EOL · eliagbayani · Feb 26, 2025 · Feb 27, 2025 · Feb 27, 2025 · Feb 27, 2025
diff --git a/.gitignore b/.gitignore
@@ -56,6 +56,21 @@ applications/xls2EOL/WhyReef-EOL(2).xls
 applications/xls2EOL/WhyReef-EOL.xls
 applications/xls2EOL/WhyReef-EOL.xml
 applications/xls2EOL/xml/*.xml
+
+applications/xls2dwca_jenkins/temp/*
+applications/specimen_export/temp/*
+applications/specimen_image_export/temp/*
+applications/trait_data_import/temp/*
+applications/specimen_export/zdev_samples/*
+applications/specimen_export/zbak/*
+applications/BOLD2iNAT/temp/*
+applications/BOLD2iNAT_csv/temp/*
+applications/dwc_validator_jenkins/temp/*
+applications/CheckListBank_tool/temp/*
+applications/CheckListBank_tool/temp/
+applications/CheckListBank_tool/temp
+
+
 config/constants.php
 config/database.yml
 config/environments/*
@@ -91,6 +106,8 @@ update_resources/connectors/CDC.php
 update_resources/connectors/CDC2.php
 update_resources/connectors/files/*
 !update_resources/connectors/files/Avibase
+!update_resources/connectors/files/wikipedia
+
 update_resources/connectors/files/Avibase/cache/*.xml
 !update_resources/connectors/files/IUCN
 update_resources/connectors/files/IUCN/cache/*.html
@@ -101,6 +118,10 @@ update_resources/connectors/XML_check.php
 vendor/eol_content_schema_v2/extension_cache/*
 !vendor/eol_content_schema_v2/extension_cache/.gitignore
 vendor/google_api/config.php
+vendor/geoPHP/
+applications/genHigherClass/sample/
+applications/genHigherClass_jenkins/temp/
+applications/genHigherClass_jenkins/temp
 
 .DS_Store
 
@@ -191,3 +212,25 @@ applications/partner_requests/DiscoverLife_EOL_tc_list.php
 applications/partner_requests/TaxonConcept_check_if_name_inEOL.php
 
 applications/partner_requests/DiscoverLife_multiple_map_per_taxon.php
+vendor/google_client_library/json/sheets.googleapis.com-php-quickstart.json
+update_resources/connectors/files/wikimedia/.gitignore
+applications/content_server/resources_2
+applications/iNaturalist_OAuth2/readmeli_secret.txt
+update_resources/connectors/173_42.php
+update_resources/connectors/173_45.php
+update_resources/connectors/173_58.php
+lib/connectors/StatsAPI.php
+update_resources/connectors/173_49.php
+tmp2
+lib/connectors/SmasherLastAPI Jul 25.php
+update_resources/connectors/terminal_fill_up_undefined_parents.txt
+update_resources/connectors/terminal_fill_up_undefined_parents.out
+update_resources/connectors/terminal_gnparser_wikidataTaxonomy.out
+update_resources/connectors/terminal_inat_images_select.out
+terminal.out
+terminal.out.txt
+applications/content_server/resources_3
+update_resources/connectors/helpers/anystyle/biblio.txt
+update_resources/connectors/test.qs
+vendor/google_client_lib_2023/json/credentials.json
+query.json
diff --git a/README.rdoc b/README.rdoc
@@ -118,7 +118,7 @@ the line should be:
 The simplest approach is to provide a symbolic link in your Apache
 DocumentRoot, e.g.:
 
-  sudo ln -s $ROOT/eol_php_code /Library/WebServer/Documents/eol_php_code
+  sudo ln -s $ROOT/eol_php_code /opt/homebrew/var/www/eol_php_code
 
 This will allow you to test the local install using:
 

diff --git a/app/models/Activity.php b/app/models/Activity.php
diff --git a/app/models/AgentRoles.php b/app/models/AgentRoles.php
diff --git a/app/models/Agents.php b/app/models/Agents.php
diff --git a/app/models/AgentsDataObject.php b/app/models/AgentsDataObject.php
