tina directories refactoring 1/2

00.DOCUMENTATION/00. Introduction/README.md

@@ -31,7 +31,9 @@ There are two exceptions are:
 
   - optionally, the backends under `twbackends`:
     - they are the only server-side elements of the tina distribution
+    - while part of the distribution, they are **standalone micro-servers**
     - they contain their own readme as to how to run them on a server
+    - once they are configured or run, the communication between them and the main tinaweb client module happens via XHR requests: therefore they can actually reside in any convenient place for your deployment.
 
 
 

explorerjs.html

@@ -54,19 +54,19 @@
 
 
   <!-- CSS -->
-  <link rel="stylesheet" href="libs/css2/twjs.css">
-  <link rel="stylesheet" href="libs/css2/twjs-mobile.css">
-  <link rel="stylesheet" href="libs/css2/selection-panels.css">
-  <link rel="stylesheet" href="libs/css2/selection-panels-mobile.css">
+  <link rel="stylesheet" href="twlibs/css2/twjs.css">
+  <link rel="stylesheet" href="twlibs/css2/twjs-mobile.css">
+  <link rel="stylesheet" href="twlibs/css2/selection-panels.css">
+  <link rel="stylesheet" href="twlibs/css2/selection-panels-mobile.css">
 
-  <link rel="stylesheet" href="libs/jquery-3/jquery-ui-1.12.1/jquery-ui.min.css" media="screen">
-  <link rel="stylesheet" href="libs/bootstrap-3/css/bootstrap.min.css" media="screen">
+  <link rel="stylesheet" href="twlibs/jquery-3/jquery-ui-1.12.1/jquery-ui.min.css" media="screen">
+  <link rel="stylesheet" href="twlibs/bootstrap-3/css/bootstrap.min.css" media="screen">
   <!-- NB bs2/3 not used for main grid (graph + bars) but inside the bars -->
-  <link rel="stylesheet" href="libs/css2/freshslider.css" media="screen">
+  <link rel="stylesheet" href="twlibs/css2/freshslider.css" media="screen">
 
-  <link type="text/css" href="libs/tweets/tweet.light.ltr.css" rel="stylesheet"/>
-  <link type="text/css" href="libs/tweets/custom.css" rel="stylesheet"/>
-  <link type="text/css" href="libs/css2/user_form.css" rel="stylesheet"/>
+  <link type="text/css" href="twlibs/tweets/tweet.light.ltr.css" rel="stylesheet"/>
+  <link type="text/css" href="twlibs/tweets/custom.css" rel="stylesheet"/>
+  <link type="text/css" href="twlibs/css2/user_form.css" rel="stylesheet"/>
 
   <!-- JS -->
   <!-- <script src="script.js"></script> -->
@@ -116,11 +116,11 @@
           <li><a href="http://www.cnrs.fr" target="_blank"
                 class="navbar-higher"
                 title="CNRS">
-                <img src="libs/img2/logo_cnrs_transparent.gif" height="23"></a></li>
+                <img src="twlibs/img2/logo_cnrs_transparent.gif" height="23"></a></li>
           <li><a href="http://iscpif.fr" target="_blank"
                 class="navbar-higher"
                 title="ISC-PIF">
-                <img src="libs/img2/logo_ISCPIF_small.svg" height="23"></a></li>
+                <img src="twlibs/img2/logo_ISCPIF_small.svg" height="23"></a></li>
 
         </ul>
 
@@ -160,7 +160,7 @@
             <li><a href="https://communityexplorer.org"
                   class="navbar-higher"
                   title="Community Explorer">
-                  <img src="libs/img2/logo.png"
+                  <img src="twlibs/img2/logo.png"
                        style="width:60px; position:absolute; top:-60px; left:-75px; z-index:5; overflow:visible;">
             </a></li>
 
@@ -194,7 +194,7 @@
 
              <li id="setcolorsMenu" class="dropdown">
                <a class="dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">
-               Set Colors <img title="Set Colors" src="libs/img2/colors.png" width="20px"><span class="caret"></span>
+               Set Colors <img title="Set Colors" src="twlibs/img2/colors.png" width="20px"><span class="caret"></span>
                </a>
                 <ul id="colorgraph-menu" class="dropdown-menu">
                 </ul>
@@ -314,7 +314,7 @@
               <!--
                <li>
                   <a href="#" id="geomapicon" onclick="$('#geomapmodal').modal('show'); callGeomapADEME();">
-                    <img title="World Map Distribution" width="34px" src="libs/img2/world.png"></img>
+                    <img title="World Map Distribution" width="34px" src="twlibs/img2/world.png"></img>
                   </a>
               </li>
               -->
@@ -322,13 +322,13 @@
 
