Merge pull request #7 from nyuhsl/master

Merging changes from NYU
pitthsls · Jul 27, 2021 · f3f33d7 · f3f33d7
2 parents 0489dee + ea5ae34
commit f3f33d7
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Showing 17 changed files with 451 additions and 93 deletions.
diff --git a/.gitignore b/.gitignore
@@ -56,6 +56,7 @@ app/config/**/parameters.yml
 app/config/common/security.yml
 app/Resources/views/institution/*
 web/css/institution/*
+web/js/institution/*
 src/AppBundle/Form/Type/ContactFormEmailType.php
 SolrIndexer.py
 
diff --git a/app/Resources/views/analytics.html.twig b/app/Resources/views/analytics.html.twig
@@ -1,3 +1 @@
 {# Insert your analytics code snippet here #}
-<script>
-</script>
diff --git a/app/Resources/views/default/add_dataset_admin.html.twig b/app/Resources/views/default/add_dataset_admin.html.twig
@@ -148,6 +148,7 @@ col-sm-4
     <legend>Grants and Publications</legend>
       {{ form_row(form.publications) }}
       {{ form_row(form.awards) }}
+      {{ form_row(form.projects) }}
       {% if userIsAdmin %}
       {# RELATED DATASETS #}
       <div class="form-group multiple">

diff --git a/app/Resources/views/default/admin-manage.html.twig b/app/Resources/views/default/admin-manage.html.twig
@@ -20,6 +20,7 @@
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'Publisher'}) }}">Publishers</a>
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'Publication'}) }}" >Cited Publications</a>
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'Award'}) }}">Awards</a>
+  <a class="list-group-item" href="{{ path('update_entity', {'entityName':'Project'}) }}">Projects</a>
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'DataType'}) }}">Data Types</a>
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'DataCollectionInstrument'}) }}">Data Collection Instruments</a>
   <a class="list-group-item" href="{{ path('update_entity', {'entityName':'DatasetFormat'}) }}">Dataset Formats</a>

diff --git a/app/Resources/views/default/update_dataset_admin.html.twig b/app/Resources/views/default/update_dataset_admin.html.twig
@@ -158,6 +158,7 @@ col-sm-4
     <legend>Grants and Publications</legend>
       {{ form_row(form.publications) }}
       {{ form_row(form.awards) }}
+      {{ form_row(form.projects) }}
      {% if userIsAdmin %}
       {# RELATED DATASETS #}
       <div class="form-group multiple">

diff --git a/app/Resources/views/default/view_dataset_external.html.twig b/app/Resources/views/default/view_dataset_external.html.twig
@@ -4,61 +4,7 @@
 
 
 {% block page_scripts %}
-<script>
-/**
-* Record outbound link clicks for Analytics
-*/
-var trackOutboundLink = function(url, label) {
-  ga('send', 'event', 'outbound', 'click', label);
-}
-
-/**
-* Initialize page popovers
-*/
-$(function () {
-  // initialize Author popovers
-  $('.dataset-authors-section [data-toggle="popover"]').popover({
-     'html':'true',
-     'animation':false,
-     'trigger':'manual',
-     'placement':'bottom',
-  }).on("mouseenter", function () {
-    var _this = this;
-    $(this).popover("show");
-    $(".popover").on("mouseleave", function () {
-      $(_this).popover('hide');
-    });
-  }).on("mouseleave", function () {
-    var _this = this;
-    setTimeout(function () {
-        if (!$(".popover:hover").length) {
-            $(_this).popover("hide");
-        }
-    }, 200);
-  });
-
-  // initialize Publisher popovers
-  $('.publishers-list [data-toggle="popover"]').popover({
-     'html':'true',
-     'animation':false,
-     'trigger':'manual',
-     'placement':'top',
-  }).on("mouseenter", function () {
-    var _this = this;
-    $(this).popover("show");
-    $(".popover").on("mouseleave", function () {
-      $(_this).popover('hide');
-    });
-  }).on("mouseleave", function () {
-    var _this = this;
-    setTimeout(function () {
-        if (!$(".popover:hover").length) {
-            $(_this).popover("hide");
-        }
-    }, 200);
-  });
-})
-</script>
+<script src="{{ asset('js/dataset_details.js') }}"></script>
 {% endblock %}
 
 
@@ -153,6 +99,12 @@ $(function () {
         {% endfor %}
         </h5>
       {% endif %}
+      </span>
+ {% if dataset.getProjects is not empty %}
+      {% for project in dataset.getProjects %}
+         <div class="dataset-detail-projects">Part of: <a href="{{ project.getProjectUrl }}" target="_blank">{{ project.getProjectName }}</a> | {{ project.getProjectDescription }}</div>
+       {% endfor %}
+    {% endif %}
       <p>
           <span class="dataset-detail-id">UID: {{ dataset.id }}</span>
       </p>

diff --git a/app/Resources/views/default/view_dataset_internal.html.twig b/app/Resources/views/default/view_dataset_internal.html.twig
@@ -1,39 +1,8 @@
 {% extends 'base.html.twig' %}
 {% from 'default/_JSONLD_output.html.twig' import JSONLD_output %}
-{% block page_scripts %}
-<script>
-/**
-* Record outbound link clicks for Analytics
-*/
-var trackOutboundLink = function(url, label) {
-  ga('send', 'event', 'outbound', 'click', label);
-}
 