diff --git a/app/models/AgentsHierarchyEntries.php b/app/models/AgentsHierarchyEntries.php
diff --git a/app/models/AgentsSynonyms.php b/app/models/AgentsSynonyms.php
diff --git a/app/models/Audiences.php b/app/models/Audiences.php
diff --git a/app/models/AudiencesDataObject.php b/app/models/AudiencesDataObject.php
diff --git a/app/models/CanonicalForms.php b/app/models/CanonicalForms.php
diff --git a/app/models/ChangeableObjectTypes.php b/app/models/ChangeableObjectTypes.php
diff --git a/app/models/Collections.php b/app/models/Collections.php
diff --git a/app/models/ContentPartners.php b/app/models/ContentPartners.php
diff --git a/app/models/CuratorActivityLogs.php b/app/models/CuratorActivityLogs.php
diff --git a/app/models/CuratorLevels.php b/app/models/CuratorLevels.php
diff --git a/app/models/DataObjects.php b/app/models/DataObjects.php
diff --git a/app/models/DataObjectsHierarchyEntry.php b/app/models/DataObjectsHierarchyEntry.php
diff --git a/app/models/DataObjectsInfoItem.php b/app/models/DataObjectsInfoItem.php
diff --git a/app/models/DataObjectsRef.php b/app/models/DataObjectsRef.php
diff --git a/app/models/DataObjectsTableOfContent.php b/app/models/DataObjectsTableOfContent.php
diff --git a/app/models/DataObjectsTaxonConcept.php b/app/models/DataObjectsTaxonConcept.php
diff --git a/app/models/DataTypes.php b/app/models/DataTypes.php
diff --git a/app/models/HarvestEvents.php b/app/models/HarvestEvents.php
diff --git a/app/models/HarvestEventsHierarchyEntries.php b/app/models/HarvestEventsHierarchyEntries.php
diff --git a/app/models/HarvestProcessLogs.php b/app/models/HarvestProcessLogs.php
diff --git a/app/models/Hierarchies.php b/app/models/Hierarchies.php
diff --git a/app/models/HierarchyEntries.php b/app/models/HierarchyEntries.php
diff --git a/app/models/HierarchyEntriesRefs.php b/app/models/HierarchyEntriesRefs.php
diff --git a/app/models/InfoItems.php b/app/models/InfoItems.php
diff --git a/app/models/Languages.php b/app/models/Languages.php
diff --git a/app/models/Licenses.php b/app/models/Licenses.php
diff --git a/app/models/MimeTypes.php b/app/models/MimeTypes.php
diff --git a/app/models/Names.php b/app/models/Names.php
diff --git a/app/models/NotificationFrequencies.php b/app/models/NotificationFrequencies.php
diff --git a/app/models/Ranks.php b/app/models/Ranks.php
diff --git a/app/models/RefIdentifierTypes.php b/app/models/RefIdentifierTypes.php
diff --git a/app/models/RefIdentifiers.php b/app/models/RefIdentifiers.php
diff --git a/app/models/Refs.php b/app/models/Refs.php
diff --git a/app/models/ResourceAgentRoles.php b/app/models/ResourceAgentRoles.php
diff --git a/app/models/ResourceStatuses.php b/app/models/ResourceStatuses.php
diff --git a/app/models/Resources.php b/app/models/Resources.php
diff --git a/app/models/ServiceTypes.php b/app/models/ServiceTypes.php
diff --git a/app/models/SpecialCollections.php b/app/models/SpecialCollections.php
diff --git a/app/models/Statuses.php b/app/models/Statuses.php
diff --git a/app/models/SynonymRelations.php b/app/models/SynonymRelations.php
diff --git a/app/models/Synonyms.php b/app/models/Synonyms.php
diff --git a/app/models/TableOfContents.php b/app/models/TableOfContents.php
diff --git a/app/models/TaxonConceptMetrics.php b/app/models/TaxonConceptMetrics.php
