Merge branch 'development'

SpeciesFileGroup · Jun 5, 2020 · d4a144e · d4a144e
2 parents 72c08d8 + bdce820
commit d4a144e
Show file tree

Hide file tree

Showing 58 changed files with 498 additions and 344 deletions.
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -119,7 +119,7 @@ GEM
     closure_tree (7.1.0)
       activerecord (>= 4.2.10)
       with_advisory_lock (>= 4.0.0)
-    coderay (1.1.2)
+    coderay (1.1.3)
     concurrent-ruby (1.1.6)
     coveralls (0.8.23)
       json (>= 1.8, < 3)
@@ -161,13 +161,13 @@ GEM
     factory_bot_rails (5.2.0)
       factory_bot (~> 5.2.0)
       railties (>= 4.2.0)
-    faker (2.11.0)
+    faker (2.12.0)
       i18n (>= 1.6, < 2)
     faraday (0.17.3)
       multipart-post (>= 1.2, < 3)
     faraday_middleware (0.14.0)
       faraday (>= 0.7.4, < 1.0)
-    ffi (1.12.2)
+    ffi (1.13.0)
     ffi-geos (2.1.0)
       ffi (>= 1.0.0)
     formatador (0.2.5)
@@ -210,7 +210,7 @@ GEM
     hashery (2.1.2)
     hashie (3.6.0)
     hiredis (0.6.3)
-    i18n (1.8.2)
+    i18n (1.8.3)
       concurrent-ruby (~> 1.0)
     indefinite_article (0.2.4)
       activesupport
@@ -362,7 +362,7 @@ GEM
     rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rdf (3.1.1)
+    rdf (3.1.2)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdoc (6.2.1)
@@ -413,10 +413,11 @@ GEM
     rspec-support (3.9.3)
     rtesseract (3.0.5)
       nokogiri
-    rubocop (0.84.0)
+    rubocop (0.85.0)
       parallel (~> 1.10)
       parser (>= 2.7.0.1)
       rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.7)
       rexml
       rubocop-ast (>= 0.0.3)
       ruby-progressbar (~> 1.7)
@@ -437,7 +438,7 @@ GEM
     ruby-units (2.3.1)
     rubyzip (2.3.0)
     safe_yaml (1.0.5)
-    sassc (2.3.0)
+    sassc (2.4.0)
       ffi (~> 1.9)
     sassc-rails (2.1.2)
       railties (>= 4.0.0)
@@ -532,7 +533,7 @@ GEM
       semantic_range (>= 2.3.0)
     websocket-driver (0.7.2)
       websocket-extensions (>= 0.1.0)
-    websocket-extensions (0.1.4)
+    websocket-extensions (0.1.5)
     wikidata-client (0.0.12)
       excon (~> 0.40)
       faraday (~> 0.9)

diff --git a/app/controllers/observation_matrix_columns_controller.rb b/app/controllers/observation_matrix_columns_controller.rb
@@ -2,6 +2,7 @@ class ObservationMatrixColumnsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
 
   before_action :set_observation_matrix_column, only: [:show]
+  after_action -> { set_pagination_headers(:observation_matrix_columns) }, only: [:index], if: :json_request?
 
   # GET /matrix_columns
   # GET /matrix_columns.json
@@ -12,7 +13,10 @@ def index
         render '/shared/data/all/index'
       end
       format.json { 
-        @observation_matrix_columns = ObservationMatrixColumn.where(filter_params).where(project_id: sessions_current_project_id).order('observation_matrix_columns.position')
+        @observation_matrix_columns = ObservationMatrixColumn.where(filter_params)
+        .where(project_id: sessions_current_project_id)
+        .order('observation_matrix_columns.position')
+        .page(params[:page]).per(params[:per])
       }
     end
   end

