	"text"
+"python is nice"	"2001"	"Asher,Lutz"	"areview"	"python, forest"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"python is cool"	"2003"	"-cc-"	"areview"	"python, ocean"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"scala is great"	"2003"	"Odersky"	"areviewB"	"scala, crop"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"php is expressive"	"2005"	"Nixon"	"areview"	"php, mysql"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"php is expressive2"	"2010"	"-bb-"	"areviewB"	"php, web"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"javascript rules the web"	"2005"	"someguy,anotherguy"	"areviewC"	"javascript, web"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"a cool article"	"2008"	"-dd-"	"areview"	"coolness, ecosystem"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"another cool article"	"2001"	"-aa-"	"areview"	"coastal, coolness"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"a js primer"	"2004"	"mandelbrot"	"areviewC"	"coolness, ecosystem, grain yield"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"
+"a scala js primer"	"2004"	"somebody"	"areviewC"	"keyword, ecosystem, growth response"	"hic in Palatio prima urbi fundamenta ieci. arcem iam scelere emptam Sabini habent"

db.json

 {
-  "data/comexjsons": {
-    "first" : "graph_example.json",
-    "graphs": {
-      "graph_example.json": {
-        "node0": { "name": "NGram" },
-        "node1": { "name": "Document" }
-      }
-    }
-  },
   "data/gargistex": {
     "first" : "shale_and_ice.gexf",
     "graphs":{
@@ -17,7 +8,7 @@
           "reldbtype": "csv",
           "reldbfile": "shale_and_ice.csv",
           "reldbqcols": ["title"],
-          "reltemplate": "_todo"
+          "reltemplate": "bib_details"
         }
       },
       "model_calibration.gexf": {
@@ -26,11 +17,20 @@
           "reldbtype": "csv",
           "reldbfile": "model_calibration.csv",
           "reldbqcols": ["title"],
-          "reltemplate": "_todo"
+          "reltemplate": "bib_details"
         }
       }
     }
   },
+  "data/comexjsons": {
+    "first" : "graph_example.json",
+    "graphs": {
+      "graph_example.json": {
+        "node0": { "name": "NGram" },
+        "node1": { "name": "Document" }
+      }
+    }
+  },
   "data/test": {
     "first" : "mini_for_csv.gexf",
     "graphs": {
@@ -40,24 +40,22 @@
           "reldbtype": "csv",
           "reldbfile": "mini_for_csv.csv",
           "reldbqcols": ["title","keywords","text"],
-          "reltemplate": "_todo"
+          "reltemplate": "bib_details"
         },
         "node1": {
           "name": "person",
           "reldbtype": "csv",
           "reldbfile": "mini_for_csv.csv",
           "reldbqcols": ["author"],
-          "reltemplate": "_todo"
+          "reltemplate": "bib_details"
         }
       },
       "test_with_various_atts.gexf": {}
     }
   },
   "data/politoscope": {
-    "dbname":null,
     "title":"Politoscope",
     "date":"2017",
-    "abstract":"",
     "first" : "ProgrammeDesCandidats.enrichi.gexf",
     "graphs": {
       "ProgrammeDesCandidats.enrichi.gexf": {
@@ -69,14 +67,14 @@
     }
   },
   "data/ClimateChange": {
-    "abstract":"ISIABSTRACT",
     "graphs": {
       "Maps_S_800.gexf": {
           "node0": {
             "name": "ISItermsWhitelistV2Oct_5 & ISItermsWhitelistV2Oct_5",
-            "reldbtable": "ISItermsWhitelistV2Oct_5",
-            "reldbname" : "wos_climate-change_title_2014-2015.db",
-            "reldbtype": "CortextDB"
+            "reldbqtable": "ISItermsWhitelistV2Oct_5",
+            "reldbfile" : "wos_climate-change_title_2014-2015.db",
+            "reldbtype": "CortextDB",
+            "reltemplate": "cortext_with_link"
           }
       }
     }

explorerjs.html

@@ -58,7 +58,7 @@
   <!-- NB bootstrap 3 not used for main grid (graph + bars) but inside the bars -->
   <link rel="stylesheet" href="twlibs3/bootstrap-3/css/bootstrap.min.css" media="screen">
   <link rel="stylesheet" href="twlibs3/freshslider/freshslider.css" media="screen">
-  <link rel="stylesheet" href="twlibs3/tweets/tweet.light.ltr.css" />
+  <link rel="stylesheet" href="twlibs3/tweets/tweet.light.excerpt.css" />
   <link rel="stylesheet" href="twlibs3/tweets/custom.css"/>
 
   <link rel="stylesheet" href="twlibs/css/twjs.css">
@@ -73,7 +73,14 @@
 
 
 <body>
+  <a id='mainlogo' href="https://github.com/moma/ProjectExplorer"
+        class="navbar-higher"
+        title="Project Explorer">
+        <img src="twlibs/img/logo.png"
+             style="width:50px; position:absolute; top:-8px; left:-4px; z-index:5; overflow:visible;">
+  </a>
   <div id="topbar" class="navbar navbar-default">
+
     <div class="container">
 
       <div class="navbar-collapse collapse" id="navbar-main">
@@ -82,6 +89,7 @@
             <!-- name will be replaced by TW.conf.branding, link by TW.conf.brandingLink -->
             <a href="#" class="navbar-middle navbar-brand twbrand-link">
               <span id="twbrand">TinaWebJS</span>
+
             </a>
           </li>
 
@@ -130,7 +138,7 @@
 
   <!-- ex-defaultop -->
   <div id="toolbar" class="navbar navbar-default">
-    <div id="defaultop" class="container">
+    <div id="defaultop" class="container-fluid">
 
       <div class="navbar-header">
         <button id="toolbar-open" type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#left" aria-expanded="false" aria-controls="navbar">
@@ -143,7 +151,7 @@
 
         <div id="left" class="navbar-collapse collapse">
 
-          <ul class="nav navbar-nav">
+          <ul class="nav navbar-nav navbar">
 
             <!--
             <li>
@@ -156,13 +164,6 @@
             </li>
             -->
 
-            <li><a href="https://communityexplorer.org"
-                  class="navbar-higher"
-                  title="Community Explorer">
-                  <img src="twlibs/img/logo.png"
-                       style="width:60px; position:absolute; top:-60px; left:-75px; z-index:5; overflow:visible;">
-            </a></li>
-
             <li>
                <a>
                 <button type="button" id="changetype" class="btn btn-success btn-sm">Change<br>Type</button>
@@ -256,9 +257,7 @@
 
           </ul>
 
-
-
-          <ul id="searchnav" class='nav navbar-nav'>
+          <ul id="searchnav" class='nav navbar-nav navbar-left'>
             <li class="navbar-lower">
               <div id="search_input_group" class="input-group input-group-sm my-nav-input-group">
                 <span class="input-group-btn crowdsourcingModule">
@@ -441,7 +440,10 @@
     </div>
   </div>
   <div id="sidebar">
-    <div id="tab-container" class='tab-container'>
+    <!-- manual file chooser if run locally -->
+    <div id="localInput"></div>
+
+    <div id="selection-tabs-contnr" class='selection-tabs-contnr'>
 
        <ul class='etabs'>
          <!-- for related elements from the combined graph (eg soc => sem) -->
@@ -460,21 +462,25 @@
        </div>
     </div>
 
-    <div class="question reldocs">
-      <div class="input-group">
-        <label for="reldocs-type" class="smlabel input-group-addon">Related documents type</label>
-        <select id="reldocs-type" name="reldocs-type"
-                class="custom-select form-control"
-                 onchange="TW.conf.relatedDocsType=this.value; getTopPapers()">
-            <option value="twitter">Twitter API</option>
-            <option value="LocalDB">Local DB query</option>
-        </select>
+    <!-- topPapers tabs -->
+    <div id="reldocs-tabs-wrapper" class="reldocs">
+
+      <!-- NB:  data-reldocstype should match TW.conf.relatedDocsType
+                and will be filled from TW.conf.relatedDocsAPIS keys
+          -->
+      <ul id="reldocs-tabs" class="nav nav-tabs" role="tablist">
+
+      </ul>
+
+      <!-- One tab pane
+           (only one with topPapers, we change content ourselves)
+         -->
+      <div class="tab-content">
+        <div id="topPapers" role="tabpanel" class="tab-pane active">
+        </div>
       </div>
-    </div>
-    <div id="topPapers">
-    </div>
 
-    <div id="localInput"></div>
+    </div>
 
     <div id="information"></div>
 
@@ -483,13 +489,14 @@
 
       open/close panel from: jsfiddle.net/KyleMit/kcpma
     -->
-    <div class="panel-group" id="accordion">
+    <div class="panel-group" id="varinfos-accordion">
 
 
       <div class="panel panel-default" id="video_explanation">
         <div class="panel-heading">
           <h4 class="panel-title">
-            <a data-toggle="collapse" data-target="#le_tutorial" href="#le_tutorial">
+            <a data-toggle="collapse" data-target="#le_tutorial" href="#le_tutorial"
+               data-parent="#varinfos-accordion">
               <span class="glyphicon glyphicon-eye-open" aria-hidden="true"></span>
               &nbsp;Tutorial video
             </a>
@@ -497,29 +504,35 @@
         </div>
 
         <!-- TODO: outcloud the video for better stream+player -->
-        <!-- <div class="panel-collapse collapse" id="le_tutorial">
+        <div class="panel-collapse collapse" id="le_tutorial">
+          <p>here video</p>
           <video width="100%"
-            src="video/AXA2015.mp4" controls=""  frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></video>
-        </div> -->
+            src="" controls=""  frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></video>
+        </div>
       </div>
 
       <div class="panel panel-default" id="tips_panel">
         <div class="panel-heading">
           <h4 class="panel-title">
-            <a data-toggle="collapse" data-target="#tips" href="#tips">
+            <a data-toggle="collapse" data-target="#tips" href="#tips"
+               data-parent="#varinfos-accordion">
               <span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
               &nbsp;Tips
             </a>
           </h4>
         </div>
 
-        <div class="panel-collapse collapse in" id="tips"></div>
+        <div class="panel-collapse collapse in" id="tips">
+          <p>here tips inserted by twmain/Tinaweb.js</p>
+        </div>
       </div>
 
-      <div class="panel panel-default" id="credits_panel">
+
+      <div class="panel panel-default" id="video_explanationw">
         <div class="panel-heading">
           <h4 class="panel-title">
-            <a data-toggle="collapse" data-target="#credits" href="#credits">
+            <a data-toggle="collapse" data-target="#credits" href="#credits"
+               data-parent="#varinfos-accordion">
               <span class="glyphicon glyphicon-flag" aria-hidden="true"></span>
               &nbsp;Credits
             </a>
@@ -527,19 +540,21 @@
         </div>
 
         <div class="panel-collapse collapse" id="credits">
-          <a href="https://bigdata.iscpif.fr/" target="_blank">
-              <img src="https://bigdata.iscpif.fr/images/logos/BIGDATA-Logo-PoweredBy-light.jpg"
-              alt="Powered by Big Data at ISCPIF"
-              style="width:85%; ">
-          </a>
-          <a href="https://github.com/moma" target="_blank">
-              <img src="twlibs/img/moma.png"
-              alt="Sciencemapping"
-              style="width:85%; ">
-          </a>
+          <p>
+            <a href="https://bigdata.iscpif.fr/" target="_blank">
+                <img src="https://bigdata.iscpif.fr/images/logos/BIGDATA-Logo-PoweredBy-light.jpg"
+                alt="Powered by Big Data at ISCPIF"
+                style="width:85%; ">
+            </a>
+            <a href="https://github.com/moma" target="_blank">
+                <img src="twlibs/img/moma.png"
+                alt="Sciencemapping"
+                style="width:85%; ">
+            </a>
+          </p>
         </div>
-
       </div>
+
     </div>
 