diff --git a/app/models/TaxonConceptNames.php b/app/models/TaxonConceptNames.php
diff --git a/app/models/TaxonConcepts.php b/app/models/TaxonConcepts.php
diff --git a/app/models/TranslatedAgentRoles.php b/app/models/TranslatedAgentRoles.php
diff --git a/app/models/TranslatedAudience.php b/app/models/TranslatedAudience.php
diff --git a/app/models/TranslatedInfoItems.php b/app/models/TranslatedInfoItems.php
diff --git a/app/models/TranslatedLanguages.php b/app/models/TranslatedLanguages.php
diff --git a/app/models/TranslatedLicenses.php b/app/models/TranslatedLicenses.php
diff --git a/app/models/TranslatedMimeTypes.php b/app/models/TranslatedMimeTypes.php
diff --git a/app/models/TranslatedRanks.php b/app/models/TranslatedRanks.php
diff --git a/app/models/TranslatedResourceStatuses.php b/app/models/TranslatedResourceStatuses.php
diff --git a/app/models/TranslatedServiceTypes.php b/app/models/TranslatedServiceTypes.php
diff --git a/app/models/TranslatedStatuses.php b/app/models/TranslatedStatuses.php
diff --git a/app/models/TranslatedSynonymRelations.php b/app/models/TranslatedSynonymRelations.php
diff --git a/app/models/TranslatedTableOfContents.php b/app/models/TranslatedTableOfContents.php
diff --git a/app/models/TranslatedVetted.php b/app/models/TranslatedVetted.php
diff --git a/app/models/TranslatedVisibilities.php b/app/models/TranslatedVisibilities.php
diff --git a/app/models/User.php b/app/models/User.php
diff --git a/app/models/Vetted.php b/app/models/Vetted.php
diff --git a/app/models/Visibilities.php b/app/models/Visibilities.php
diff --git a/applications/BOLD2iNAT/form_result.php b/applications/BOLD2iNAT/form_result.php
@@ -0,0 +1,86 @@
+<?php
+namespace php_active_record;
+include_once(dirname(__FILE__) . "/../../config/environment.php");
+
+// /* normal operation
+ini_set('error_reporting', false);
+ini_set('display_errors', false);
+$GLOBALS['ENV_DEBUG'] = false; //set to false in production
+// */
+
+/* during development
+ini_set('error_reporting', E_ALL);
+ini_set('display_errors', true);
+$GLOBALS['ENV_DEBUG'] = true; //set to true during development
+*/
+
+// echo "<pre>"; print_r($_FILES); exit("</pre>");
+$form_url = '';
+/* from copied template
+$form_url = @get_val_var('form_url');
+if($form_url) { //URL is pasted.
+    $orig_file = pathinfo($form_url, PATHINFO_BASENAME);
+    $newfile = time() . "." . pathinfo($orig_file, PATHINFO_EXTENSION);
+    if(!in_array(pathinfo($form_url, PATHINFO_EXTENSION), array('xls', 'xlsx', 'zip'))) exit("\nERROR: Wrong file format.\n\n");
+    // print_r(pathinfo($form_url)); exit;
+    // good debug
+    echo "<hr>form_url: [$form_url]";
+    echo "<hr>orig_file: [$orig_file]";
+    echo "<hr>newfile: [$newfile]<hr>";
+    // exit;
+    //
+}
+elseif($file_type = @$_FILES["file_upload"]["type"]) {
+    if(in_array($file_type, array("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/vnd.ms-excel", "application/zip"))) {
+        if($_FILES["file_upload"]["error"] > 0) {}
+        else {
+            $orig_file = $_FILES["file_upload"]["name"];
+            $url = "temp/" . time() . "." . pathinfo($orig_file, PATHINFO_EXTENSION);
+            if(move_uploaded_file($_FILES["file_upload"]["tmp_name"] , $url)) {
+                debug("<br>file uploaded - OK<br>");
+            }
+            else echo "<br>uploading file - ERROR<br>";
+        }
