reorganized json path and added new examples

annot_desc.php

@@ -13,9 +13,9 @@
 // load annotation links in hash
 $annot_hash;
 
-if ( file_exists("$annotation_links_path/annotation_links.json") ) {
+if ( file_exists("$json_files_path/tools/annotation_links.json") ) {
 
-    $annot_json_file = file_get_contents("$annotation_links_path/annotation_links.json");
+    $annot_json_file = file_get_contents("$json_files_path/tools/annotation_links.json");
     // var_dump($annot_json_file);
     $annot_hash = json_decode($annot_json_file, true);
     // var_dump($annot_hash);

annot_desc_file.php

@@ -6,8 +6,8 @@
 
   <!-- COMMANDS -->
   <?php
-    if (file_exists("$annotation_links_path/annotation_links.json")) {
-      $annot_json_file = file_get_contents("$annotation_links_path/annotation_links.json");
+    if (file_exists("$json_files_path/tools/annotation_links.json")) {
+      $annot_json_file = file_get_contents("$json_files_path/tools/annotation_links.json");
       $annot_hash = json_decode($annot_json_file, true);
     }
 

footer.php

@@ -6,20 +6,21 @@
             include_once realpath("$custom_text_path/custom_footer.php");
           }
           else {
-            $logos_path = $root_path."".$images_path."/logos";
+            // $logos_path = $root_path."".$images_path."/logos";
 
-            $logos_json = file_get_contents($logos_path."/logos.json");
-            // var_dump($labs_json);
+            // $logos_json = file_get_contents($logos_path."/logos.json");
+            $logos_json = file_get_contents($json_files_path."/customization/logos.json");
+
+
+            //var_dump($logos_json);
             $jlogo = json_decode($logos_json, true);
 
             foreach($jlogo["logos"] as $logo) {
               echo "<a href='".$logo["link"]."' target='_blank'><img class='m-2' height='".$logo["height"]."' src='".$images_path."/logos/".$logo["image"]."'></a>";
             }
-
-            echo '<br>';
           }
         ?>
-
+        <br>
         <p style="display:inline">
           <a href="/easy_gdb/cookies.php">Cookie policy</a>.
           This site is based on <a href="https://github.com/noefp/easy_gdb" target="_blank">easyGDB</a> software.

gene.php

@@ -19,8 +19,8 @@
   $annot_file = $annotations_path."/".trim($_GET["annot"]);
   // list($gene_name, $annot_file) = explode("@", trim($_GET["name"]));
 
-  if (file_exists("$annotation_links_path/annotation_links.json")) {
-    $annot_json_file = file_get_contents("$annotation_links_path/annotation_links.json");
+  if (file_exists("$json_files_path/tools/annotation_links.json")) {
+    $annot_json_file = file_get_contents("$json_files_path/tools/annotation_links.json");
     $annotation_hash = json_decode($annot_json_file, true);
   }
 

groups.php

@@ -1,60 +1,58 @@
   <br>
   <h1>People</h1>
+  <br>
 
-      <?php 
-      if ($dh = opendir($lab_path)){
-        // echo "<ul>";
-        while (($file_name = readdir($dh)) !== false){ //iterate all files in dir
+  <?php 
+    $labs_json_file = $json_files_path."/customization/labs.json";
+
+    if ( file_exists($labs_json_file) ){
+      $labs_json = file_get_contents($labs_json_file);
+      // var_dump($labs_json);
+      $lab_hash = json_decode($labs_json, true);
+
+      foreach($lab_hash as $key => $value) {
+
+        echo '<h2>'.$lab_hash[$key]["group_name"].'</h2>';
+        echo '<div class="row">';
+        echo '<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">';
+
+        foreach($lab_hash[$key]["people"] as $person) {
 