     <br><br>
@@ -610,12 +625,12 @@
     </div>
 
 
-    <div id="modalloader" class="modal fade">
+    <!-- <div id="modalloader" class="modal fade">
         <div id="loader" class="loader">
             <img src="twlibs/img/loader.gif"></img>
         </div>
         <div id="closeloader" data-dismiss="modal"></div>
-    </div>
+    </div> -->
 
 
     <div id="facet-options" class="modal fade">
@@ -725,10 +740,9 @@
       </div>
     </div>
 
-
+<!--
     <div id="geomapmodal" class="modal fade">
 
-        <!-- <div class="modal-content"> -->
           <div class="modal-header">
             <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
             <h4 class="modal-title">Geomap</h4>
@@ -736,12 +750,10 @@
           <div class="modal-body">
             <div class="geomapCont"></div>
           </div>
-        <!-- </div> -->
-          <!-- <div class="geomapCont"></div> -->
           <div id="closegeomap" data-dismiss="modal"></div>
-    </div>
+    </div> -->
 
-    <div id="heatgraph"></div>
+    <!-- <div id="heatgraph"></div> -->
 
   </div>
 

settings_explorerjs.js

@@ -6,8 +6,8 @@ TW.conf = (function(TW){
 
   let TWConf = {}
 
-  TWConf.branding = 'Community Explorer 2'  // <--- name displayed in upper left
-  TWConf.brandingLink = 'https://communityexplorer.org'   // <--- link to "home"
+  TWConf.branding = 'ProjectExplorer'  // <--- name displayed in upper left
+  TWConf.brandingLink = 'https://github.com/moma/ProjectExplorer'   // <--- link to "home"
 
 
   // ==========================
@@ -17,13 +17,7 @@ TW.conf = (function(TW){
   // Graph data source
   // -----------------
   // the graph input depends on TWConf.sourcemode (or manual url arg 'sourcemode')
-  TWConf.sourcemode = "api"   // accepted: "api" | "serverfile" | "servermenu" | "localfile"
-
-  // server-side .gexf|.json default source
-  TWConf.sourceFile = ""
-
-  // ...or server-side gexf default source list
-  TWConf.sourceMenu = "db.json"
+  TWConf.sourcemode = "servermenu"   // accepted: "api" | "serverfile" | "servermenu" | "localfile"
 
   // ...or remote bridge to default source api ajax queries
   TWConf.sourceAPI={};
@@ -34,9 +28,8 @@ TW.conf = (function(TW){
   // Related documents (topPapers) data source
   // -----------------------------------------
 
-  TWConf.getRelatedDocs = false
+  TWConf.getRelatedDocs = true
   TWConf.relatedDocsMax = 10
-  TWConf.relatedDocsAPI = "http://127.0.0.1:5000/twitter_search"
 
   TWConf.relatedDocsType = "twitter"      // accepted: "twitter" | "LocalDB"
                                           // POSSible: "elastic"
@@ -115,7 +108,7 @@ TW.conf = (function(TW){
     'weight'          : {'col': "heatmap" , 'n': 5,  'binmode': 'samerange'  },
     'Weighted Degree' : {'col': "heatmap", 'n': 8,  'binmode': 'samerange'  },
     'out-degree'      : {'col': "heatmap" , 'n': 3,  'binmode': 'samepop'  },
-    'CC'              : {'col': "cluster" ,          'binmode': 'off'},
+    'country'         : {'col': "cluster" ,          'binmode': 'off'},
     'ACR'             : {'col': "cluster" ,          'binmode': 'off'},
 'cluster_universal_index': {'col': "cluster" ,         'binmode': 'off'      },
        'community_orphan' : {'col': "cluster" ,        'binmode': 'off'      }
@@ -165,8 +158,12 @@ TW.conf = (function(TW){
   // Modules path
   // ------------
   TWConf.paths = {
-    'ourlibs': 'static/tinawebJS/twlibs',
-    'modules': 'twmodules'
+    'ourlibs': 'twlibs',
+    'templates': "twlibs/hit_templates",
+    'modules': 'twmodules',
+
+    'sourceFile': "",           // server-side .gexf|.json default source
+    'sourceMenu': "db.json"     // ...or server-side gexf default source list
   }
   Object.freeze(TWConf.paths)  // /!\ to prevent path modification before load
 
@@ -216,7 +213,7 @@ TW.conf = (function(TW){
   // if fa2Available, the auto-run config:
 
     TWConf.fa2Enabled= true;        // fa2 auto-run at start and after graph modified ?
-    TWConf.fa2Milliseconds=10000;    // duration of auto-run
+    TWConf.fa2Milliseconds=2000;    // duration of auto-run
     TWConf.minNodesForAutoFA2 = 5   // graph size threshold to auto-run
 
 

twbackends/phpAPI/DirScan_main.php

-<?php
-
-header('Content-Type: application/json');
-
-include("DirectoryScanner.php");
-$projectFolderPat = dirname(dirname(getcwd())) . "/";
-$instance = new scanTree($projectFolderPat);
-$instance->getDirectoryTree("data");
-
-//pr(var_dump($instance->folders));
-$output = array();
-$output["folders"] = $instance->folders;
-$output["gexf_idfolder"] = $instance->gexf_folder;
-echo json_encode($output);
-
-// ** Debug Functions: **
-function br() {
-    echo "----------<br>";
-}
-
-function pr($msg) {
-    echo $msg . "<br>";
-}
-
-?>

twbackends/phpAPI/README.md

@@ -58,18 +58,47 @@ TWConf.relatedDocsType = "LocalDB"  (CSV or CortextDB)
 Finally, to match the correct DB with the correct graph file:
   - both should reside in `data/yoursubdir`
   - the appropriate source database information needs to appear in `db.json` in order to associate the graph source file (eg gexf) with this related docs API:
+
+
 ```json
 "data/yoursubdir": {
-      "dbname":"your.sqlite.db",
-      "title":"yourDocumentTitlesTable",
-      "date":"yourDocumentPubDatesTable",
-      "abstract":"yourDocumentContentsTable",
       "graphs": {
           "your.graph.gexf": {
-              "semantic": { "table":"yourTableWithTerms"},
-              "social": { "table":"yourTableWithSocialNodes"}
+              "node0": {
+                        "name": "terms",
+                        "reldbtype": "CortextDB",
+                        "reldbfile": "yourDB.db",
+                        "reldbqtable": "yourTableWithTerms"
+                      },
+              "node1": {
+                        "name": "people",
+                        "reldbtype": "CortextDB",
+                        "reldbfile": "yourDB.db",
+                        "reldbqtable": "yourTableWithSocialNodes"
+                      },
+          }
+      }
+},
+
+"data/anothersubdir": {
+      "graphs": {
+          "another.graph.gexf": {
+              "node0": {
+                        "name": "terms",
+                        "reldbtype": "csv",
+                        "reldbfile": "aCsvByDocs.csv",
+                        "reldbqcols": ["title", "text", "keywords"]
+                      },
+              "node1": {
+                        "name": "people",
+                        "reldbtype": "csv",
+                        "reldbfile": "aCsvByDocs.csv",
+                        "reldbqcols": ["authors", "editors"]
+                      },
           }
       }
 }
+
 ```
-£TODO update after new specifications implemented
+
+See more exemples and explanations in [servermenu_config.md](https://github.com/moma/ProjectExplorer/blob/master/00.DOCUMENTATION/A-Introduction/servermenu_config.md).

twbackends/phpAPI/clear_favorites.php

-<?php
-
-echo 'toto';
-?>
\ No newline at end of file

twbackends/phpAPI/csv_div.php

@@ -7,47 +7,50 @@ error_reporting(-1);
 
 
 // DISPLAY THE RESULTS
-function displayDoc($docId, $score, $base) {
-
-  $output = "";
+function displayDoc($docId, $score, $base, $outmode) {
 
   // POSS score should have a data-score attribute
-  $output = "<li class='searchhit' title='".$score."'>";
 
   // shortcut to doc
   $doc = $base[$docId];
 
-  // £TODO new concept: use searchhit-templates
-  $has_template = False ;
-  if ($has_template) {
+  // fallback "universal" values
+  $title = try_attrs_until_you_find($doc, ['title', 'tit', 't']);
+  $source = try_attrs_until_you_find($doc, ['source', 'journal', 'j']);
+  $keywords = try_attrs_until_you_find($doc, ['keywords', 'keyword', 'kw']);
+  $author = try_attrs_until_you_find($doc, ['authors', 'author', 'auth', 'au']);
+  $doccontent = try_attrs_until_you_find($doc, ['text', 'txt', 'abstract', 'content']);
 
-  }
-  else {
-    // fallback "universal" values
-    $title = try_attrs_until_you_find($doc, ['title', 'tit', 't']);
-    $source = try_attrs_until_you_find($doc, ['source', 'journal', 'j']);
-    $keywords = try_attrs_until_you_find($doc, ['keywords', 'keyword', 'kw']);
-    $author = try_attrs_until_you_find($doc, ['authors', 'author', 'auth', 'au']);
-    $doccontent = try_attrs_until_you_find($doc, ['text', 'txt', 'abstract', 'content']);
-
-    $date = try_attrs_until_you_find($doc, ['pubdate', 'publication_year', 'date']);
-
-    // detailed dates, gargantext-compatible
-    $month = try_attrs_until_you_find($doc, ['publication_month']);
-    $day = try_attrs_until_you_find($doc, ['publication_day']);
-    if ($month) {       $date .= "/".$month;
-      if ($day) {         $date .= "/".$day;  } }
-
-    // "universal" template
+  $date = try_attrs_until_you_find($doc, ['pubdate', 'publication_year', 'date']);
+
+  // detailed dates, gargantext-compatible
+  $month = try_attrs_until_you_find($doc, ['publication_month']);
+  $day = try_attrs_until_you_find($doc, ['publication_day']);
+  if ($month) {       $date .= "/".$month;
+    if ($day) {         $date .= "/".$day;  } }
+
+  // "universal" template
+  if ($outmode == 'html') {
+    $output = "<li class='searchhit' title='".$score."'>";
     $output.="<p><b>$title</b> by <span class='author'>$author</span>, <i>$source</i> [$date]</p>";
     if (strlen($keywords)) {
       $output.="<p><b>keywords:</b> $keywords</p>";
     }
     $output.="<p><span class='hit-text'>$doccontent</span></p>";
+    $output.="</li>";
+  }
+  // json mode
+  else {
+    $output = array(
+      "tit" => $title,
+      "au" => $author,
+      "src" => $source,
+      "kws" => $keywords,
+      "txt" => $doccontent,
+      "date" => $date,
+      "score" => $score
+    );
   }
-
-  $output.="</li>";
-
   return $output;
 }
 
@@ -67,6 +70,7 @@ function try_attrs_until_you_find($doc_obj, $attr_names_array) {
 
 
 $htmlout = "<ul class=infoitems>\n";
+$jsonout = array();
 $nb_displayed = 0;
 foreach ($sims as $doc => $freq) {
   // doc limit
@@ -75,16 +79,30 @@ foreach ($sims as $doc => $freq) {
   }
 
   $rowid = ltrim($doc, 'd');
-  $thisdoc = displayDoc($rowid, $freq, $base);
+  $thisdoc = displayDoc($rowid, $freq, $base, $output_mode);
   // echodump("doc", $thisdoc);
-  $htmlout .= $thisdoc."\n";
 
+  if ($output_mode == "html") {
+    $htmlout .= $thisdoc."\n";
+  }
+  else {
+    array_push($jsonout, $thisdoc);
+  }
   // doc limit
   $nb_displayed++;
 }
 $htmlout .= "</ul>\n";
 
-echo '<br/><h4><font color="#0000FF"> Full text of top '.$max_item_displayed."/".count($sims).' related publications:</font></h4>'.$htmlout;
+if ($output_mode == "html") {
+  echo '<br/><h4><font color="#0000FF"> Full text of top '.$nb_displayed."/".count($sims).' related publications:</font></h4>';
+  echo $htmlout;
+}
+else {
+  echo json_encode(array(
+    'hits' => $jsonout,
+    'nhits' => $nb_displayed
+  ));
+}
 
