Merge branch 'main' into task/des-2569-add-facilities-to-all-project-…

…types
DesignSafe-CI · Nov 14, 2023 · 47f5a93 · 47f5a93
2 parents 7e6d7ea + 59120ce
commit 47f5a93
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diff --git a/.dockerignore b/.dockerignore
@@ -7,4 +7,5 @@ coverage
 .git
 .docs
 .github
-.pytest_cache
+.pytest_cache
+data
diff --git a/designsafe/apps/projects/models/agave/base.py b/designsafe/apps/projects/models/agave/base.py
@@ -499,7 +499,7 @@ def to_datacite_json(self):
         # remember, related works are not required, so they can be missing...
         for a_proj in self.associated_projects: #relatedwork
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= a_proj.keys():
                 identifier['relationType'] = mapping[a_proj['type']]
                 identifier['relatedIdentifierType'] = a_proj['hrefType']

diff --git a/designsafe/apps/projects/models/agave/experimental.py b/designsafe/apps/projects/models/agave/experimental.py
@@ -82,7 +82,7 @@ def to_datacite_json(self):
         attributes['relatedIdentifiers'] = []
         for r_work in self.related_work:
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= r_work.keys():
                 identifier['relationType'] = mapping[r_work['type']]
                 identifier['relatedIdentifierType'] = r_work['hrefType']

diff --git a/designsafe/apps/projects/models/agave/hybrid_simulation.py b/designsafe/apps/projects/models/agave/hybrid_simulation.py
@@ -100,7 +100,7 @@ def to_datacite_json(self):
         attributes['relatedIdentifiers'] = []
         for r_work in self.related_work:
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= r_work.keys():
                 identifier['relationType'] = mapping[r_work['type']]
                 identifier['relatedIdentifierType'] = r_work['hrefType']

diff --git a/designsafe/apps/projects/models/agave/rapid.py b/designsafe/apps/projects/models/agave/rapid.py
@@ -98,7 +98,7 @@ def to_datacite_json(self):
         attributes['relatedIdentifiers'] = []
         for r_work in self.related_work:
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= r_work.keys():
                 identifier['relationType'] = mapping[r_work['type']]
                 identifier['relatedIdentifierType'] = r_work['hrefType']
@@ -256,7 +256,7 @@ def to_datacite_json(self):
         attributes['relatedIdentifiers'] = []
         for r_work in self.related_work:
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= r_work.keys():
                 identifier['relationType'] = mapping[r_work['type']]
                 identifier['relatedIdentifierType'] = r_work['hrefType']

diff --git a/designsafe/apps/projects/models/agave/simulation.py b/designsafe/apps/projects/models/agave/simulation.py
@@ -84,7 +84,7 @@ def to_datacite_json(self):
         attributes['relatedIdentifiers'] = []
         for r_work in self.related_work:
             identifier = {}
-            mapping = {'Linked Project': 'IsSupplementTo', 'Linked Dataset': 'IsSupplementTo', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
+            mapping = {'Linked Project': 'IsPartOf', 'Linked Dataset': 'IsPartOf', 'Cited By': 'IsCitedBy', 'Context': 'IsDocumentedBy'}
             if {'type', 'href', 'hrefType'} <= r_work.keys():
                 identifier['relationType'] = mapping[r_work['type']]
                 identifier['relatedIdentifierType'] = r_work['hrefType']

diff --git a/designsafe/apps/search/templates/designsafe/apps/search/index.j2 b/designsafe/apps/search/templates/designsafe/apps/search/index.j2
@@ -8,12 +8,15 @@
 
 {% block content %}
 <div class="container">
-    <ui-view></ui-view>
+    <div class="gcse-search"></div>
   {{message}}
   </div>
 </div>
 {% addtoblock "js" %}
   <script src="<%= htmlWebpackPlugin.files.js %>"></script>
+  <script async src="https://cse.google.com/cse.js?cx=7671a7caca0a643c1">
+</script>
 {% endaddtoblock %}
 