diff --git a/app/javascript/vue/tasks/descriptor/app.vue b/app/javascript/vue/tasks/descriptor/app.vue
@@ -77,7 +77,7 @@
                     <component
                       v-if="descriptor.type && showDescriptor"
                       :is="loadComponent + 'Component'"
-                      @save="saveDescriptor"
+                      @save="saveDescriptor($event, false)"
                       v-model="descriptor"
                     />
                   </div>
@@ -201,14 +201,14 @@ export default {
         short_name: undefined
       }
     },
-    saveDescriptor (descriptor) {
+    saveDescriptor (descriptor, redirect = true) {
       this.saving = true
       if (this.descriptor.id) {
         UpdateDescriptor(descriptor).then(response => {
           this.descriptor = response
           this.saving = false
           TW.workbench.alert.create('Descriptor was successfully updated.', 'notice')
-          if (this.matrix) {
+          if (this.matrix && redirect) {
             window.open(`/tasks/observation_matrices/new_matrix/${this.matrixId}`, '_self')
           }
         }, rejected => {
@@ -221,7 +221,7 @@ export default {
           this.setParameters()
           TW.workbench.alert.create('Descriptor was successfully created.', 'notice')
           if (this.matrix) {
-            this.addToMatrix(this.descriptor)
+            this.addToMatrix(this.descriptor, redirect)
           }
         }, rejected => {
           this.saving = false
@@ -235,15 +235,17 @@ export default {
         TW.workbench.alert.create('Descriptor was successfully deleted.', 'notice')
       })
     },
-    addToMatrix (descriptor) {
+    addToMatrix (descriptor, redirect) {
       const data = {
         descriptor_id: descriptor.id,
         observation_matrix_id: this.matrix.id,
         type: 'ObservationMatrixColumnItem::SingleDescriptor'
       }
       CreateObservationMatrixColumn(data).then(() => {
         TW.workbench.alert.create('Descriptor was successfully added to the matrix.', 'notice')
-        window.open(`/tasks/observation_matrices/new_matrix/${this.matrixId}`, '_self')
+        if (redirect) {
+          window.open(`/tasks/observation_matrices/new_matrix/${this.matrixId}`, '_self')
+        }
       })
     },
     loadMatrix (id) {

diff --git a/app/javascript/vue/tasks/new_matrix/app.vue b/app/javascript/vue/tasks/new_matrix/app.vue
@@ -1,36 +1,46 @@
 <template>
   <div id="vue_new_matrix_task">
+    <spinner-component
+      v-if="settings.loadingRows || settings.loadingColumns"
+      legend="Loading..."
+      :full-screen="true"/>
     <div class="flex-separate middle">
-      <h1>{{ (matrix.id ? 'Edit' : 'New') }} matrix</h1>
+      <h1>{{ (matrix.id ? 'Edit' : 'New') }} observation matrix</h1>
       <div class="horizontal-left-content">
         <ul class="context-menu">
-          <li> 
-            <a 
+          <li>
+            <a
               href="/tasks/observation_matrices/observation_matrix_hub/index">
               Hub
             </a>
           </li>
+          <li>
+            <a
+              href="/tasks/observation_matrices/dashboard/index">
+              Dashboard
+            </a>
+          </li>
           <li>
             <a :href="`/tasks/observation_matrices/view/${matrix.id}`">
               View
             </a>
           </li>
 
           <li>
-            <a href="/otus/new">New Otu</a>
+            <a href="/otus/new">New OTU</a>
           </li>
           <li>
             <a
               v-if="matrix.id"
-              :href="`/tasks/descriptors/new_descriptor?observation_matrix_id=${matrix.id}`">New Descriptor
+              :href="`/tasks/descriptors/new_descriptor?observation_matrix_id=${matrix.id}`">New descriptor
             </a>
             <a
               v-else
-              :href="`/tasks/descriptors/new_descriptor`">New Descriptor
+              :href="`/tasks/descriptors/new_descriptor`">New descriptor
             </a>
           </li>
           <li>
-            <a href="/tasks/accessions/comprehensive/index">New Collection Object</a>
+            <a href="/tasks/accessions/comprehensive/index">New collection object</a>
           </li>
           <li>
             <pin-component
@@ -80,6 +90,7 @@ import RowsFixed from './components/rows/fixed'
 import columnsFixed from './components/columns/fixed'
 import RadialAnnotator from 'components/radials/annotator/annotator'
 import PinComponent from 'components/pin.vue'
+import SpinnerComponent from 'components/spinner'
 
 import rowsDynamic from './components/rows/dynamic'
 import columnDynamic from './components/columns/dynamic'
@@ -96,23 +107,27 @@ export default {
     columnsFixed,
     columnDynamic,
     RadialAnnotator,
-    PinComponent
+    PinComponent,
+    SpinnerComponent
   },
   computed: {
-    matrix() {
+    matrix () {
       return this.$store.getters[GetterNames.GetMatrix]
     },
-    isRow() {
+    isRow () {
       return (this.$store.getters[GetterNames.GetMatrixView] == 'row' ? true : false) 
     },
-    isFixed() {
+    isFixed () {
       return (this.$store.getters[GetterNames.GetMatrixMode] == 'fixed' ? true : false)
     },
-    columnList() {
+    columnList () {
       return this.$store.getters[GetterNames.GetMatrixColumns]
     },
-    matrixId() {
+    matrixId () {
       return this.$store.getters[GetterNames.GetMatrix].id
+    },
+    settings () {
+      return this.$store.getters[GetterNames.GetSettings]
     }
   },
   data() {