                <li>
                   <a href="#" id="snapicon" onclick="saveGraphIMG();" class="zoombarbuttons">
-                    <img title="Take a photo!" style="width:30px" src="libs/img2/camera.png"></img>
+                    <img title="Take a photo!" style="width:30px" src="twlibs/img2/camera.png"></img>
                   </a>
               </li>
 
               <li>
                   <a href="#savemodal" id="saveAs" class="zoombarbuttons" data-toggle="modal" data-target="#savemodal">
-                    <img style="width:28px" title="Save As..." src="libs/img2/save.png"></img>
+                    <img style="width:28px" title="Save As..." src="twlibs/img2/save.png"></img>
                   </a>
               </li>
 
@@ -348,21 +348,21 @@
               <li>
                   <a href="#" id="lensButton" class="zoombarbuttons"
                      title="Center View">
-                    <img src="libs/img2/target.png">
+                    <img src="twlibs/img2/target.png">
                   </a>
               </li>
 
               <li>
                   <a href="#" id="layoutButton" class="zoombarbuttons"
                      title="Force Atlas Layout">
-                    <img src="libs/img2/edges.png">
+                    <img src="twlibs/img2/edges.png">
                   </a>
               </li>
 
               <li>
                   <a href="#" id="noverlapButton" class="zoombarbuttons"
                      title="Disperse Overlapping Nodes">
-                    <img src="libs/img2/disperse.png">
+                    <img src="twlibs/img2/disperse.png">
                   </a>
               </li>
 
@@ -371,7 +371,7 @@
                   <a href="#facet-options" id="facets" class="zoombarbuttons"
                      title="Facets coloring options"
                      data-toggle="modal" data-target="#facet-options">
-                    <img src="libs/img2/facet_options.png"></img>
+                    <img src="twlibs/img2/facet_options.png"></img>
                   </a>
               </li>
 
@@ -420,7 +420,7 @@
 
       <!-- to reopen the panel -->
       <div id="sideunfold">
-        <img title="Open sidepanel" src="libs/img2/unfold2.png"></img>
+        <img title="Open sidepanel" src="twlibs/img2/unfold2.png"></img>
       </div>
 
     </div>
@@ -518,7 +518,7 @@
               style="width:85%; ">
           </a>
           <a href="https://github.com/moma" target="_blank">
-              <img src="libs/img2/moma.png"
+              <img src="twlibs/img2/moma.png"
               alt="Sciencemapping"
               style="width:85%; ">
           </a>
@@ -529,7 +529,7 @@
 
     <br><br>
     <div id="sidefold">
-      <img title="Close sidepanel" src="libs/img2/fold2.png"></img>
+      <img title="Close sidepanel" src="twlibs/img2/fold2.png"></img>
     </div>
   </div>
   <div id="hidden-elements">
@@ -597,7 +597,7 @@
 
     <div id="modalloader" class="modal fade">
         <div id="loader" class="loader">
-            <img src="libs/img2/loader.gif"></img>
+            <img src="twlibs/img2/loader.gif"></img>
         </div>
         <div id="closeloader" data-dismiss="modal"></div>
     </div>
@@ -731,13 +731,13 @@
   </div>
 
   <!--         SCRIPTS        -->
-  <script src="libs/jquery-3/jquery-3.2.0.min.js" type="text/javascript"></script>
-  <script src="libs/jquery-3/jquery-ui-1.12.1/jquery-ui.min.js" type="text/javascript"></script>
-  <script src="libs/jquery-3/jquery.easytabs.js" type="text/javascript"></script>
-  <script src="libs/freshslider.1.0.js" type="text/javascript" ></script>
-  <script src="libs/readmore.js" type="text/javascript"></script>
-  <script src="libs/tweets/widgets.js" type="text/javascript" language="javascript"></script>
-  <script src="libs/bootstrap-native/bootstrap-native.min.js"></script>
+  <script src="twlibs/jquery-3/jquery-3.2.0.min.js" type="text/javascript"></script>
+  <script src="twlibs/jquery-3/jquery-ui-1.12.1/jquery-ui.min.js" type="text/javascript"></script>
+  <script src="twlibs/jquery-3/jquery.easytabs.js" type="text/javascript"></script>
+  <script src="twlibs/freshslider.1.0.js" type="text/javascript" ></script>
+  <script src="twlibs/readmore.js" type="text/javascript"></script>
+  <script src="twlibs/tweets/widgets.js" type="text/javascript" language="javascript"></script>
+  <script src="twlibs/bootstrap-native/bootstrap-native.min.js"></script>
 