 // to see the entire results array:
 // --------------------------------

twbackends/phpAPI/csv_indexation.php

@@ -55,14 +55,14 @@ function parse_and_index_csv($filename, $typed_cols_to_index, $separator, $quote
           $base[$rowid][$colname] = $line_fields[$c];
 
           // fill our search index if the type+col was asked in postings
-          foreach (['semantic', 'social'] as $swtype){
-            if (array_key_exists($swtype, $postings)) {
-              if (array_key_exists($colname, $postings[$swtype])) {
+          for ($ndtypeid = 0 ; $ndtypeid < $GLOBALS["ntypes"] ; $ndtypeid++) {
+            if (array_key_exists($ndtypeid, $postings)) {
+              if (array_key_exists($colname, $postings[$ndtypeid])) {
                 // basic tokenisation (TODO specify tokenisation delimiters etc.)
                 $tokens = preg_split("/\W/", $line_fields[$c]);
 
                 // for debug
-                // echo("indexing column:".$colname." under type:".$swtype.'<br>');
+                // echo("indexing column:".$colname." under type:".$ndtypeid.'<br>');
                 // var_dump($tokens);
 
                 foreach($tokens as $tok) {
@@ -70,16 +70,16 @@ function parse_and_index_csv($filename, $typed_cols_to_index, $separator, $quote
                   if (strlen($tok)) {
 
                     // POSS : stopwords could be used here
-                    if (! array_key_exists($tok, $postings[$swtype][$colname])) {
-                      $postings[$swtype][$colname][$tok] = array();
+                    if (! array_key_exists($tok, $postings[$ndtypeid][$colname])) {
+                      $postings[$ndtypeid][$colname][$tok] = array();
                     }
                     // in a csv, rowid is a pointer to the document
-                    if (array_key_exists($docid, $postings[$swtype][$colname][$tok])) {
+                    if (array_key_exists($docid, $postings[$ndtypeid][$colname][$tok])) {
                       // we keep the frequencies
-                      $postings[$swtype][$colname][$tok][$docid]++ ;
+                      $postings[$ndtypeid][$colname][$tok][$docid]++ ;
                     }
                     else {
-                      $postings[$swtype][$colname][$tok][$docid] = 1;
+                      $postings[$ndtypeid][$colname][$tok][$docid] = 1;
                     }
                   }
                 }

twbackends/phpAPI/default_doc_details.php

 <?php
+include('tools.php');
 include('parameters_details.php');
-$db = $gexf_db[$gexf];
 
-$base = new PDO("sqlite:../" .$db);
+$base = new PDO("sqlite:" .$mainpath.$graphdb);
 $query = str_replace( '__and__', '&', $_GET["query"] );
 $terms_of_query = json_decode($query);
 
 // echo "mainpath: ".$mainpath."<br>";
-// echo "thedb: ".$db."<br>";
+// echo "thedb: ".$mainpath.$graphdb."<br>";
 // echo "thequery: ".var_dump($terms_of_query);
 
 echo '
@@ -18,7 +18,7 @@ echo '
   <link rel="stylesheet" href="js/jquery-ui.css" />
   <script src="js/jquery-1.9.1.js"></script>
   <script src="js/jquery-ui.js"></script>
-  
+
   <script>
   $(function() {
     $( "#tabs" ).tabs({
@@ -27,12 +27,12 @@ echo '
   });
   </script>
 </head>
-          
+
     <body>
     <div id="tabs">
   <ul>
     <li><a href="#tabs-1">Selected Document</a></li>
-    <li><a href="full_doc_list.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&index='.$_GET["index"].'&type='.urlencode($_GET["type"]).'">Full list</a></li>';    
+    <li><a href="full_doc_list.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&index='.$_GET["index"].'&type='.urlencode($_GET["type"]).'">Full list</a></li>';
   echo '</ul>';
 
 echo '<div id="tabs-1">';
@@ -43,14 +43,14 @@ $id=$_GET["id"];
 // //$elems = json_decode($query);
 //   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
 //         foreach ($base->query($sql) as $row) {
-//           $country=$CC[strtoupper($row['data'])];         
+//           $country=$CC[strtoupper($row['data'])];
 //         }
 
 	$sql = 'SELECT data FROM ISITITLE WHERE id='.$id.' group by data';
 
 	foreach ($base->query($sql) as $row) {
 		$output.='<h2>'.$row['data'].'</h2>';
-		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";		
+		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";
 	}
 
 
@@ -76,7 +76,7 @@ $id=$_GET["id"];
 //   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
 //   foreach ($base->query($sql) as $row) {
 //     $country=$CC[strtoupper($row['data'])];
-  
+
 //     $output.=strtoupper($country).'<br/>   ';
 //   }
 
@@ -118,7 +118,7 @@ $id=$_GET["id"];
     $abs.=". ".$row['data'];
 	}
   $abs=str_replace('ISSUES:'  ,'<br/><br/><b>Issues:</b>',$abs);
-  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);    
+  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);
   $abs=str_replace('IMPACT:'  ,'<br/><br/><b>Impact:</b>',$abs);
   $abs=str_replace('NOVELTY:'  ,'<br/><br/><b>Novelty:</b>',$abs);
   $abs=str_replace('BOLD INNOVATION:'  ,'<br/><br/><b>Bold innovation:</b>',$abs);
@@ -131,7 +131,7 @@ $id=$_GET["id"];
   $abs=str_replace('_x000D_', ' ', $abs);
   $abs=str_replace('•', ' ', $abs);
   $abs=str_replace('’', '\'', $abs);
-  
+
   foreach ($terms_of_query as $key => $value) {
     $abs=str_ireplace($value,'<font color="green"><b> '.$value.'</b></font>',$abs);
   }
@@ -140,7 +140,7 @@ $id=$_GET["id"];
   }
 
   $output.='<br/><p align="justify"><b>Abstract : </b><i>'.$abs.' </i></p>';
-  $output.="<br>"; 
+  $output.="<br>";
 
 
 

twbackends/phpAPI/full_doc_list.php

 <?php
+include('tools.php');
 include('parameters_details.php');
-$db = $gexf_db[$gexf];
 
-$base = new PDO("sqlite:../" .$db);
+$base = new PDO("sqlite:" .$mainpath.$graphdb);
 
 
 $output = "<ul>"; // string sent to the javascript for display
-#http://localhost/branch_ademe/php/test.php?type=social&query=[%22marwah,%20m%22]
 
 
 $type = $_GET["type"];
@@ -14,7 +13,7 @@ $query = str_replace( '__and__', '&', $_GET["query"] );
 $terms_of_query=json_decode($_GET["query"]);
 $elems = json_decode($query);
 
-// nombre d'item dans les tables 
+// nombre d'item dans les tables
 $sql='SELECT COUNT(*) FROM ISIABSTRACT';
 foreach ($base->query($sql) as $row) {
   $table_size=$row['COUNT(*)'];
@@ -23,7 +22,6 @@ foreach ($base->query($sql) as $row) {
 $table = "";
 $column = "";
 $id="";
-$twjs=end( explode("/",getcwd()) )."/"; // LOCALDB folder.
 
 if($type=="social"){
   $table = "ISIAUTHOR";
@@ -63,9 +61,9 @@ $sum=0;
 //The final query!
 // array of all relevant documents with score
 
-foreach ($base->query($sql) as $row) {        
+foreach ($base->query($sql) as $row) {
         // on pondère le score par le nombre de termes mentionnés par l'article
-        
+
         //$num_rows = $result->numRows();
         $wos_ids[$row[$id]] = $row["count(*)"];
         $sum = $row["count(*)"] +$sum;
@@ -76,8 +74,8 @@ foreach ($base->query($sql) as $row) {
 
 $number_doc=ceil(count($wos_ids)/3);
 $count=0;
-foreach ($wos_ids as $id => $score) { 
-  if ($count<1000){
+foreach ($wos_ids as $id => $score) {
+  if ($count<200){
     // retrieve publication year
     $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
     foreach ($base->query($sql) as $row) {
@@ -85,23 +83,16 @@ foreach ($wos_ids as $id => $score) {
     }
 
     // to filter under some conditions
-    $to_display=true; 
+    $to_display=true;
     if ($to_display){
       $count+=1;
       $output.="<li title='".$score."'>";
-      $output.=imagestar($score,$factor,$twjs).' '; 
+      $output.=imagestar($score,$factor,'./').' ';
       $sql = 'SELECT data FROM ISITITLE WHERE id='.$id." group by data";
 
       foreach ($base->query($sql) as $row) {
-         $output.='<a href="default_doc_details.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
-
-                        //this should be the command:
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
-
-                        //the old one:  
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
-        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="twlibs/img/gs.png"></a>'; 
-        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+        $output.='<a href="default_doc_details.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>';
       }
 
   // get the authors
@@ -110,9 +101,7 @@ foreach ($wos_ids as $id => $score) {
         $output.=strtoupper($row['data']).', ';
       }
 
-  //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
-
-      $output.=$external_link."</li><br>";      
+      $output.=$external_link."</li><br>";
     }
 
   }else{
@@ -126,21 +115,4 @@ $output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$ou
 
 echo $output;
 
-
-function imagestar($score,$factor,$twjs) {
-// produit le html des images de score
-  $star_image = '';
-  if ($score > .5) {
-    $star_image = '';
-    for ($s = 0; $s < min(5,$score/$factor); $s++) {
-      $star_image.='<img src="twlibs/img/star.gif" border="0" >';
-    }
-  } else {
-    $star_image.='<img src="twlibs/img/stargrey.gif" border="0">';
-  }
-  return $star_image;
-}
-
 ?>
-
-

twbackends/phpAPI/info_div.php

@@ -7,24 +7,54 @@ ini_set('display_startup_errors',1);
 // exemple call:
 // http://blabla/LOCALDB/info_div.php?type=semantic&bi=0&query=[%22Monte%20Carlo%22]&gexf=%22line/AXA/RiskV2PageRank1000.gexf%22&index=ISItermsAxa_2015
 
+include('tools.php');
 include('parameters_details.php');
 
-if ($_GET['dbtype'] == "CortextDB") {
-  $base = new PDO("sqlite:".$mainpath.$graphdb);
-  include('default_div.php');
+if ($output_mode == "json") {
+  header('Content-Type: application/json');
 }
 
+$dbtype = null;
+if (array_key_exists('reldbtype', $my_conf[$ntid])) {
+  $dbtype = $my_conf[$ntid]['reldbtype'];
+}
 else {
-  // to index: the "searchable columns"
-  if (! array_key_exists('toindex', $_GET)) {
-    echo('<br> info_div.php (csv mode): please provide columns to index <br>');
+  $guess_src = '';
+  if (array_key_exists('dbtype', $_GET))  {
+    $dbtype = $_GET['dbtype'];
+    $guess_src = "via url parameters";
   }
   else {
-    $idxcolsbytype = json_decode($_GET['toindex']);
+    $dbtype = 'csv'; // new default
+    $guess_src = "by default";
 
-    // echodump("columns to index",$idxcolsbytype);
+  }
+  errmsg("not filled", "$gexf -> node$ntid -> 'reldbtype'", "...Assuming dbtype is $dbtype ($guess_src).");
+}
 
 
+if ($dbtype == "CortextDB") {
+  $base = new PDO("sqlite:".$mainpath.$graphdb);
+  include('default_div.php');
+}
+
+else {
+  // to index: the union of "searchable columns" qcols for all nodetypes
+  $idxcolsbytype = [];
+  for ($i = 0; $i < $ntypes ; $i++) {
+    if ($my_conf[$i]['active']) {
+      $idxcolsbytype[$i] = [];
+      $idxcolsbytype[$i] = $my_conf[$i]['reldbqcols'];
+    }
+    // else {
+    //   echo("no nodetype ".$i."<br>");
+    // }
+  }
+
+  if (! $idxcolsbytype) {
+    echo('<br> info_div.php (csv mode): please provide reldbqcols param in db.json <br>');
+  }
+  else {
     // DO THE INDEXATION (or RETRIEVE CACHED ONE)
     // we use cache if memcached is present (and if we indexed the csv already)
     include('csv_indexation.php');
@@ -68,7 +98,7 @@ else {
 