 {% endblock %}
+{% block footer %}{% include 'includes/footer.html' %}{% endblock footer %}
diff --git a/designsafe/static/scripts/applications/controllers/application-add.js b/designsafe/static/scripts/applications/controllers/application-add.js
@@ -270,7 +270,7 @@ export function applicationAddCtrl(window, angular, $, _) {
                     },
                     'defaultProcessorsPerNode': {
                         'type': 'integer',
-                        'description': 'Default number of processors per node to be used when running this app if no processor count is given in the job request',
+                        'description': 'Total number of processors across all nodes to be used when running this app if no processor count is given in the job request',
                         'maxLength': 12,
                         'title': 'Default processor count',
                         'x-schema-form': {

diff --git a/...e/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js b/...e/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js
@@ -246,6 +246,7 @@ class FilesListingCtrl {
     browse($event, file) {
         $event.preventDefault();
         $event.stopPropagation();
+        if (this.doi) file.doi = this.doi;
         this.onBrowse({ file });
     }
 

diff --git a/...e/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js b/...e/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js
@@ -68,7 +68,8 @@ class DataDepotToolbarCtrl {
     copy() {
         const { api, scheme, system, path } = this.FileListingService.listings.main.params;
         const files = this.getAllSelected();
-        this.FileOperationService.openCopyModal({api, scheme, system, path, files});
+        const doi = this.FileListingService.currentDOI || this.$stateParams.doi;
+        this.FileOperationService.openCopyModal({api, scheme, system, path, files, doi});
     }
     move() {
         const { api, scheme, system, path } = this.FileListingService.listings.main.params;

diff --git a/designsafe/static/scripts/data-depot/components/published/published-view.component.js b/designsafe/static/scripts/data-depot/components/published/published-view.component.js
@@ -659,6 +659,7 @@ class PublishedViewCtrl {
     }
 
     onBrowse(file, doi) {
+        if (!doi) {doi = file.doi}
         if (!doi) {doi = this.$stateParams.doi}
         if (file.type === 'dir') {
             this.$state.go(this.$state.current.name, { filePath: file.path, query_string: null, doi: doi });

diff --git a/designsafe/static/scripts/navbar.js b/designsafe/static/scripts/navbar.js
@@ -13,7 +13,7 @@
     var radioValue = $('input[name="search-radio"]:checked').val();
     var searchstring = $('#searchfield').val();
     if (ev.which === 13 || ev.type === 'click') {
-      if (radioValue==='website') window.location = '/search?type_filter=all&query_string=' + searchstring;
+      if (radioValue==='website') window.location = '/search?q=' + searchstring;
       if (radioValue ==='datasets') {
         var datasetSearchUrl = `/data/browser/public/?query_string=%257B%2522queries%2522%253A%257B%2522searchString%2522%253A%2522${searchstring}%2522%252C%2522publicationYear%2522%253A%2522%2522%257D%252C%2522typeFilters%2522%253A%257B%2522experimental%2522%253Afalse%252C%2522simulation%2522%253Afalse%252C%2522field_recon%2522%253Afalse%252C%2522other%2522%253Afalse%252C%2522hybrid_simulation%2522%253Afalse%257D%252C%2522advancedFilters%2522%253A%257B%2522experimental%2522%253A%257B%2522experimentType%2522%253A%2522%2522%252C%2522experimentalFacility%2522%253A%257B%2522name%2522%253A%2522%2522%252C%2522label%2522%253A%2522%2522%257D%257D%252C%2522simulation%2522%253A%257B%2522simulationType%2522%253A%2522%2522%257D%252C%2522field_recon%2522%253A%257B%2522naturalHazardType%2522%253A%2522%2522%252C%2522naturalHazardEvent%2522%253A%2522%2522%252C%2522frType%2522%253A%2522%2522%252C%2522frDate%2522%253A%2522%2522%257D%252C%2522other%2522%253A%257B%2522dataType%2522%253A%2522%2522%257D%252C%2522hybrid_simulation%2522%253A%257B%2522hybridSimulationType%2522%253A%2522%2522%257D%257D%257D`
         window.location = datasetSearchUrl;

diff --git a/...gnsafe/components/modals/data-browser-service-copy/data-browser-service-copy.component.js b/...gnsafe/components/modals/data-browser-service-copy/data-browser-service-copy.component.js
@@ -118,6 +118,7 @@ class DataBrowserCopyCtrl {
             destSystem: dest.system,
             destPath: dest.path,
             successCallback: this.successCallback,
+            doi: this.resolve.doi
         });
     }
 