   <script src="tinawebJS/globalUtils.js" type="text/javascript"></script>
 

settings_explorerjs.js

@@ -42,7 +42,7 @@ TW.conf = (function(TW){
 
   TWConf.relatedDocsAPIS = {
     // routes by corresponding type
-    "wosLocalDB": "LOCALDB",
+    "wosLocalDB": "twbackends/phpAPI",
     "twitter": "http://127.0.0.1:5000/twitter_search"
   }
 

LOCALDB/README.md → twbackends/phpAPI/README.md

@@ -3,8 +3,11 @@
 
 ##### Provides an API for "topPapers" search queries in tinawebJS
 
+These php files provide access to a CSV or sqlite database as an ajax endpoint for a "related documents" search in tinawebJS client.
+
 Main use case is support for one-doc-by-row CSV files.
 
+
 #### Prerequisites
 
 You need any kind of php server support with php > 5.0.
@@ -20,8 +23,9 @@ location ~ \.php$ {
   include snippets/fastcgi-php.conf;
   fastcgi_pass unix:/run/php/php7.0-fpm.sock;
 
- fastcgi_param SCRIPT_FILENAME /your/path/to/LOCALDB/$fastcgi_script_name;
- #                             ---------------------
+ fastcgi_param SCRIPT_FILENAME
+   /your/path/to/twbackends/phpAPI/$fastcgi_script_name;
+ # --------------------------------
 }
 ```
 
@@ -36,11 +40,36 @@ sudo service php7.0-fpm restart
 
 For legacy cortext-style databases, you'll also need sqlite:
 ```
-sudo apt install sqlite3
+sudo apt install sqlite3 php7.0-sqlite3
 ```
 
 
 #### Usage
-For a given graph source and database, you will need to **fill in the right settings in `db.json`**  in order to associate the graph source file (eg gexf) with this related docs API.
 
-£TODO explain after new specifications implemented
+###### Configuration
+
+To use the API for the "topPapers" embedded search in ProjectExplorer, the corresponding settings should be picked either:
+  - via the interface (side panel menu)
+  - or directly in settings_explorerjs.js:
+```
+TWConf.relatedDocsType = "wosLocalDB"
+```
+
+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",
+      "gexfs": {
+          "your.graph.gexf": {
+              "semantic": { "table":"yourTableWithTerms"},
+              "social": { "table":"yourTableWithSocialNodes"}
+          }
+      }
+}
+```
+£TODO update after new specifications implemented

LOCALDB/info_div.php → twbackends/phpAPI/info_div.php

@@ -4,16 +4,13 @@ ini_set('display_errors',1);
 ini_set('display_startup_errors',1);
 // error_reporting(-1);
 
-// relative path to dirname "/line"
-$project_root = "../";
-
 // 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('parameters_details.php');
 
 if ($_GET['dbtype'] == "sql") {
-  $base = new PDO("sqlite:".$project_root.$graphdb);
+  $base = new PDO("sqlite:".$mainpath.$graphdb);
   include('default_div.php');
 }
 
@@ -51,7 +48,8 @@ else {
 
       // indexing ----------------------------------------------------------------------
       // must know about all (sem+soc) cols typed, even if each search doesn't need them
-      $csv_search_base = parse_and_index_csv($project_root.$graphdb,
+      // echodump("filename CSV", $mainpath.$graphdb);
+      $csv_search_base = parse_and_index_csv($mainpath.$graphdb,
                                              $idxcolsbytype,
                                             $csvsep, $csvquote);
       // -------------------------------------------------------------------------------

LOCALDB/parameters_details.php → twbackends/phpAPI/parameters_details.php

@@ -17,7 +17,10 @@ $gexf_db["data/gargistex/model_calibration.gexf"] = "data/gargistex/model_calibr
 
 $gexf= str_replace('"','',$_GET["gexf"]);
 
-$mainpath=dirname(getcwd())."/";
+// default path to ProjectExplorer root
+// (where data directory and db.json file reside)
+$mainpath=dirname(getcwd())."/../";
+
 $graphdb = $gexf_db[$gexf];