     // DO THE SEARCH
     // -------------
-    $searchcols = json_decode($_GET['searchin']);
+    $searchcols = $my_conf[$ntid]['reldbqcols'];
 
     // a - split the query
     $qtokens = preg_split('/\W/', $_GET["query"]);
@@ -93,7 +123,7 @@ else {
       for ($l=0 ; $l < count($searchcols) ; $l++) {
 
         // set of values we could find a match in
-        $searchable = $postings[$_GET['type']][$searchcols[$l]];
+        $searchable = $postings[$ntid][$searchcols[$l]];
 
         if (array_key_exists($tok, $searchable)) {
 

twbackends/phpAPI/parameters_details.php

 <?php
 
 
-# loading an associated db for a given gexf as relatedDocs php API
-$gexf_db = array();
+// GLOBAL PARAMS
+// -------------
+// 0 - output mode: 'json' or 'html'
+//  > json is for new use cases where styling is applied via template import in the js
+//  > html is the classical use where data is styled in this php scripts
+$output_mode = "json";
 
-# £££TODO read the db.json
-$gexf_db["data/ClimateChange/Maps_S_800.gexf"] = "data/ClimateChange/wos_climate-change_title_2014-2015.db";
-$gexf_db["data/AXA/RiskV2PageRank1000.gexf"] = "data/AXA/data.db";
-$gexf_db["data/AXA/RiskV2PageRank2500.gexf"] = "data/AXA/data.db";
-$gexf_db["data/AXA/RiskV2PageRank5000.gexf"] = "data/AXA/data.db";
-$gexf_db["data/test/mini_for_csv.gexf"] = "data/test/mini_for_csv.csv";
-$gexf_db["data/gargistex/shale_and_ice.gexf"] = "data/gargistex/shale_and_ice.csv";
-$gexf_db["data/gargistex/model_calibration.gexf"] = "data/gargistex/model_calibration.csv";
+// 1 - relative urls
+$our_php_root="twbackends/phpAPI";        // our php scripts relative URL
+$our_libs_root="twbackends/phpAPI";       // for our few icons and jquery-ui
+                                          // POSS could be merged with our_php_root
 
-// $gexf_db["data/ProgrammeDesCandidats.gexf"] = "foobar";
 
-$gexf= str_replace('"','',$_GET["gexf"]);
+// 2 - paths
+$mainpath=dirname(dirname(getcwd()))."/"; // default fs path to ProjectExplorer root
+                                          // (where data dir and db.json file reside)
 
-// default path to ProjectExplorer root
-// (where data directory and db.json file reside)
-$mainpath=dirname(getcwd())."/../";
+$project_menu_path = "db.json";
 
-$graphdb = $gexf_db[$gexf];
+// 3 - others
+$ntypes = 2;         // max node types
 
+// number of docs to display setting
+$max_item_displayed = 7;
 
 // for csv parsing
 $csvsep = "\t";
@@ -32,15 +34,36 @@ $csvquote = '"';
 $memserver = 'localhost';
 $memport = 11211;
 
-// number of docs to display setting
-$max_item_displayed = 7;
 
-// echodump("graphdb", $graphdb);
+// CONFIGURATION PARAMS
+// --------------------
+// parse db.json project menu and create a conf by file
+$conf = read_conf($mainpath.$project_menu_path, $ntypes);
+
+// =======================================
+// echodump("== READ CONF ==<br>", $conf);
+// =======================================
 
-function echodump($title, $anyObj) {
-  echo "<br>".$title.": ";
-  echo (json_encode($anyObj, JSON_PRETTY_PRINT));
-  echo "<br>";
+$gexf= str_replace('"','',$_GET["gexf"]);
+$ndtype = $_GET["type"];
+$ntid = null;
+$my_conf = null;
+
+// legacy types => generic types with 0 as default
+if ($ndtype == 'social')   {  $ntid = 1;  }
+else                       {  $ntid = 0;  }
+
+// echodump("params: node type id", $ntid);
+
+if (! $conf[$gexf][$ntid]['active']) {
+  errmsg("not active", "your graph ($gexf)");
+  exit(1);
+}
+else {
+  $my_conf = $conf[$gexf];
+  $graphdb = $my_conf[$ntid]['dir'].'/'.$my_conf[$ntid]['reldbfile'];
 }
 
+// echodump("params: reldb", $graphdb);
+
 ?>

twbackends/phpAPI/tools.php

+<?php
+
+
+function echodump($title, $anyObj) {
+  echo "<br>".$title.": ";
+  echo (preg_replace_callback("/\n(\s*)/", function($capt){
+    return('<br>'.str_repeat('&nbsp;', strlen($capt[0])));
+  }, json_encode($anyObj, JSON_PRETTY_PRINT)));
+  echo "<br>";
+}
+
+
+function errmsg($message, $context, $more = "") {
+  echo "<p class='micromessage'>The relatedDocs DB conf for $context is $message
+  (please read A-Introduction/servermenu_config.md).<br>$more</p>";
+}
+
+// reading db.json associations
+//    source graph file <=> (db, dbtype, cols) as relatedDocs php API
+function read_conf($filepath, $ntypes) {
+  $project_menu_fh = fopen($filepath, "r");
+  $json_st = '';
+  while (!feof($project_menu_fh)) {
+    $json_st .= fgets($project_menu_fh);
+  }
+  fclose($project_menu_fh);
+  $project_menu = json_decode($json_st);
+
+  // echodump("== db.json menu ==", $project_menu);
+
+  $conf = array();
+  foreach ($project_menu as $project_dir => $dir_items){
+    // NB access by obj property (and not array key)
+    if (! property_exists($dir_items, 'graphs')) {
+      error_log("tw/phpAPI skip error: conf file ($project_menu_path)
+                 has no 'graphs' entry for project '$project_dir' !");
+      continue;
+    }
+    foreach ($dir_items->graphs as $graph_file => $graph_conf){
+      // echodump("== $graph_file ==", $graph_conf);
+
+      $gpath = $project_dir.'/'.$graph_file;
+
+      // NB a graph conf can now have different settings for each nodetype
+      // node0 <=> classic type 'semantic'
+      // node1 <=> classic type 'social'
+
+      $conf[$gpath] = array($ntypes);
+
+      for ($i = 0 ; $i < $ntypes ; $i++) {
+        // check node0, node1, etc to see if they at least have a reldbfile
+        if (! property_exists($graph_conf, 'node'.$i)
+            || ! property_exists($graph_conf->{'node'.$i}, 'reldbfile') ) {
+          $conf[$gpath][$i] = array('active' => false);
+          continue;
+        }
+        else {
+          // we have a file for this type: copy entire conf
+          $conf[$gpath][$i] = (array)$graph_conf->{'node'.$i};
+
+          $conf[$gpath][$i]['active'] = true;
+          $conf[$gpath][$i]['dir'] = $project_dir;
+        }
+        // POSS here info on higher level may be propagated for lower ones
+        //     (ex: if dbtype is on the project level, its value should count
+        //          for each source file in the project unless overridden)
+      }
+    }
+  }
+  return $conf;
+}
+
+function imagestar($score,$factor,$static_libs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > 1) {
+    $star_image = '';
+    $yellow_star = '<img src="'.$static_libs.'/img/star.gif" border="0" >';
+    $grey_star = '<img src="'.$static_libs.'/img/stargrey.gif" border="0">';
+    $max = 5 * $score / $factor;
+    for ($s = 0; $s < 5 ; $s++) {
+      if ($s < $max) {
+        $star_image.=$yellow_star;
+      }
+      else {
+        $star_image.= $grey_star;
+      }
+    }
+  }
+  return $star_image;
+}
+
+?>

twbackends/phpAPI/unused/README.md

+#### Unused functionalities
+
+  - `tfidf.php`: compute a tfidf value per term (as pointwise metric for ranking, not similarities) table in Cortext-like databases
+  - `listFiles.php` + `DirectoryScanner.php`: alternative strategy to navigate between source files (old tina before db.json)
+  - `favorites.php` : query a favorites table in Cortext-like databases

twbackends/phpAPI/favorite.php → twbackends/phpAPI/unused/favorite.php

@@ -2,6 +2,7 @@
 $db= $_GET["db"];//I receive the specific database as string!
 $terms_of_query=json_decode($_GET["query"]);
 include('parameters_details.php');
+include('tools.php');
 $base = new PDO("sqlite:" .$mainpath.$db);
 $query=$_GET["query"];
 $gexf=$_GET["gexf"];
@@ -20,7 +21,7 @@ foreach ($base->query($sql) as $row){
 
 $favorite_keywords=array();
 
-foreach ($wos_ids as $id => $score) { 
+foreach ($wos_ids as $id => $score) {
   if ($count<1000){
     // retrieve publication year
     $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
@@ -38,8 +39,8 @@ foreach ($wos_ids as $id => $score) {
         }else{
           $favorite_keywords[$row['data']]=1;
         }
-      }  
-      
+      }
+
 
 
       $sql = 'SELECT data FROM ISITITLE WHERE id='.$id;
@@ -47,12 +48,12 @@ foreach ($wos_ids as $id => $score) {
          $output.='<a href="default_doc_details.php?db='.urlencode($db).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
 
                         //this should be the command:
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> ";
 
-                        //the old one:  
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
-        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>'; 
-        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+                        //the old one:
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>';
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>';
       }
 
   // get the authors
@@ -62,7 +63,7 @@ foreach ($wos_ids as $id => $score) {
       }
 
       if($project_folder!='nci'){
-        
+
         $output.='('.$pubdate.') ';
 
       }else {
@@ -73,15 +74,15 @@ foreach ($wos_ids as $id => $score) {
   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
   foreach ($base->query($sql) as $row) {
     $country=$CC[strtoupper($row['data'])];
-  
+
     $output.=strtoupper($country).'  ';
   }
 
 
   //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
 
-      $output.=$external_link."</li><br>";      
-    
+      $output.=$external_link."</li><br>";
+
 
   }else{
     continue;
@@ -106,22 +107,6 @@ foreach ($favorite_keywords as $key => $value) {
 $output= '<h3>'.$num_favorite.' favorite items </h3>'.$tag_could.'<br/>'.$output;
 
 
-echo $output;                
-
-function imagestar($score,$factor,$twjs) {
-// produit le html des images de score
-  $star_image = '';
-  if ($score > .5) {
-    $star_image = '';
-    for ($s = 0; $s < min(5,$score/$factor); $s++) {
-      $star_image.='<img src="twlibs/img/star.gif" border="0" >';
-    }
-  } else {
-    $star_image.='<img src="twlibs/img/stargrey.gif" border="0">';
-  }
-  return $star_image;
-}
-        
-        
+echo $output;
 
 ?>

twbackends/phpAPI/unused/variants/README.md

+
+### phpAPI old use-case specific variants
+
+They are quasi-identical to info_div.php and full_doc_list.php, kept for future decision to remove or add as conditional behavior.
+
+Apparent use-cases:
+  - `info_div2.php`: tweetoscope
+  - `full_doc_list2.php`: pasteur
+  - `default_doc_details2.php`: pasteur
+  - `full_doc_list_tidf.php`: ???

twbackends/phpAPI/default_doc_details2.php → twbackends/phpAPI/unused/variants/default_doc_details2.php

 <?php
+include('tools.php');
 include('parameters_details.php');
 $db = $gexf_db[$gexf];
 