-/**
-* Initialize Author popovers
-*/
-$(function () {
-  $('[data-toggle="popover"]').popover({
-     'html':'true',
-     'animation':false,
-     'trigger':'manual',
-     'placement':'bottom',
-  }).on("mouseenter", function () {
-    var _this = this;
-    $(this).popover("show");
-    $(".popover").on("mouseleave", function () {
-      $(_this).popover('hide');
-    });
-  }).on("mouseleave", function () {
-    var _this = this;
-    setTimeout(function () {
-        if (!$(".popover:hover").length) {
-            $(_this).popover("hide");
-        }
-    }, 200);
-  });
-})
-</script>
+{% block page_scripts %}
+<script src="{{ asset('js/dataset_details.js') }}"></script>
 {% endblock %}
 
 
@@ -132,6 +101,11 @@ $(function () {
 					</h5>
 				{% endif %}
 			</span>
+ {% if dataset.getProjects is not empty %}
+      {% for project in dataset.getProjects %}
+         <div class="dataset-detail-projects">Part of: <a href="{{ project.getProjectUrl }}" target="_blank">{{ project.getProjectName }}</a> | {{ project.getProjectDescription }}</div>
+       {% endfor %}
+    {% endif %}
 			<p>
 				<span class="dataset-detail-id">UID: {{ dataset.id }}</span>
 			</p>

diff --git a/app/config/common/config.yml b/app/config/common/config.yml
@@ -23,6 +23,7 @@ framework:
         # handler_id set to null will use default session handler from php.ini
         handler_id:  session.handler.native_file
         save_path:   "%kernel.root_dir%/sessions"
+        cookie_secure: true
     fragments:       ~
     http_method_override: true
 

diff --git a/app/config/common/services.yml b/app/config/common/services.yml
@@ -32,3 +32,7 @@ services:
 #    service_name:
 #        class: AppBundle\Directory\ClassName
 #        arguments: ["@another_service_name", "plain_value", "%parameter_name%"]
+  app.security_headers_listener:
+    class: AppBundle\EventListener\ResponseListener
+    tags:
+      - { name: kernel.event_listener, event: kernel.response, method: onKernelResponse  }
diff --git a/src/AppBundle/Entity/Dataset.php b/src/AppBundle/Entity/Dataset.php
@@ -209,6 +209,16 @@ class Dataset implements JsonSerializable {
   protected $awards;
 
 
+  /**
+   * @ORM\ManyToMany(targetEntity="Project", cascade={"persist"}, inversedBy="datasets")
+   * @ORM\JoinTable(name="datasets_projects",
+   *                joinColumns={@ORM\JoinColumn(name="dataset_uid",referencedColumnName="dataset_uid")},
+   *                inverseJoinColumns={@ORM\JoinColumn(name="project_id",referencedColumnName="project_id")}
+   *                )
+   */
+  protected $projects;
+
+
   /**
    * @ORM\ManyToMany(targetEntity="AccessRestriction", cascade={"persist"}, inversedBy="datasets")
    * @ORM\JoinTable(name="datasets_access_restrictions",
@@ -460,6 +470,7 @@ public function __construct()
     $this->date_added = new \DateTime("now");
     $this->dataset_formats = new \Doctrine\Common\Collections\ArrayCollection();
     $this->awards = new \Doctrine\Common\Collections\ArrayCollection();
+    $this->projects = new \Doctrine\Common\Collections\ArrayCollection();
     $this->access_restrictions = new \Doctrine\Common\Collections\ArrayCollection();
     $this->data_collection_instruments = new \Doctrine\Common\Collections\ArrayCollection();
     $this->subject_genders = new \Doctrine\Common\Collections\ArrayCollection();
@@ -1109,6 +1120,40 @@ public function getAwards()
         return $this->awards;
     }
 