-          if (!preg_match('/^\./', $file_name)) { //discard hidden files
-            if (!is_dir($lab_path."/".$file_name) && preg_match('/\.json/', $file_name) ){
-
-              $labs_json = file_get_contents($lab_path."/".$file_name);
-              // var_dump($labs_json);
-              $lab = json_decode($labs_json, true);
-              // var_dump($lab);
-              echo '<h2>'.$lab["group_name"].'</h2><br>';
-              echo '<div class="row">';
-              echo '<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">';
-
-              foreach($lab["people"] as $person) {
-                if ($person["link"]) {
-                  if (preg_match('/www|http/', $person["link"])) { //external link
-
-                    echo '<a href="'.$person["link"].'" target="blank" class="float-left card egdb_person_card" style="color:#333">';
-                  } else {
-                    echo '<a href="person_view.php?person_file='.$person["link"].'" class="float-left card egdb_person_card" style="color:#333">';
-                  }
-                } else {
-                  echo '<a href="" class="float-left card egdb_person_card" style="color:#333">';
-                }
-                echo '<img class="card-img-top egdb_person_img" src="'.$images_path.'/people/'.$person["picture"].'" alt="Lab member">';
-                echo '<div class="card-body" style="white-space: nowrap; padding: 5px;">';
-                echo '<h4 style="margin-bottom: 5px">'.$person["person_name"].'</h4>';
-                echo '<p class="person-card-text">'.$person["position"].'</p>';
-                if ($person["more_info"]) {
-                  foreach($person["more_info"] as $person_item) {
-                    echo '<p class="person-card-text">'.$person_item.'</p>';
-                  }
-                }
-                echo '</div>';
-                echo '</a>';
-
-              }
-
-              echo '</div></div><br>';
-
+          if ($person["link"]) {
+            if (preg_match('/www|http/', $person["link"])) { //external link
+
+              echo '<a href="'.$person["link"].'" target="blank" class="float-left card egdb_person_card" style="color:#333">';
+            } else {
+              echo '<a href="person_view.php?person_file='.$person["link"].'" class="float-left card egdb_person_card" style="color:#333">';
             }
+          } else {
+            echo '<a href="" class="float-left card egdb_person_card" style="color:#333">';
           }
+          echo '<img class="card-img-top egdb_person_img" src="'.$images_path.'/people/'.$person["picture"].'" alt="Lab member">';
+          echo '<div class="card-body" style="white-space: nowrap; padding: 5px;">';
+          echo '<h4 style="margin-bottom: 5px">'.$person["person_name"].'</h4>';
+          echo '<p class="person-card-text">'.$person["position"].'</p>';
+          if ($person["more_info"]) {
+            foreach($person["more_info"] as $person_item) {
+              echo '<p class="person-card-text">'.$person_item.'</p>';
+            }
+          }
+          echo '</div>';
+          echo '</a>';
 
-        }
-      }
-      ?>      
+        }//close foreach person
+
+        echo '</div></div><br>'; //close row
+
+      } //close foreach lab
+    } //close if json file exists
+
+
+  ?>      
 
-    </div>
-  </div>
+    <!-- </div>
+  </div> -->
 
-  <br>
 <style>
   .egdb_person_card {
     min-height:150px;

species.php

@@ -8,9 +8,13 @@
     <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
   <?php 
-    if ( file_exists("$species_path/species_list.json") ) {
+    // if ( file_exists("$species_path/species_list.json") ) {
+      //$logos_json = file_get_contents($json_files_path."/customization/logos.json");
+
+    if ( file_exists($json_files_path."/customization/species_list.json") ) {
 
-        $sps_json_file = file_get_contents("$species_path/species_list.json");
+        // $sps_json_file = file_get_contents("$species_path/species_list.json");
+        $sps_json_file = file_get_contents("$json_files_path/customization/species_list.json");
         // var_dump($sps_json_file);
         $species_hash = json_decode($sps_json_file, true);
         // var_dump($$species_hash);

species_view.php

@@ -14,9 +14,11 @@
   <div class="row" style="margin-bottom: 10px;">
     <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
       <?php 
-        if ( file_exists("$species_path/species_list.json") ) {
+        if ( file_exists("$json_files_path/customization/species_list.json") ) {
 
-            $sps_json_file = file_get_contents("$species_path/species_list.json");
+            // $sps_json_file = file_get_contents("$species_path/species_list.json");
+
+            $sps_json_file = file_get_contents("$json_files_path/customization/species_list.json");
             // var_dump($sps_json_file);
             $species_hash = json_decode($sps_json_file, true);
             // var_dump($species_hash);

templates/egdb_files/egdb_conf/easyGDB_conf.php

@@ -7,18 +7,18 @@
 $images_path = "/$egdb_files_folder/egdb_images";
 $custom_text_path = "$root_path/$egdb_files_folder/egdb_custom_text";
 $downloads_path = "downloads";
+$annotations_path = "$root_path/annotations";
 $blast_dbs_path = "$root_path/blast_dbs";
 $lookup_path = "$root_path/lookup"; //from root 
 $species_path = "$root_path/$egdb_files_folder/egdb_species";
 $lab_path = "$root_path/$egdb_files_folder/egdb_labs";
+$json_files_path = "$root_path/$egdb_files_folder/json_files";
 
   //Expression
 $expression_path = "$root_path/expression_data";
 $private_expression_path = "$root_path/private_expression_data";
+$comparator_lookup = 0;
 
-  //Annotations
-$annotation_links_path = "$root_path/$egdb_files_folder/annotations";
-$annotations_path = "$root_path/annotations";
 
   //Passport
 $passport_path = "$root_path/passport";
@@ -40,7 +40,7 @@
 
 $tb_about = 1;
 $tb_downloads = 1;
-$tb_species = 0;
+$tb_species = 1;
 $tb_search_box = 0;
 