@@ -18,7 +19,7 @@ echo '
   <link rel="stylesheet" href="js/jquery-ui.css" />
   <script src="js/jquery-1.9.1.js"></script>
   <script src="js/jquery-ui.js"></script>
-  
+
   <script>
   $(function() {
     $( "#tabs" ).tabs({
@@ -27,12 +28,12 @@ echo '
   });
   </script>
 </head>
-          
+
     <body>
     <div id="tabs">
   <ul>
     <li><a href="#tabs-1">Selected Document</a></li>
-    <li><a href="full_doc_list2.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&type='.urlencode($_GET["type"]).'">Full list</a></li>';    
+    <li><a href="full_doc_list2.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&type='.urlencode($_GET["type"]).'">Full list</a></li>';
   echo '</ul>';
 
 echo '<div id="tabs-1">';
@@ -43,7 +44,7 @@ $id=$_GET["id"];
 // //$elems = json_decode($query);
 //   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
 //         foreach ($base->query($sql) as $row) {
-//           $country=$CC[strtoupper($row['data'])];         
+//           $country=$CC[strtoupper($row['data'])];
 //         }
 
 
@@ -59,7 +60,7 @@ $id=$_GET["id"];
 
 	foreach ($base->query($sql) as $row) {
 		$output.='<h2>'.$row['data'].'</h2>';
-		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";		
+		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";
 	}
 
 
@@ -77,13 +78,13 @@ $id=$_GET["id"];
 
 
     $output.=' (2014) ';
- 
+
 
 // // get the country
 //   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
 //   foreach ($base->query($sql) as $row) {
 //     $country=$CC[strtoupper($row['data'])];
-  
+
 //     $output.=strtoupper($country).'<br/>   ';
 //   }
 
@@ -125,7 +126,7 @@ $id=$_GET["id"];
     $abs.=". ".$row['data'];
 	}
   $abs=str_replace('ISSUES:'  ,'<br/><br/><b>Issues:</b>',$abs);
-  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);    
+  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);
   $abs=str_replace('IMPACT:'  ,'<br/><br/><b>Impact:</b>',$abs);
   $abs=str_replace('NOVELTY:'  ,'<br/><br/><b>Novelty:</b>',$abs);
   $abs=str_replace('BOLD INNOVATION:'  ,'<br/><br/><b>Bold innovation:</b>',$abs);
@@ -138,7 +139,7 @@ $id=$_GET["id"];
   $abs=str_replace('_x000D_', ' ', $abs);
   $abs=str_replace('•', ' ', $abs);
   $abs=str_replace('’', '\'', $abs);
-  
+
   foreach ($terms_of_query as $key => $value) {
     $abs=str_ireplace($value,'<font color="green"><b> '.$value.'</b></font>',$abs);
   }
@@ -147,7 +148,7 @@ $id=$_GET["id"];
   }
 
   $output.='<br/><p align="justify"><b>Abstract : </b><i>'.$abs.' </i></p>';
-  $output.="<br>"; 
+  $output.="<br>";
 
 
 

twbackends/phpAPI/full_doc_list2.php → twbackends/phpAPI/unused/variants/full_doc_list2.php

 <?php
+include('tools.php');
 include('parameters_details.php');
 $db = $gexf_db[$gexf];
 
@@ -14,7 +15,7 @@ $query = str_replace( '__and__', '&', $_GET["query"] );
 $terms_of_query=json_decode($_GET["query"]);
 $elems = json_decode($query);
 
-// nombre d'item dans les tables 
+// nombre d'item dans les tables
 $sql='SELECT COUNT(*) FROM ISIABSTRACT';
 foreach ($base->query($sql) as $row) {
   $table_size=$row['COUNT(*)'];
@@ -23,7 +24,6 @@ foreach ($base->query($sql) as $row) {
 $table = "";
 $column = "";
 $id="";
-$twjs="pasteurapi/"; // submod path of TinaWebJS
 
 if($type=="social"){
   $table = "ISIAUTHOR";
@@ -64,9 +64,9 @@ $sum=0;
 //The final query!
 // array of all relevant documents with score
 
-foreach ($base->query($sql) as $row) {        
+foreach ($base->query($sql) as $row) {
         // on pondère le score par le nombre de termes mentionnés par l'article
-        
+
         //$num_rows = $result->numRows();
         $wos_ids[$row[$id]] = $row["count(*)"];
         $sum = $row["count(*)"] +$sum;
@@ -77,7 +77,7 @@ foreach ($base->query($sql) as $row) {
 
 $number_doc=ceil(count($wos_ids)/3);
 $count=0;
-foreach ($wos_ids as $id => $score) { 
+foreach ($wos_ids as $id => $score) {
   if ($count<1000){
     // retrieve publication year
     $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
@@ -86,23 +86,22 @@ foreach ($wos_ids as $id => $score) {
     }
 
     // to filter under some conditions
-    $to_display=true; 
+    $to_display=true;
     if ($to_display){
       $count+=1;
       $output.="<li title='".$score."'>";
-      $output.=imagestar($score,$factor,$twjs).' '; 
+      $output.=imagestar($score,$factor,$our_libs_root).' ';
       $sql = 'SELECT data FROM ISITITLE WHERE id='.$id." group by data";
 
       foreach ($base->query($sql) as $row) {
-         $output.='<a href="default_doc_details2.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+         $output.='<a href="'.$our_php_root.'/default_doc_details2.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
 
                         //this should be the command:
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> ";
 
-                        //the old one:  
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
-        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="twlibs/img/gs.png"></a>'; 
-        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+                        //the old one:
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="'.$our_libs_root.'/img/gs.png"></a>';
       }
 
   // get the authors
@@ -113,7 +112,7 @@ foreach ($wos_ids as $id => $score) {
 
   //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
 
-      $output.=$external_link."</li><br>";      
+      $output.=$external_link."</li><br>";
     }
 
   }else{
@@ -127,21 +126,4 @@ $output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$ou
 
 echo $output;
 
-
-function imagestar($score,$factor,$twjs) {
-// produit le html des images de score
-  $star_image = '';
-  if ($score > .5) {
-    $star_image = '';
-    for ($s = 0; $s < min(5,$score/$factor); $s++) {
-      $star_image.='<img src="twlibs/img/star.gif" border="0" >';
-    }
-  } else {
-    $star_image.='<img src="twlibs/img/stargrey.gif" border="0">';
-  }
-  return $star_image;
-}
-
 ?>
-
-

twbackends/phpAPI/full_doc_list_tidf.php → twbackends/phpAPI/unused/variants/full_doc_list_tidf.php

 <?php
+include('tools.php');
 include('parameters_details.php');
-  
+
 $db= $_GET["db"];//I receive the specific database as string!
 $query=$_GET["query"];
 $gexf=$_GET["gexf"];
@@ -21,7 +22,7 @@ $output = "<ul>"; // string sent to the javascript for display
 $type = $_GET["type"];
 $query = str_replace( '__and__', '&', $_GET["query"] );
 $elems = json_decode($query);
-// nombre d'item dans les tables 
+// nombre d'item dans les tables
 $sql='SELECT COUNT(*) FROM ISIABSTRACT';
 foreach ($base->query($sql) as $row) {
   $table_size=$row['COUNT(*)'];
@@ -31,7 +32,7 @@ foreach ($base->query($sql) as $row) {
 // Other restrictions
 // extracting the project folder and the year
 if (strpos($gexf,'2013')>0){
-  $year='2013'; 
+  $year='2013';
   $year_filter=true;
 }elseif (strpos($gexf,'2012')>0){
   $year='2012';
@@ -42,14 +43,13 @@ if (strpos($gexf,'2013')>0){
 
 // identification d'une année pour echoing
 if($project_folder=='nci'){
-  $year_filter=true;  
-  
+  $year_filter=true;
+
 }
 
 $table = "";
 $column = "";
 $id="";
-$twjs="tinawebJS/"; // submod path of TinaWebJS
 
 if($type=="social"){
   $table = "ISIAUTHOR";
@@ -95,7 +95,7 @@ $sum=0;
 //echo $sql;//The final query!
 // array of all relevant documents with score
 $count=0;
-foreach ($corporadb ->query($sql) as $row) {  
+foreach ($corporadb ->query($sql) as $row) {
   //if ($count<4*$max_item_displayed){
     $wos_ids[$row[$id]] = $row['sum(tfidf)'];//$row["count(*)"];
     $sum = $row["count(*)"] +$sum;
@@ -109,7 +109,7 @@ foreach ($corporadb ->query($sql) as $row) {
 
 $number_doc=ceil(count($wos_ids)/3);
 $count=0;
-foreach ($wos_ids as $id => $score) { 
+foreach ($wos_ids as $id => $score) {
   if ($count<1000){
     // retrieve publication year
     $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
@@ -118,37 +118,37 @@ foreach ($wos_ids as $id => $score) {
     }
 
     // to filter under some conditions
-    $to_display=true; 
+    $to_display=true;
     if ($project_folder=='echoing'){
       if ($year_filter){
         if ($pubdate!=$year){
           $to_display=false;
         }
-      }     
+      }
     }elseif($project_folder=='nci'){
       if ($year_filter){
         if ($pubdate!='2013'){
           $to_display=false;
         }
-      } 
+      }
     }
 
     if ($to_display){
       $count+=1;
       $output.="<li title='".$score."'>";
-      $output.=imagestar($score,$factor,$twjs).' '; 
+      $output.=imagestar($score,$factor,$our_libs_root).' ';
       $sql = 'SELECT data FROM ISITITLE WHERE id='.$id;
 
       foreach ($base->query($sql) as $row) {
-         $output.='<a href="default_doc_details.php?db='.urlencode($db).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+         $output.='<a href="'.$our_php_root.'/default_doc_details.php?db='.urlencode($db).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
 
                         //this should be the command:
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> ";
 
-                        //the old one:  
-      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
-        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="twlibs/img/gs.png"></a>'; 
-        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+                        //the old one:
+      //$output.='<a href="JavaScript:newPopup(\''.$our_php_root.'/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="'.$our_libs_root.'/img/gs.png"></a>';
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>';
       }
 
   // get the authors
@@ -158,7 +158,7 @@ foreach ($wos_ids as $id => $score) {
       }
 
       if($project_folder!='nci'){
-        
+
         $output.='('.$pubdate.') ';
 
       }else {
@@ -169,7 +169,7 @@ foreach ($wos_ids as $id => $score) {
 
   //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
 
-      $output.=$external_link."</li><br>";      
+      $output.=$external_link."</li><br>";
     }
 
   }else{
@@ -183,21 +183,4 @@ $output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$ou
 
 echo $output;
 
-
-function imagestar($score,$factor,$twjs) {
-// produit le html des images de score
-  $star_image = '';
-  if ($score > .5) {
-    $star_image = '';
-    for ($s = 0; $s < min(5,$score/$factor); $s++) {
-      $star_image.='<img src="twlibs/img/star.gif" border="0" >';
-    }
-  } else {
-    $star_image.='<img src="twlibs/img/stargrey.gif" border="0">';
-  }
-  return $star_image;
-}
-
 ?>
-
-

twbackends/phpAPI/info_div2.php → twbackends/phpAPI/unused/variants/info_div2.php

@@ -13,7 +13,6 @@ $elems = json_decode($query);
 $table = "";
 $column = "";
 $id="";
-$twjs="API_CNRS/"; // submod path of TinaWebJS
 
 
 if($type=="semantic"){
@@ -65,9 +64,9 @@ $sum=0;
 //The final query!
 // array of all relevant documents with score
 
-foreach ($base->query($sql) as $row) {        
+foreach ($base->query($sql) as $row) {
         // on pondère le score par le nombre de termes mentionnés par l'article
-        
+
         //$num_rows = $result->numRows();
         $wos_ids[$row[$id]] = $row["count(*)"];
         $sum = $row["count(*)"] +$sum;
@@ -76,21 +75,21 @@ foreach ($base->query($sql) as $row) {
 
 // /// nombre de document associés $related
 $total_count=0;
-$count_max=500; 
+$count_max=500;
 $number_doc=count($wos_ids);
 $count=0;
 
 $all_terms_from_selected_projects=array();// list of terms for the top 6 project selected
 
 // to filter under some conditions
-$to_display=true; 
+$to_display=true;
 $count=0;
 
 
-foreach ($wos_ids as $id => $score) { 
+foreach ($wos_ids as $id => $score) {
   if ($total_count<$count_max) {
     // retrieve publication year
-    
+
     if ($to_display){
       $total_count+=1;
 