+        $newfile = "temp/" . time() . "." . pathinfo($orig_file, PATHINFO_EXTENSION);
+        // echo "<hr>orig_file: [$orig_file]";
+        // echo "<hr>url: [$url]";
+        // echo "<hr>newfile: [$newfile]<hr>";
+        // exit;
+    }
+    else exit("<hr>$file_type<hr>Invalid file. <br> <a href='javascript:history.go(-1)'> &lt;&lt; Go back</a><hr>");
+}
+else exit("<hr>Please browse an Excel file OR enter its URL to continue. <br> <a href='javascript:history.go(-1)'> &lt;&lt; Go back</a><hr>");
+*/
+// /* current section from copied template section
+$newfile = time(); //implemented mainly just a unique ID
+// */
+
+/* replaced by Jenkins call
+print "<br><b>Processing, please wait...</b><br><hr>";
+print"<META HTTP-EQUIV='Refresh' Content='0; URL=generate.php?file=$newfile&orig_file=$orig_file'>";
+exit;
+*/
+
+if(Functions::is_production()) {
+    $for_DOC_ROOT =  '/var/www/html/eol_php_code/'; //'/html/eol_php_code/';
+    $true_DOC_ROOT = DOC_ROOT;
+}
+else {
+    $for_DOC_ROOT = DOC_ROOT;
+    $true_DOC_ROOT = $for_DOC_ROOT;
+}
+
+// if($form_url)   require_once("jenkins_call_4url.php");
+// else            require_once("jenkins_call.php");
+
+$form = $_POST;
+require_once("jenkins_call.php");
+
+function get_val_var($v)
+{
+    if     (isset($_GET["$v"])) $var = $_GET["$v"];
+    elseif (isset($_POST["$v"])) $var = $_POST["$v"];
+    if(isset($var)) return $var;
+    else return NULL;
+}
+?>
diff --git a/applications/BOLD2iNAT/generate_jenkins.php b/applications/BOLD2iNAT/generate_jenkins.php
@@ -0,0 +1,2 @@
+<?php
+?>
diff --git a/applications/BOLD2iNAT/jenkins_call.php b/applications/BOLD2iNAT/jenkins_call.php
@@ -0,0 +1,106 @@
+<?php
+require_once("../../../LiteratureEditor/Custom/lib/Functions.php");
+require_once("../../../FreshData/controllers/other.php");
+require_once("../../../FreshData/controllers/freshdata.php");
+
+/* during development
+ini_set('error_reporting', E_ALL);
+ini_set('display_errors', true);
+$GLOBALS['ENV_DEBUG'] = true; //set to true when debugging
+*/
+
+$ctrler = new freshdata_controller(array());
+$job_name = 'xls2dwca_job';
+$task = $ctrler->get_available_job($job_name);
+$postfix = "_xls2dwca";
+
+// /* for debugging:
+$server_http_host = $_SERVER['HTTP_HOST'];
+$server_script_name = $_SERVER['SCRIPT_NAME'];
+$server_script_name = str_replace("form_result.php", "generate_jenkins.php", $server_script_name);
+// */
+
+$params['true_root'] = $true_DOC_ROOT;
+$params['uuid'] = pathinfo($newfile, PATHINFO_FILENAME);
+
+/* IMPORTANT: un-comment during development
+echo "<pre>"; print_r($form); echo "</pre>";
+*/
+
+/*Array(
+    [form_url] => 
+    [Proj] => KANB
+    [Dept] => fishes
+    [Lic] => CreativeCommons – Attribution Non-Commercial Share-alike (by-nc-sa)
+    [Lic_yr] => my_year
+    [Lic_inst] => my_inst
+    [Lic_cont] => my_contact
+)*/
+$dept_map['fishes'] = 'FISH';
+$dept_map['mammals'] = 'MAMMALS';
+$dept_map['herps'] = 'HERPS'; //'AMPHIBIANS & REPTILES';
+$dept_map['birds'] = 'BIRDS';
+$dept_map['botany'] = 'BOTANY';
+$dept_map['paleo'] = 'PALEOBIOLOGY';
+
+if(isset($form['Proj_refresh'])) $Proj_refresh = 1;
+else                             $Proj_refresh = 0;
+
+$json = '{"JWT":"'.$form['JWT'].'" , "token_type":"'.$form['token_type'].'", "Proj":"'.$form['Proj'].'", "Taxon":"'.$form['Taxon'].'", "Dept":"'.$dept_map[$form['Dept']].'"