 $tb_tools = 1;

templates/egdb_files/json_files/customization/labs.json

@@ -0,0 +1,52 @@
+{
+  "Lab1":
+    {
+    "group_name":"The Wall Lab",
+    "people":
+      [
+      	{"person_name":"Daenerys Targaryen","position":"Principal Investigator","picture":"placeholder1.png","link":"person.php",
+      		"more_info":[
+      			"phone: 555-123456",
+      			"email: [email protected]"
+      		]
+      	},
+      	{"person_name":"John Snow","position":"Research Assistant","picture":"placeholder2.png","link":"person.php",
+      		"more_info":[
+      			"phone: 555-123456",
+      			"email: [email protected]"
+      		]
+      	},
+      	{"person_name":"White Walker","position":"PhD Student","picture":"placeholder1.png","link":"person.php",
+      		"more_info":[
+      			"phone: 555-123456",
+      			"email: [email protected]"
+      		]
+      	}
+      ]
+    },
+  "Lab2":
+    {
+    "group_name":"Mordor Lab",
+    "people":
+    [
+      {"person_name":"Sauron","position":"Principal Investigator","picture":"placeholder2.png","link":"person.php",
+      	"more_info":[
+      		"phone: 555-123456",
+      		"email: [email protected]"
+      	]
+      },
+      {"person_name":"Uruk hai","position":"Research Assistant","picture":"placeholder1.png","link":"person.php",
+      	"more_info":[
+      		"phone: 555-123456",
+      		"email: [email protected]"
+      	]
+      },
+      {"person_name":"Orc","position":"PhD Student","picture":"placeholder2.png","link":"person.php",
+      	"more_info":[
+      		"phone: 555-123456",
+      		"email: [email protected]"
+      	]
+      }
+    ]
+  }
+}

templates/egdb_files/json_files/tools/comparator_link.json

@@ -0,0 +1 @@
+{"link":"https://peatmoss.plantcode.cup.uni-freiburg.de/ppatens_db/pp_annot.php?name=query_id"}

templates/expression_data/expression_info.json → templates/egdb_files/json_files/tools/expression_info.json

@@ -1,5 +1,5 @@
 {
-  "Example1 - Plant_gene_expression (RPKM).txt":
+  "Example1 - Plant_gene_expression_RPKM.txt":
     {"link":"",
       "annotation_file":"example/gene_annotations.txt",
       "description":"example1_description.php",
@@ -17,7 +17,7 @@
           "Cold":"cold.jpeg"
         }
     },
-  "Example2 - Organism dataset name (Units).txt":
+  "Example2 - Organism dataset name.txt":
     {"link":"#",
       "description":"example2_description.php"
     },

templates/egdb_files/json_files/tools/vcf.json

@@ -0,0 +1,17 @@
+{
+  "gene_names_file":"gene_names.txt",
+  "gff_file":"gene_models.gff.gz",
+  "jb_data_folder":"easy_gdb_sample",
+  "passport_folder":"passport_folder",
+  "chr_files":
+    {
+      "chr1":"chr1.ann.vcf.gz",
+      "chr2":"chr2.ann.vcf.gz",
+      "chr3":"chr3.ann.vcf.gz",
+      "chr4":"chr4.ann.vcf.gz",
+      "chr5":"chr5.ann.vcf.gz",
+      "chr6":"chr6.ann.vcf.gz",
+      "chr7":"chr7.ann.vcf.gz",
+      "chr8":"chr8.ann.vcf.gz"
+    }
+}

tools/annot_output_db.php

@@ -26,8 +26,8 @@
 	// load annotation links in hash
 	$annot_hash;
 
-	if ( file_exists("$annotation_links_path/annotation_links.json") ) {
-	    $annot_json_file = file_get_contents("$annotation_links_path/annotation_links.json");
+	if ( file_exists("$json_files_path/tools/annotation_links.json") ) {
+	    $annot_json_file = file_get_contents("$json_files_path/tools/annotation_links.json");
 	    $annot_hash = json_decode($annot_json_file, true);
 	}
 

tools/annot_output_file.php

@@ -133,8 +133,8 @@ function print_annot_table($desc_input, $annot_file, $annot_hash, $dataset_name,
     }
 
     // create HASH with ANNOTATION links
-    if (file_exists("$annotation_links_path/annotation_links.json")) {
-      $annot_json_file = file_get_contents("$annotation_links_path/annotation_links.json");
+    if (file_exists("$json_files_path/tools/annotation_links.json")) {
+      $annot_json_file = file_get_contents("$json_files_path/tools/annotation_links.json");
       $annotation_hash = json_decode($annot_json_file, true);
     }