@@ -99,27 +98,27 @@ foreach ($wos_ids as $id => $score) {
 
         $sql = 'SELECT data FROM ISITITLE WHERE id='.$id.' group by data';
         foreach ($base->query($sql) as $row) {
-          $external_link="<a href=http://google.com/webhp?#q=".urlencode('"'.utf8_decode($row['data']).'"')." target=blank>".' <img width=15px src="twlibs/img/google.png"></a>';  
+          $external_link="<a href=http://google.com/webhp?#q=".urlencode('"'.utf8_decode($row['data']).'"')." target=blank>".' <img width=15px src="'.$our_libs_root.'/img/google.png"></a>';
           $output.="<li title='".$score."'>";
-          $output.=$external_link.imagestar($score,$factor,$twjs).' '; 
-          $output.='<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
+          $output.=$external_link.imagestar($score,$factor,$our_libs_root).' ';
+          $output.='<a href="JavaScript:newPopup(\''.$our_php_root.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
           // $output.='<a>'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
-          
+
         }
 
         $sql = 'SELECT data FROM ISIDOI WHERE id='.$id.' group by data';
         foreach ($base->query($sql) as $row) {
-          $output.=$external_link.imagestar($score,$factor,$twjs).' ';  
-          $output.='<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
-          
+          $output.=$external_link.imagestar($score,$factor,$our_libs_root).' ';
+          $output.='<a href="JavaScript:newPopup(\''.$our_php_root.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
+
         }        // get the authors
         $sql2 = 'SELECT data FROM ISIAUTHOR WHERE id='.$id. ' group by data';
         foreach ($base->query($sql2) as $row2) {
           $output.=(str_replace("\r", "", $row2['data'])).', ';
-          
+
         }
         $output = rtrim($output, ", ");
-        $output.="</li><br>"; 
+        $output.="</li><br>";
 
       }
     }
@@ -154,10 +153,10 @@ function getDB ($directory)  {
     $result = "";
     $handler = opendir($directory);
     while ($file = readdir($handler)) {
-      if ($file != "." && $file != ".." 
-              && 
+      if ($file != "." && $file != ".."
+              &&
         ((strpos($file,'.db~'))==false && (strpos($file,'.db'))==true )
-              || 
+              ||
         ((strpos($file,'.sqlite~'))==false && (strpos($file,'.sqlite'))==true)
       ) {
             //$results[] = $file;
@@ -170,19 +169,4 @@ function getDB ($directory)  {
     return $result;
 }
 
-
-function imagestar($score,$factor,$twjs) {
-// produit le html des images de score
-  $star_image = '';
-  if ($score > .5) {
-    $star_image = '';
-    for ($s = 0; $s < min(5,$score/$factor); $s++) {
-      $star_image.='<img src="twlibs/img/star.gif" border="0" >';
-    }
-  } else {
-    $star_image.='<img src="twlibs/img/stargrey.gif" border="0">';
-  }
-  return $star_image;
-}
-
 ?>

twlibs/css/selection-panels.css

@@ -117,11 +117,16 @@
 
 .zoombarbuttons {
   position:relative;  /* b/c they can contain absolute wait icon */
+  width:100%;
+  height:100%;
 }
 
 .zoombarbuttons:hover {
     opacity: .7;
 }
+/*.zoombarbuttons:hover > img {
+    box-shadow: 0px 0px 1px 3px #033;
+}*/
 
 #zoomMinusButton, #zoomPlusButton {
     display: block;

twlibs/css/twjs-mobile.css

@@ -23,7 +23,7 @@
     bottom: 0;
     height: 25%;
     width: 100%;
-    background-color: #CCC;
+    background-color: #BBB;
   }
 
   #topPapers {

twlibs/css/twjs.css

@@ -94,7 +94,7 @@ html.waiting {
 }
 
 #defaultop #searchnav {
-  padding-left: 40px;
+  padding-left: 30px;
 }
 #defaultop .my-nav-input-group {
   width: 2vw !important;
@@ -118,6 +118,8 @@ html.waiting {
 #defaultop .slider-legend {
     margin: 10px 0 0 0 ;
 }
+
+
 #defaultop .settingslider {
     max-width: 90px !important;
     display: inline-block ;
@@ -135,6 +137,10 @@ html.waiting {
   line-height: 12px;
 }
 
+#left {
+  max-width:
+}
+
 /* override navbar toggle on right side when collapsed */
 #toolbar-open {
   float:left !important;
@@ -143,8 +149,8 @@ html.waiting {
 
 
 /* right info panel */
-#accordion {
-  display:none
+#varinfos-accordion {
+  display:block;
 }
 
 /* VARIAE */
@@ -178,7 +184,9 @@ html.waiting {
 
 .searchhit {
   font-family: "Roboto", "Droid Sans", sans-serif;
-  border: 1px solid #222;
+  border: 1px solid #888;
+  border-radius: 7px;
+  background-color: #FFF;
   padding: 7px 0 7px 12px;
   margin: 10px 10px 0 0;
 }
@@ -188,22 +196,11 @@ html.waiting {
   font-family: "Crete Round", "garamond", serif ;
   padding: 5px;
 }
-
-#tab-container {
-  margin: 7px;
-}
-
-#topPapers{
-    display: none;
-    margin: 7px;
-    padding: 10px 0px 10px 10px;
-    border-style:solid;
-    background-color:white;
-    color:black;
-    border: 1px solid #666;
-    -moz-border-radius: 3px;
-    -webkit-border-radius: 3px;
-    -border-radius: 3px;
+.hit-keywords {
+  color: #000;
+  font-style: italic;
+  font-family: "Crete Round", "garamond", serif ;
+  padding: 5px;
 }
 
 /* small messages */
@@ -216,21 +213,10 @@ p.micromessage{
 	font-weight: bold;
 }
 
-/* Example Styles for Demo */
-.etabs { margin: 0; padding: 0; line-height: 15px;}
-.tab { display: inline-block; zoom:1; *display:inline; background: #eee; border: solid 1px #999; border-bottom: none; -moz-border-radius: 4px 4px 0 0; -webkit-border-radius: 4px 4px 0 0; }
-.tab a { font-size: 12px; line-height: 15px; display: block; padding: 0 5px 2px 5px; outline: none; }
-.tab a:hover { text-decoration: underline; }
-.tab.active { background: #fff; padding-top: 6px; position: relative; top: 1px; border-color: #666; }
-.tab a.active { font-weight: bold; }
-.tab-container .panel-container { background: #fff; border: solid #666 1px; padding: 10px; -moz-border-radius: 0 4px 4px 4px; -webkit-border-radius: 0 4px 4px 4px; }
-.panel-container { margin-bottom: 10px; }
-
-
-
 
 /* SIDEBAR CONTENT */
 
+
 #sidebar {
   padding: 5px 0 0 5px;
 }
@@ -253,7 +239,7 @@ p.micromessage{
 
 #localInput {
     font-size: 80%;
-    padding: 10px;
+    height: 0;  /* before activation if explorerjs.html run locally */
 }
 
 #localgraphfile {
@@ -288,8 +274,71 @@ p.micromessage{
 
 ul.infoitems {
   list-style: none;
+  padding: 0 !important;
 }
 
+/* etabs => easytabs (for selection)
+ * nav-tabs => bootstrap[-native] tabs (for reldocs)
+ */
+
+
+#selection-tabs-contnr, #reldocs-tabs-wrapper {
+ margin: 7px;
+ display: none; /* shown when selection */
+}
+
+.etabs{ margin: 0; padding: 0; line-height: 15px;}
+.tab {
+  display: inline-block; zoom:1; *display:inline; background: #eee; border: solid 1px #999; border-bottom: none; -moz-border-radius: 4px 4px 0 0; -webkit-border-radius: 4px 4px 0 0; }
+.tab a { font-size: 12px; line-height: 15px; display: block; padding: 0 5px 2px 5px; outline: none; }
+.tab a:hover { text-decoration: underline; }
+.tab.active { background: #fff; padding-top: 6px; position: relative; top: 1px; border-color: #666; }
+.tab a.active { font-weight: bold; }
+.selection-tabs-contnr .panel-container { background: #fff; border: solid #666 1px; padding: 10px; -moz-border-radius: 0 4px 4px 4px; -webkit-border-radius: 0 4px 4px 4px; }
+.panel-container { margin-bottom: 10px; }
+
+
+.tab-content {
+    padding: 10px;
+    border: 1px solid #555;
+    border-radius: 0 4px 4px 4px;
+    background-color: #BBB;
+    display: block;
+}
+
+.nav-tabs > li > a,
+.nav-tabs > li:hover > a {
+    margin-bottom: -1px;
+    padding: 4px 7px;
+    border-top: 1px solid rgb(204, 204, 204);
+    border-left: 1px solid rgb(204, 204, 204);
+    border-right: 1px solid rgb(204, 204, 204);
+}
+
+.nav-tabs > li.active > a,
+.nav-tabs > li.active > a:hover,
+.nav-tabs > li.active > a:focus {
+    color: white !important;
+    background-color: #3E6280;
+    border-top: 1px solid #222;
+    border-left: 1px solid #222;
+    border-right: 1px solid #222;
+}
+
+#topPapers{
+    display: none;
+    color:black;
+}
+
+
+
+
+
+
+
+
+
+
 /* switch css -- generic (src: proto.io/freebies/onoff/)*/
 .onoffswitch {
     position: relative; width: 38px;

twlibs/hit_templates/cortext_with_link.html

+<li class="searchhit" title='$${score}'>
+    <a href="$${link}">$${tit}</a> <span class="author">$${au}</span>
+</li>

twlibs/hit_templates/universal.html

+<li class="searchhit" title="$${score}">
+  <p>
+   <a href="$${link}"><b>$${tit}</b></a>
+    by
+   <span class="author">$${au}</span>
+   ,
+   <i>$${src}</i>
+   [$${date}]
+  </p>
+
+  <p>
+    <span class="hit-keywords">
+     $${kws}
+    </span>
+    <span class="hit-text">
+     $${txt}
+    </span>
+  </p>
+</li>

twlibs3/tweets/custom.css

 blockquote.Tweet {
   display: inline-block !important;
+  background-color: #FFF;
   font-family: Roboto, "Helvetica Neue", "Segoe UI", Calibri, sans-serif !important;
   font-size: 12px !important;
   font-weight: bold !important;
-  line-height: 16px !important;
+  line-height: 14px !important;
   border-color: #eee #ddd #bbb !important;
   border-radius: 5px !important;
   border-style: solid !important;
   border-width: 1px !important;
   box-shadow: 0 1px 3px rgba(0, 0, 0, 0.15) !important;
   margin: 10px 5px !important;
-  padding: 0 16px 16px 16px !important;
+  padding: 8px 16px !important;
   min-width: 330px !important;
   width: 330px !important;
   max-width: 330px !important;
 }
 
 p.Tweet-text {
-  font-size: 16px !important;
+  padding: .4em 0 0 0 !important;
+  margin-bottom: -1em !important;
+  font-size: 12px !important;
   font-weight: normal !important;
-  line-height: 20px !important;
-  min-height: 90px !important;
+  line-height: 16px !important;
+  min-height: 70px !important;
 }
 
 blockquote.Tweet a {
@@ -32,7 +35,8 @@ blockquote.Tweet a {
 
 blockquote.Tweet a:hover,
 blockquote.Tweet a:focus {
-  text-decoration: underline !important;
+  /*text-decoration: underline !important;*/
+  text-decoration: none !important;
 }
 
 .Tweet-metadata {
@@ -41,3 +45,7 @@ blockquote.Tweet a:focus {
 .Tweet-authorScreenName {
   font-size: .9em;
 }
+
+.Tweet-actions {
+    padding-left: .5em;
+}

twmain/Tinaweb.js

@@ -381,11 +381,59 @@ var TinaWebJS = function ( sigmacanvas ) {
           }
         }
 