diff --git a/.../components/modals/data-browser-service-preview/data-browser-service-preview.component.js b/.../components/modals/data-browser-service-preview/data-browser-service-preview.component.js
@@ -138,7 +138,7 @@ class DataBrowserServicePreviewCtrl {
     copy() {
         const { api, scheme, system, path } = this.FileListingService.listings.main.params;
         const files = [this.resolve.file];
-        this.FileOperationService.openCopyModal({ api, scheme, system, path, files });
+        this.FileOperationService.openCopyModal({ api, scheme, system, path, files, doi: this.resolve.doi });
     }
 
     move() {

diff --git a/...nsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-collections-template.html b/...nsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-collections-template.html
@@ -71,7 +71,8 @@
                               published="true"
                               on-scroll="$ctrl.scrollToBottom()"
                               listing="$ctrl.FileListingService.listings[collection.uuid]"
-                              on-browse="$ctrl.onBrowse(file)">&nbsp;
+                              on-browse="$ctrl.onBrowse(file)"
+                              doi="mission.doi">&nbsp;
               </files-listing>
           </div>
       </div>
@@ -206,7 +207,8 @@
                                   published="true"
                                   on-scroll="$ctrl.scrollToBottom()"
                                   listing="$ctrl.FileListingService.listings[collection.uuid]"
-                                  on-browse="$ctrl.onBrowse(file)">&nbsp;
+                                  on-browse="$ctrl.onBrowse(file)"
+                                  doi="mission.doi">&nbsp;
                   </files-listing>
               </div>
           </div>
@@ -299,7 +301,8 @@
                                   published="true"
                                   on-scroll="$ctrl.scrollToBottom()"
                                   listing="$ctrl.FileListingService.listings[collection.uuid]"
-                                  on-browse="$ctrl.onBrowse(file)">&nbsp;
+                                  on-browse="$ctrl.onBrowse(file)"
+                                  doi="mission.doi">&nbsp;
                   </files-listing>
               </div>
               </div>
@@ -347,7 +350,8 @@
                                   published="true"
                                   on-scroll="$ctrl.scrollToBottom()"
                                   listing="$ctrl.FileListingService.listings[collection.uuid]"
-                                  on-browse="$ctrl.onBrowse(file)">&nbsp;
+                                  on-browse="$ctrl.onBrowse(file)"
+                                  doi="mission.doi">&nbsp;
                   </files-listing>
               </div>    
           </div>

diff --git a/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js b/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js
@@ -3,7 +3,7 @@ import { map, tap, catchError } from 'rxjs/operators';
 import { takeLatestSubscriber } from './_rxjs-utils';
 
 export class FileOperationService {
-    constructor($http, $state, $rootScope, $uibModal, $q, ProjectService, Django, toastr) {
+    constructor($http, $state, $stateParams, $rootScope, $uibModal, $q, ProjectService, Django, toastr) {
         'ngInject';
         this.$state = $state;
         this.$uibModal = $uibModal;
@@ -12,6 +12,7 @@ export class FileOperationService {
         this.toastr = toastr;
         this.$rootScope = $rootScope;
         this.$http = $http;
+        this.$stateParams = $stateParams;
         this.ProjectService = ProjectService;
         this.from = from; // bind rxjs method for mocking
 
@@ -125,7 +126,7 @@ export class FileOperationService {
      * @param {string} params.system System to copy files from.
      * @param {Object[]} params.files Array of file objects {name, system, path} to copy.
      */
-    openCopyModal({ api, scheme, system, files }) {
+    openCopyModal({ api, scheme, system, files, doi }) {
         this.operations.copy.status = {};
         var modal = this.$uibModal.open({
             component: 'copyModal',
@@ -134,6 +135,7 @@ export class FileOperationService {
                 scheme: () => scheme,
                 system: () => system,
                 files: () => files,
+                doi: () => doi,
             },
             size: 'lg',
         });
@@ -154,14 +156,15 @@ export class FileOperationService {
      * @param {string} params.destPath Path of directory to copy files into.
      * @param {function} params.successCallback Callback on successful copy of all files.
      */
-    handleCopy({ srcApi, srcFiles, destApi, destSystem, destPath, successCallback }) {
+    handleCopy({ srcApi, srcFiles, destApi, destSystem, destPath, successCallback, doi}) {
         const copyParams = {
             srcApi,
             srcFiles,
             destApi,
             destSystem,
             destPath,
             successCallback,
+            doi,
         };
 