+
+    /**
+     * Add projects
+     *
+     * @param \AppBundle\Entity\Project $projects
+     * @return Dataset
+     */
+    public function addProject(\AppBundle\Entity\Project $projects)
+    {
+        $this->projects[] = $projects;
+
+        return $this;
+    }
+
+    /**
+     * Remove projects
+     *
+     * @param \AppBundle\Entity\Project $projects
+     */
+    public function removeProject(\AppBundle\Entity\Project $projects)
+    {
+        $this->projects->removeElement($projects);
+    }
+
+    /**
+     * Get projects
+     *
+     * @return \Doctrine\Common\Collections\Collection
+     */
+    public function getProjects()
+    {
+        return $this->projects;
+    }
+
     /**
      * Add access_restrictions
      *
@@ -1731,7 +1776,7 @@ public function getDatasetUid()
      * @return array
      */
     public function jsonSerialize() {
-      $formats = $awards = $restrictions = $stds = $genders = $sexes = $ages = [];
+      $formats = $awards = $projects = $restrictions = $stds = $genders = $sexes = $ages = [];
       $equipment = $software = $subject_of_study = $others = [];
       $locs = $rel = $areas = $area_details = $domains = $publications = $keywords = $publishers = [];
       $authors = $data_type_array = $types_of_study = $corresponding_authors = $experts = [];
@@ -1755,6 +1800,7 @@ public function jsonSerialize() {
       foreach ($this->data_types as $data_type) { $data_type_array[]=$data_type->getDisplayName(); }
       foreach ($this->data_collection_instruments as $std) { $stds[]=$std->getDisplayName(); }
       foreach ($this->awards as $award) { $awards[]=$award->getDisplayName(); }
+      foreach ($this->projects as $project) { $projects[]=$project->getDisplayName(); }
       foreach ($this->local_experts as $expert) { $experts[]=$expert->getDisplayName(); }
       foreach ($this->subject_domains as $domain) { $domains[]=$domain->getDisplayName(); }
       foreach ($this->subject_genders as $gender) { $genders[]=$gender->getDisplayName(); }
@@ -1793,6 +1839,7 @@ public function jsonSerialize() {
         'data_types'                => $data_type_array,
         'data_collection_standards' => $stds,
         'awards'                    => $awards,
+        'projects'                  => $projects,
         'local_experts'             => $experts,
         'subject_domains'           => $domains,
         'subject_genders'           => $genders,
@@ -1813,13 +1860,14 @@ public function jsonSerialize() {
      */
      public function serializeForSolr() {
 
-       $formats = $awards = $restrictions = $stds = $genders = $sexes = $ages = $equipment = $software = $subject_of_study = [];
+       $formats = $projects = $awards = $restrictions = $stds = $genders = $sexes = $ages = $equipment = $software = $subject_of_study = [];
        $areas = $area_details = $domains = $publications = $keywords = $publishers = [];
        $authors = $data_type_array = $types_of_study = $corresponding_authors = $experts = $data_locations = $akas = $related_datasets = [];
        $other_resource_names = $other_resource_descriptions = $related_pubs = $data_location_contents = [];
        $accession_numbers = $access_instructions = [];
        foreach ($this->dataset_formats as $format) { $formats[]=$format->getDisplayName(); }
        foreach ($this->awards as $award) { $awards[]=$award->getDisplayName(); }
+       foreach ($this->projects as $project) { $projects[]=$project->getDisplayName(); }
        foreach ($this->access_restrictions as $restriction) { $restrictions[]=$restriction->getDisplayName(); }
        foreach ($this->data_collection_instruments as $std) { $stds[]=$std->getDisplayName(); }
        foreach ($this->subject_genders as $gender) { $genders[]=$gender->getDisplayName(); }
@@ -1868,6 +1916,7 @@ public function serializeForSolr() {
          'study_types'           => $types_of_study,
          'collection_standards'  => $stds,
          'awards'                => $awards,
+         'projects'              => $projects,
          'access_restrictions'   => $restrictions,
          'subject_population_ages'=>$ages,
          'subject_geographic_area'=>$areas,
@@ -1897,7 +1946,7 @@ public function serializeForSolr() {
      * @return array
      */
     public function serializeComplete() {
-      $formats = $awards = $restrictions = $stds = $genders = $sexes = $ages = [];
+      $formats = $projects = $awards = $restrictions = $stds = $genders = $sexes = $ages = [];
       $equipment = $software = $subject_of_study = $others = [];
       $locs = $rel = $areas = $area_details = $domains = $publications = $keywords = $publishers = [];
       $authors = $data_type_array = $types_of_study = $corresponding_authors = $experts = [];
@@ -1918,6 +1967,7 @@ public function serializeComplete() {
       foreach ($this->data_types as $data_type) { $data_type_array[]=$data_type->getDisplayName(); }
       foreach ($this->data_collection_instruments as $std) { $stds[]=$std->getAllProperties(); }
       foreach ($this->awards as $award) { $awards[]=$award->getAllProperties(); }
+      foreach ($this->projects as $project) { $projects[]=$project->getAllProperties(); }
       foreach ($this->local_experts as $expert) { $experts[]=$expert->getAllProperties(); }
       foreach ($this->subject_domains as $domain) { $domains[]=$domain->getAllProperties(); }
       foreach ($this->subject_genders as $gender) { $genders[]=$gender->getDisplayName(); }
@@ -1956,6 +2006,7 @@ public function serializeComplete() {
         'data_types'                => $data_type_array,
         'data_collection_standards' => $stds,
         'awards'                    => $awards,
+        'projects'                  => $projects,
         'local_experts'             => $experts,
         'subject_domains'           => $domains,
         'subject_genders'           => $genders,