-        $('#tab-container').easytabs({
+        // initialize selection tabs (POSS: swap from easytabs lib to bs-native)
+        $('#selection-tabs-contnr').easytabs({
           updateHash:false,
           defaultTab: 'li#tabneigh'
         });
 
+        // initialize reldocs tabs
+        if (TW.conf.getRelatedDocs) {
+          // POSSible: create them on a settings list (currently in the HTML)
+
+          let ul = document.getElementById('reldocs-tabs')
+
+          let tabEls = []
+          for (var possibleAPI in TW.conf.relatedDocsAPIS) {
+            // create valid tabs
+            let newLi = document.createElement('li')
+            newLi.setAttribute("role", "presentation")
+            let newRDTab =  document.createElement('a')
+            newRDTab.text = possibleAPI
+            newRDTab.href = '#topPapers'
+            newRDTab.setAttribute("role", "tab")
+            newRDTab.dataset.toggle = 'tab'
+            newRDTab.dataset.reldocstype = possibleAPI
+
+            if (possibleAPI == TW.conf.relatedDocsType) {
+              newLi.setAttribute("class", "active")
+            }
+
+            // add to DOM
+            ul.append(newLi)
+            newLi.append(newRDTab)
+
+            // keep access
+            TW.gui.reldocTabs[possibleAPI] = newRDTab
+          }
+
+          // afterwards to get all types and the active type
+          for (let rdtype in TW.gui.reldocTabs) {
+            let tab = TW.gui.reldocTabs[rdtype]
+
+            // init toggle mecanisms (bootstrap.native/#componentTab)
+            // (just used for the tabs active/inactive handling,
+            //  content is *always* topPapers and we modify it ourselves)
+            new Tab(tab);
+
+            // add handler to switch relatedDocsType
+            tab.addEventListener('click', function(){
+              TW.conf.relatedDocsType = this.dataset.reldocstype
+              getTopPapers()
+            })
+          }
+        }
+
         // show any already existing panel
         document.getElementById("graph-panels").style.display = "block"
 
@@ -715,17 +763,15 @@ var TinaWebJS = function ( sigmacanvas ) {
           }
         })
 
-        if (TW.conf.getRelatedDocs && document.getElementById('reldocs-type')) {
-          document.getElementById('reldocs-type').value = TW.conf.relatedDocsType
+        // select currently preferred reldoc tab
+        if (TW.conf.getRelatedDocs && document.getElementById('reldocs-tabs')) {
+          TW.gui.reldocTabs[TW.conf.relatedDocsType].Tab.show()
         }
 
         $("#tips").html(getTips());
 
-        // a bit costly, TODO make conditional or deprecated
-        // showMeSomeLabels(6);
-
-        // updateDownNodeEvent(false);
-
+        // we start with no selection
+        $("#selection-tabs-contnr").hide();
 
         // #saveAs => toggle #savemodal initialized in html + bootstrap-native
 
@@ -1072,15 +1118,6 @@ var TinaWebJS = function ( sigmacanvas ) {
         }
       });
 
-      if (TW.conf.getRelatedDocs) {
-        let reldocsEls = document.querySelectorAll('.reldocs')
-        for (var k in reldocsEls) {
-          if (reldocsEls[k].style) {
-            reldocsEls[k].style.display = 'block'
-          }
-        }
-      }
-
       if (TW.conf.filterSliders) {
 
         // the indice of the first cat to be active (ex: '1')

twmain/enviroment.js

@@ -24,6 +24,7 @@ TW.gui.foldedSide=false;
 TW.gui.manuallyChecked = false;
 TW.gui.handpickedcolor = false;     // <= changes edge rendering strategy
 TW.gui.lastFilters = {}
+TW.gui.reldocTabs = []
 
 TW.gui.sizeRatios = [1,1]           // sizeRatios per nodetype
 

twmain/extras_explorerjs.js

@@ -373,12 +373,12 @@ function getTopPapers(){
     topPapersFetcher(
       swNodetypes[0],
       qWordsbySwType[swNodetypes[0]],
-      `<h2>${swNodetypes[0]}</h2>`,
-      function(enrichedHtml) {
+      [[],[]],
+      function(priorJsonHits) {
         topPapersFetcher(
           swNodetypes[1],
           qWordsbySwType[swNodetypes[1]],
-          enrichedHtml+`<p class=centered>---</p><h2>${swNodetypes[1]}</h2>`,
+          priorJsonHits,
           displayTopPapers
         )
       }
@@ -396,31 +396,30 @@ function getTopPapers(){
 //  - cbNext is a partial function to handle the follow-up
 //    (just pass it resHTML, to continue enriching or display)
 //
-function topPapersFetcher(swType, qWords, priorHtml, cbNext){
+function topPapersFetcher(swType, qWords, accumulHits, cbNext){
 
-  if (isUndef(priorHtml))    priorHtml = ''
-  if (isUndef(cbNext))       cbNext = displayTopPapers
+  // list of json object with hit metadata (title, author, etc.) by nodetype
+  if (isUndef(accumulHits))      accumulHits = [[],[]]
+
+  // callback to continue accumulating json hits or display to html
+  if (isUndef(cbNext))           cbNext = displayTopPapers
 
   // introducing the modern node type thanks to updated db.json specs
   let nodetype = (swType == 'semantic') ? 0 : 1
 
-  let stockErrMsg = `<p class="micromessage">
-    Your settings for relatedDocsType are set on ${TW.conf.relatedDocsType}
-    API but it couldn't be connected to.</p>`
-
-  if (TW.conf.relatedDocsType == "api") {
-    stockErrMsg += `<p class="micromessage">Check if it is running and
-    accessible:<br><span class=code>${TW.conf.relatedDocsAPI}</span></p>`
-  }
-
-  let resHTML = ''
-
   let apiurl = TW.conf.relatedDocsAPIS[TW.conf.relatedDocsType]
 
   if (! apiurl) {
     apiurl = TW.conf.relatedDocsAPI
   }
 
+  let stockErrMsg = `
+  <p class="micromessage">The API ${TW.conf.relatedDocsType} couldn't be connected to.</p>
+  <p class="micromessage">The queried route found in TW.conf was: <span class=code>${apiurl}</span>
+  <br>Check if it is running and accessible.</p>`
+
+  let resHTML = ''
+
   if (TW.conf.relatedDocsType == "twitter") {
     let joinedQ = qWords.map(function(w){return'('+w+')'}).join(' AND ')
     $.ajax({
@@ -430,34 +429,37 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
         contentType: "application/json",
         success : function(data){
             if (data.length) {
-              for (var k in data) {
-                let tweetJson = data[k]
-                resHTML += renderTweet(tweetJson)
-              }
+              accumulHits[nodetype] = accumulHits[nodetype].concat(data)
             }
             else {
-              resHTML += `<p class="micromessage centered">The query
-                         <span class=code>${joinedQ}</span> delivers
-                         no results on Twitter.</p>`
+              accumulHits[nodetype].push({
+                "error": `<p class="micromessage centered">The query
+                           <span class=code>${joinedQ}</span> delivers
+                           no results on Twitter.</p>`
+              })
             }
-            cbNext(priorHtml + resHTML)
+            cbNext(accumulHits)
         },
         error: function(){
           console.log(`Not found: relatedDocs for ${apiurl}`)
-          cbNext(priorHtml + stockErrMsg)
+          accumulHits[nodetype].push({
+            "error": stockErrMsg
+          })
+          cbNext(accumulHits)
         }
     });
   }
   else if (TW.conf.relatedDocsType == "LocalDB") {
     let thisRelDocsConf = TW.gmenuInfos[TW.File][nodetype]
     if (!thisRelDocsConf) {
-      resHTML =
-        `<p>Your settings for relatedDocsType are set on a local database,
+      accumulHits[nodetype].push({
+        "error": `<p>Your settings for relatedDocsType are set on a local database,
             but your servermenu file does not provide any information about
             the CSV or DB table to query for related documents
             (on nodetype ${nodetype}: ${swType})</p>`
-            cbNext(priorHtml + resHTML)
-            return
+      })
+      cbNext(accumulHits)
+      return
     }
     else {
       // /!\ documentation and specification needed for the php use cases /!\
@@ -468,53 +470,101 @@ function topPapersFetcher(swType, qWords, priorHtml, cbNext){
       //          or 'csv' (like gargantext exports)
 
       // POSS object + join.map(join)
-      let urlParams = "type="+swType+"&query="+joinedQ+"&gexf="+TW.File+"&n="+TW.conf.relatedDocsMax+"&dbtype="+thisRelDocsConf.reldbtype
-
-      if (thisRelDocsConf.reldbtype == "CortextDB") {
-        var qIndex = thisRelDocsConf.reldbtable    // a table
-        urlParams += `&index=${qIndex}`
-      }
-      else {
-        // a list of csv columns to search in
-        // ex: for semantic nodes matching we look in 'title', 'keywords' cols
-        //     for social nodes matching we look in 'authors' col... etc.
-        let joinedSearchCols = JSON.stringify(thisRelDocsConf.reldbqcols)
-        urlParams += `&searchin=${joinedSearchCols}`
-
-        // HIGHER LEVEL SCOPE (whole indexation directive) WILL BE MOVED TO PHP
-        let allCols = {}
-
-        if (TW.gmenuInfos[TW.File][0])
-          allCols.semantic = TW.gmenuInfos[TW.File][0].reldbqcols
-
-        if (TW.gmenuInfos[TW.File][1])
-          allCols.social = TW.gmenuInfos[TW.File][1].reldbqcols
-
-        let joinedAllCols = JSON.stringify(allCols)
-        urlParams += `&toindex=${joinedAllCols}`
-        // POSS use a direct access from php to db.json to avoid toindex
-      }
+      let urlParams = "type="+swType+"&query="+joinedQ+"&gexf="+TW.File+"&n="+TW.conf.relatedDocsMax ;
 
       $.ajax({
           type: 'GET',
           url: apiurl + '/info_div.php',
           data: urlParams,
+          contentType: "application/json",
           success : function(data){
-              console.log(`relatedDocs: ${apiurl}/info_div.php?${urlParams}`);
-              resHTML = data
-              cbNext(priorHtml + resHTML)
+            if (data.hits) {
+              accumulHits[nodetype] = accumulHits[nodetype].concat(data.hits)
+            }
+            cbNext(accumulHits)
           },
           error: function(){
             console.log(`Not found: relatedDocs for ${apiurl}`)
-            cbNext(priorHtml + stockErrMsg)
+            accumulHits[nodetype].push({
+              "error": stockErrMsg
+            })
+            cbNext(accumulHits)
           }
       });
     }
   }
 }
 