         const copyMapping = () => this.mapParamsToCopy(copyParams);
@@ -180,7 +183,7 @@ export class FileOperationService {
      * @param {Object[]} params.files Array of file objects {name, system, path} to copy.
      * @param {function} params.successCallback Callback on successful copy of all files.
      */
-    mapParamsToCopy({ srcApi, destApi, destSystem, destPath, srcFiles, successCallback }) {
+    mapParamsToCopy({ srcApi, destApi, destSystem, destPath, srcFiles, successCallback, doi }) {
         // Treat Shared Data as Agave for the purpose of copying files.
         if (srcApi === 'shared') {
             srcApi = 'agave';
@@ -193,7 +196,7 @@ export class FileOperationService {
             // Copying files between APIs requires the transfer endpoint.
             if (srcApi === destApi) {
                 const copyUrl = this.removeDuplicateSlashes(
-                    `/api/datafiles/${srcApi}/private/copy/${f.system}/${f.path}/`
+                    `/api/datafiles/${srcApi}/private/copy/${f.system}/${f.path}/?doi=${doi}`
                 );
                 copyRequest = this.$http.put(copyUrl, {
                     dest_system: destSystem,

diff --git a/designsafe/static/scripts/workspace/controllers/application-form.js b/designsafe/static/scripts/workspace/controllers/application-form.js
@@ -123,16 +123,16 @@ export default function ApplicationFormCtrl($scope, $rootScope, $localStorage, $
         let items = [];
         if ($scope.form.schema.properties.inputs) {
             items.push('inputs');
+            $scope.form.form.push({
+                type: 'fieldset',
+                readonly: readOnly,
+                title: 'Inputs',
+                items: items,
+            });
         }
         if ($scope.form.schema.properties.parameters) {
             items.push('parameters');
         }
-        $scope.form.form.push({
-            type: 'fieldset',
-            readonly: readOnly,
-            title: 'Inputs',
-            items: items,
-        });
 
         /* job details */
         items = [];

diff --git a/designsafe/static/scripts/workspace/html/application-form.html b/designsafe/static/scripts/workspace/html/application-form.html
@@ -12,7 +12,7 @@ <h1>Select an app</h1>
 <div ng-if="data.bin" class="app-dropdown">
     <p compile="data.bin.description" class="app-form-wrapper" ng-if="data.bin.description"></p>
     <div>Select a version of <b>{{data.bin.value.definition.label}}</b> from the dropdown:</div>
-    <select ng-model="data.selectedApp" ng-options="app.value.definition.label for app in data.bin.applications | orderBy: 'value.definition.label'">
+    <select ng-model="data.selectedApp" ng-options="app.value.definition.label for app in data.bin.applications | orderBy: 'value.definition.label'" style="color:initial;">
         <option value=''disabled selected>-- Please Select --</option>
     </select>
 </div>

diff --git a/designsafe/static/scripts/workspace/html/directives/agave-file-picker.html b/designsafe/static/scripts/workspace/html/directives/agave-file-picker.html
@@ -1,9 +1,14 @@
 <div>
     <div class="input-group">
         <span class="input-group-btn">
-          <button ng-click="wantFile($event)" class="btn btn-default" type="button">Select</button>
+            <button ng-click="wantFile($event)" class="btn btn-default" type="button">Select</button>
         </span>
-        <input type="text" class="form-control" ng-model="data.input" placeholder="{{form.placeholder || 'Click to select input data'}}" />
+        <input
+            type="text"
+            class="form-control"
+            ng-model="data.input"
+            placeholder="{{form.placeholder || 'Click Select on the left to choose input data'}}"
+        />
     </div>
     <span class="help-text" ng-if="requesting">
         <button type="button" class="btn btn-xs btn-link" ng-click="stopWant($event)">Cancel</button>
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,4 +7,5 @@ coverage @@
     .git
     .docs
     .github
-    .pytest_cache
+    .pytest_cache
+    data