+        , "Proj_refresh":"'.$Proj_refresh.'"
+        , "Lic":"'.@$form['Lic'].'", "Lic_yr":"'.@$form['Lic_yr'].'", "Lic_inst":"'.@$form['Lic_inst'].'", "Lic_cont":"'.@$form['Lic_cont'].'"}';
+$params['json'] = $json;
+
+$params['Proj_and_Taxon'] = $form['Proj']."_".str_replace(' ','_',$form['Taxon']);
+
+   $params['destination'] = $for_DOC_ROOT . "/applications/specimen_image_export/" . $newfile;
+   //always use DOC_ROOT so u can switch from jenkins to cmdline. BUT DOC_ROOT won't work here either since /config/boot.php is not called here. So use $for_DOC_ROOT instead.
+
+/* for more debugging...
+echo "<br>newfile: [$newfile]";
+echo "<br>orig_file: [$orig_file]";
+echo "<br>destination: " . $params['destination']; 
+echo "<br>uuid: " . $params['uuid']; 
+echo "<br>server_http_host: [$server_http_host]";
+echo "<br>server_script_name: [$server_script_name]";
+echo "<hr>"; //exit;
+*/
+
+// php update_resources/connectors/marine_geo_image.php _ image_input.xlsx _ _ '$json'
+// php update_resources/connectors/marine_geo_image.php _ _ 'https://github.com/eliagbayani/EOL-connector-data-files/raw/master/MarineGEO/image_input.xlsx' uuid001 '$json'
+
+$newfile = pathinfo($newfile, PATHINFO_BASENAME);
+if($form_url) $cmd = PHP_PATH.' bold2inat.php jenkins _ ' . "'" . $form_url . "' ".$params['uuid']. " '".$params['json']."'"; //no filename but there is form_url and uuid
+else          $cmd = PHP_PATH.' bold2inat.php jenkins ' . "'" . $newfile . "' _ _ ". "'".$params['json']."'";
+
+$cmd .= " 2>&1";
+$ctrler->write_to_sh($params['uuid'].$postfix, $cmd);
+$cmd = $ctrler->generate_exec_command($params['uuid'].$postfix); //pass the desired basename of the .sh filename (e.g. xxx.sh then pass "xxx")
+$c = $ctrler->build_curl_cmd_for_jenkins($cmd, $task);
+
+/* to TSV destination here... not sure purpose of this one ???
+if(file_exists($params['destination'])) unlink($params['destination']);
+*/
+
+$shell_debug = shell_exec($c);
+// sleep(10);
+
+/* for more debugging...
+echo "<pre><hr>cmd: $cmd<hr>c: $c<hr></pre>";
+echo "<pre><hr>shell_debug: [$shell_debug]<hr></pre>";
+*/
+
+require_once("show_build_status.php");
+
+function compute_destination($newfile, $orig_file)
+{
+    $filename = pathinfo($newfile, PATHINFO_FILENAME);
+    if(pathinfo($orig_file, PATHINFO_EXTENSION) == "zip") {
+        $temp = pathinfo($orig_file, PATHINFO_FILENAME);
+        $ext = pathinfo($temp, PATHINFO_EXTENSION);
+    }
+    else $ext = pathinfo($orig_file, PATHINFO_EXTENSION);
+    $final = "$filename.$ext";
+    return $final;
+}
+?>