-function displayTopPapers(enrichedHtml) {
-  $("#topPapers").html(enrichedHtml);
+function makeRendererFromTemplate(tmplName) {
+  let tmplURL = TW.conf.paths.templates + '/' + tmplName + '.html'
+  let gotTemplate = AjaxSync({ url: tmplURL });
+
+  var tmplStr = ''
+  if (gotTemplate['OK']) {
+    tmplStr = gotTemplate.data
+  }
+
+  // we return a customized renderJsonToHtml function
+  return function(jsonHit) {
+    let htmlOut = tmplStr
+    for (key in jsonHit) {
+      // our tags look like this in the template ====> by $${author}, [$${date}]
+      let reKey = new RegExp('\\$\\$\\{'+key+'\\}', 'g')
+      // we replace them by value
+      htmlOut = htmlOut.replace(reKey, jsonHit[key])
+    }
+
+    // we also replace any not found keys by 'N/A'
+    let reKeyAll = new RegExp('\\$\\$\\{[^\\}]+\\}', 'g')
+    htmlOut = htmlOut.replace(reKeyAll, "N/A")
+
+    return htmlOut
+  }
+}
+
+function displayTopPapers(jsonHits) {
+
+  // console.log('jsonHits', jsonHits)
+
+  let resHTML = '<ul class="infoitems">'
+  let toHtmlFun = function(){}
+
+  for (var ndtypeId in TW.categories) {
+    if (TW.conf.relatedDocsType == 'twitter') {
+      toHtmlFun = renderTweet
+    }
+    else {
+      let thisRelDocsConf = TW.gmenuInfos[TW.File][ndtypeId]
+      if (thisRelDocsConf && thisRelDocsConf.reltemplate) {
+        // console.log("my rendering hits template", thisRelDocsConf.reltemplate)
+        
+        toHtmlFun = makeRendererFromTemplate(thisRelDocsConf.reltemplate)
+      }
+      else {
+        console.warn(`no rendering template found in ${TW.conf.paths.sourceMenu} for this source ${TW.File}...`)
+
+        // try the universal template
+        toHtmlFun = makeRendererFromTemplate("universal")
+      }
+    }
+
+    // console.log("my rendering fun", toHtmlFun)
+
+    for (var k in jsonHits[ndtypeId]) {
+      let hitJson = jsonHits[ndtypeId][k]
+      if (hitJson.error) {
+        resHTML += hitJson.error
+      }
+      else {
+        resHTML += toHtmlFun(hitJson)
+      }
+    }
+  }
+
+  resHTML += '</ul>'
+
+  // effect the changes in topPapers
+  $("#topPapers").html(resHTML);
 }
 
 function newPopup(url) {
@@ -687,8 +737,6 @@ function renderTweet( tweet) {
 }
 
 function getTips(){
-    param='';
-
     text =
         "<br>"+
         "Basic Interactions:"+
@@ -710,9 +758,6 @@ function getTips(){
         "<li>The 'change level' button allows to change between global view and node centered view,</li>"+
         "<li>To explore the neighborhood of a selection click on the 'change level' button.</li>"+
         "</ul>";
-
-    $("#tab-container").hide();
-    $("#tab-container-top").hide();
     return text;
 }
 

twmain/main.js

@@ -79,6 +79,8 @@ if (window.location.protocol == 'file:' || sourcemode == 'localfile') {
     remark.classList.add('comment')
     remark.classList.add('centered')
     inputDiv.appendChild(remark)
+    inputDiv.style.height = "auto";
+    inputDiv.style.padding = "10px";
   }
 
   // user can open a gexf or json from his fs
@@ -215,7 +217,7 @@ function syncRemoteGraphData () {
   // cases            (2)       and     (3) : we'll read a file from server
   // sourcemode == "serverfile" or "servermenu" (several files with <select>)
   else {
-    console.log("input case: server-side file, using TW.conf.sourceMenu or getUrlParam.file or TW.conf.sourceFile")
+    console.log("input case: server-side file, using TW.conf.paths.sourceMenu or getUrlParam.file or TW.conf.paths.sourceFile")
 
     // -> @mode is servermenu, files are listed in db.json file (preRes ajax)
     //      --> if @file also in url, choose the db.json one matching
@@ -223,13 +225,13 @@ function syncRemoteGraphData () {
 
     // -> @mode is serverfile
     //      -> gexf file path is in the urlparam @file
-    //      -> gexf file path is already specified in TW.conf.sourceFile
+    //      -> gexf file path is already specified in TW.conf.paths.sourceFile
 
     // menufile case : a list of source files in ./db.json
     if (sourcemode == 'servermenu') {
-        console.log("reading from FILEMENU TW.conf.sourceMenu")
+        console.log("reading from FILEMENU TW.conf.paths.sourceMenu")
         // we'll first retrieve the menu of available files in db.json, then get the real data in a second ajax
-        var infofile = TW.conf.sourceMenu
+        var infofile = TW.conf.paths.sourceMenu
 
         if (TW.conf.debug.logFetchers)  console.info(`attempting to load filemenu ${infofile}`)
         var preRES = AjaxSync({ url: infofile, datatype:"json" });
@@ -307,12 +309,12 @@ function syncRemoteGraphData () {
       TW.File = getUrlParam.file
     }
     // direct file fallback case: specified file in settings_explorer
-    else if (TW.conf.sourceFile && linkCheck(TW.conf.sourceFile)) {
+    else if (TW.conf.paths.sourceFile && linkCheck(TW.conf.paths.sourceFile)) {
       console.log("no @file arg: trying TW.conf.sourceFile from settings")
-      TW.File = TW.conf.sourceFile;
+      TW.File = TW.conf.paths.sourceFile;
     }
     else {
-      console.error(`No specified input and neither db.json nor TW.conf.sourceFile ${TW.conf.sourceFile} are present`)
+      console.error(`No specified input and neither db.json nor TW.conf.paths.sourceFile ${TW.conf.paths.sourceFile} are present`)
     }
 
     var finalRes = AjaxSync({ url: TW.File });

twmain/methods.js

@@ -122,14 +122,17 @@ function cancelSelection (fromTagCloud, settings) {
 
     // hide all selection panels
     if(fromTagCloud==false){
+        // £TODO give them all a common class
         $("#names").html("");
-        $("#topPapers").html(""); $("#topPapers").hide();
-        $("#opossiteNodes").html(""); $("#tab-container").hide();
+        $("#topPapers").html("");
+        $("#topPapers").hide();
+        $("#oppositeNodes").html("");
+        $("#selection-tabs-contnr").hide();
+        $("#reldocs-tabs-wrapper").hide();
         $("#information").html("");
         $("#searchinput").val("");
         $("#unselectbutton").hide();
         $("#lefttopbox").hide();
-        $("#tips").html(getTips());
     }
 
     // send "eraseNodeSet" event
@@ -430,21 +433,22 @@ function updateRelatedNodesPanel( sels , same, oppos ) {
 
     //using the readmore.js (NB readmore and easytabs are not easy to harmonize)
     $("#lefttopbox").show();
-    $("#tab-container").show();
+    $("#selection-tabs-contnr").show();
     $("#names").html(namesDIV).readmore({maxHeight:100});
     if(oppos.length>0) {
       $("#oppositeNodes").html(alterNodesDIV).readmore({maxHeight:200});
     }
     $("#sameNodes").html(sameNodesDIV).readmore({maxHeight:200});
     $("#information").html(informationDIV);
-    $("#tips").html("");
 
     if (TW.conf.getRelatedDocs) {
+      $("#reldocs-tabs-wrapper").show();
       $("#topPapers").show();
       getTopPapers()
     }
     else {
       $("#topPapers").hide()
+      $("#reldocs-tabs-wrapper").hide();
     }
 }
 

twmain/sigmaUtils.js

@@ -565,12 +565,7 @@ var SigmaUtils = function () {
           else {
               if ((TW.conf.fa2Enabled || args.manual)
                   && TW.partialGraph.graph.nNodes() >= TW.conf.minNodesForAutoFA2) {
-                setTimeout(function(){
-                  // NB in here scope: 'this' is the window
-                  if (TW.partialGraph.isForceAtlas2Running())
-                    sigma_utils.ourStopFA2()
-                },
-                args.duration)
+                setTimeout(function(){sigma_utils.ourStopFA2()},args.duration)
 
                 // hide edges during work for smaller cpu load
                 if (TW.partialGraph.settings('drawEdges')) {

twpresets/settings_explorerjs.comex.js

@@ -19,12 +19,6 @@ TW.conf = (function(TW){
   // the graph input depends on TWConf.sourcemode (or manual url arg 'sourcemode')
   TWConf.sourcemode = "api"   // accepted: "api" | "serverfile" | "servermenu" | "localfile"
 
-  // server-side .gexf|.json default source
-  TWConf.sourceFile = ""
-
-  // ...or server-side gexf default source list
-  TWConf.sourceMenu = "db.json"
-
   // ...or remote bridge to default source api ajax queries
   TWConf.sourceAPI={};
   TWConf.sourceAPI["forNormalQuery"] = "services/api/graph";
@@ -47,7 +41,7 @@ TW.conf = (function(TW){
   }
 
   // fallback topPapers API if none found by type
-  TWConf.relatedDocsAPI = "twbackends/phpAPI"
+  TWConf.relatedDocsAPI = "http://127.0.0.1:5000/twitter_search"
 
   // =======================
   // DATA FACETS AND LEGENDS
@@ -114,7 +108,7 @@ TW.conf = (function(TW){
     'weight'          : {'col': "heatmap" , 'n': 5,  'binmode': 'samerange'  },
     'Weighted Degree' : {'col': "heatmap", 'n': 8,  'binmode': 'samerange'  },
     'out-degree'      : {'col': "heatmap" , 'n': 3,  'binmode': 'samepop'  },
-    'CC'              : {'col': "cluster" ,          'binmode': 'off'},
+    'country'         : {'col': "cluster" ,          'binmode': 'off'},
     'ACR'             : {'col': "cluster" ,          'binmode': 'off'},
 'cluster_universal_index': {'col': "cluster" ,         'binmode': 'off'      },
        'community_orphan' : {'col': "cluster" ,        'binmode': 'off'      }
@@ -145,9 +139,9 @@ TW.conf = (function(TW){
   TWConf.maxDiscreteValues = 15
   TWConf.legendsBins = 7
 
-  // to normalize node sizes: (NB not very useful because tina normalizes them at display)
+  // to normalize node sizes (larger range does increase visual size difference)
   TWConf.desirableNodeSizeMin=1;
-  TWConf.desirableNodeSizeMax=2;
+  TWConf.desirableNodeSizeMax=10;
 
 
   // =============
@@ -164,8 +158,12 @@ TW.conf = (function(TW){
   // Modules path
   // ------------
   TWConf.paths = {
-    'ourlibs': 'static/tinawebJS/twlibs',
-    'modules': 'twmodules'
+    'ourlibs': 'twlibs',
+    'templates': "twlibs/hit_templates",
+    'modules': 'twmodules',
+
+    'sourceFile': "",           // server-side .gexf|.json default source
+    'sourceMenu': "db.json"     // ...or server-side gexf default source list
   }
   Object.freeze(TWConf.paths)  // /!\ to prevent path modification before load
 
@@ -256,8 +254,8 @@ TW.conf = (function(TW){
       font: "Droid Sans",                // font params
       fontStyle: "bold",
       defaultLabelColor: '#000',         // labels text color
-      labelSizeRatio: 1,                 // initial label size (on the slider)
-      labelThreshold: 5,                 // min node cam size to start showing label
+      labelSizeRatio: 1,                 // label size in ratio of node size
+      labelThreshold: 4,                 // min node cam size to start showing label
                                          // (old tina: showLabelsIfZoom)
 
       // hovered nodes
@@ -272,10 +270,10 @@ TW.conf = (function(TW){
       twSelectedColor: "default",     // "node" for a label bg like the node color,
                                    // "default" for note-like yellow
 
-      // not selected <=> grey
-      twNodesGreyOpacity: .35,                       // smaller value: more grey
+      // not selected <=> (1-greyness)
+      twNodesGreyOpacity: .5,                       // smaller value: more grey
       twBorderGreyColor: "rgba(100, 100, 100, 0.5)",
-      twEdgeGreyColor: "rgba(100, 100, 100, 0.2)",
+      twEdgeGreyColor: "rgba(100, 100, 100, 0.3)",
   };
   // NB: sigmaJsDrawingProperties are available as 'settings' in all renderers
   // cf. https://github.com/jacomyal/sigma.js/wiki/Settings#renderers-settings
@@ -285,7 +283,7 @@ TW.conf = (function(TW){
   // -----------------------------------
   // mouse captor zoom limits
   TWConf.zoomMin = .015625         // for zoom IN   (ex: 1/64 to allow zoom x64)
-  TWConf.zoomMax = 2               // for zoom OUT
+  TWConf.zoomMax = 8               // for zoom OUT
 
   // circle selection cursor
   TWConf.circleSizeMin = 0;
@@ -302,7 +300,7 @@ TW.conf = (function(TW){
   // relative sizes (iff ChangeType == both nodetypes)
   TWConf.sizeMult = [];
   TWConf.sizeMult[0] = 1.0;     // ie for node type 0 (<=> sem)
-  TWConf.sizeMult[1] = 5.0;     // ie for node type 1 (<=> soc)
+  TWConf.sizeMult[1] = 10.0;     // ie for node type 1 (<=> soc)
 
 
   // ===========