diff --git a/app/javascript/vue/tasks/new_matrix/components/columns/copyDescriptors.vue b/app/javascript/vue/tasks/new_matrix/components/columns/copyDescriptors.vue
@@ -137,8 +137,8 @@ export default {
         if (newVal) {
           this.isLoading = true
           GetObservationMatrices().then(response => {
-            response.splice(response.findIndex(item => { return this.matrixId === item.id }), 1)
-            this.observationMatrices = response
+            response.body.splice(response.body.findIndex(item => { return this.matrixId === item.id }), 1)
+            this.observationMatrices = response.body
             this.isLoading = false
           })
         }
@@ -156,8 +156,8 @@ export default {
   methods: {
     loadDescriptors (matrixId) {
       this.isLoading = true
-      GetMatrixObservationColumns(matrixId).then(response => {
-        this.descriptors = response
+      GetMatrixObservationColumns(matrixId, { per: 500 }).then(response => {
+        this.descriptors = response.body
         this.isLoading = false
       })
     },

diff --git a/app/javascript/vue/tasks/new_matrix/components/columns/dynamic.vue b/app/javascript/vue/tasks/new_matrix/components/columns/dynamic.vue
@@ -58,8 +58,8 @@ export default {
   },
   mounted() {
     GetSmartSelector('keywords').then(response => {
-      this.smartOptions = this.smartOptions.filter(value => Object.keys(response).includes(value))
-      this.selectorLists = response
+      this.smartOptions = this.smartOptions.filter(value => Object.keys(response.body).includes(value))
+      this.selectorLists = response.body
     })
   },
   methods: {

diff --git a/app/javascript/vue/tasks/new_matrix/components/columns/fixed.vue b/app/javascript/vue/tasks/new_matrix/components/columns/fixed.vue
@@ -58,8 +58,8 @@
     },
     mounted() {
       GetMatrixColumnMetadata().then(response => {
-        this.smartOptions = Object.keys(response)
-        this.lists = response
+        this.smartOptions = Object.keys(response.body)
+        this.lists = response.body
       })
     },
     methods: {

diff --git a/app/javascript/vue/tasks/new_matrix/components/columns/keywordView.vue b/app/javascript/vue/tasks/new_matrix/components/columns/keywordView.vue
@@ -53,9 +53,7 @@
           batch_type: 'tags',
           klass: 'Descriptor'
         }
-        console.log(object);
         CreateColumnBatchLoad(object).then((response) => {
-          console.log(response);
           this.$store.dispatch(ActionNames.GetMatrixObservationColumns, this.matrixId)
         })
       }

diff --git a/app/javascript/vue/tasks/new_matrix/components/columns/search.vue b/app/javascript/vue/tasks/new_matrix/components/columns/search.vue
@@ -1,24 +1,17 @@
 <template>
   <div>
-    <p>Select</p>
     <div class="flex-wrap">
       <div class="field">
         <autocomplete
           min="2"
-          :display="displayAutocomplete"
-          :placeholder="`Select a descriptor`"
+          :clear-after="true"
+          placeholder="Select a descriptor"
           label="label"
-          @getItem="setResult"
+          @getItem="createColumnItem($event.id)"
           url="/descriptors/autocomplete"
           param="term"/>
       </div>
     </div>
-    <button
-      :disabled="!objectId"
-      class="normal-input button button-submit"
-      type="button"
-      @click="createColumnItem">Create
-    </button>
   </div>
 </template>
 <script>
@@ -37,26 +30,20 @@ export default {
       return this.$store.getters[GetterNames.GetMatrix]
     }
   },
-  data() {
+  data () {
     return {
       displayAutocomplete: undefined,
-      objectId: undefined,
+      objectId: undefined
     }
   },
   methods: {
-    createColumnItem() {
-      let data = {
+    createColumnItem (id) {
+      const data = {
         observation_matrix_id: this.matrix.id,
-        descriptor_id: this.objectId,
+        descriptor_id: id,
         type: 'ObservationMatrixColumnItem::SingleDescriptor'
       }
-      this.displayAutocomplete = undefined
-      this.objectId = undefined
       this.$store.dispatch(ActionNames.CreateColumnItem, data)
-    },
-    setResult(descriptor) {
-      this.objectId = descriptor.id
-      this.displayAutocomplete = descriptor.label
     }
   }
 }

diff --git a/app/javascript/vue/tasks/new_matrix/components/newMatrix/newMatrix.vue b/app/javascript/vue/tasks/new_matrix/components/newMatrix/newMatrix.vue
@@ -83,18 +83,18 @@ export default {
         this.$store.commit(MutationNames.SetMatrixMode, (value ? 'fixed' : 'dynamic'))
       }
     },
-    validateData() {
+    validateData () {
       return this.$store.getters[GetterNames.GetMatrix].name &&
             !this.$store.getters[GetterNames.GetMatrix].id
     }
   },
   methods: {
-    create() {
+    create () {
       CreateMatrix(this.matrix).then(response => {
-        this.matrix = response
-      }); 
+        this.matrix = response.body
+      })
     },
-    updateMatrix() {
+    updateMatrix () {
       this.$store.dispatch(ActionNames.UpdateMatrix)
     }
   }

diff --git a/app/javascript/vue/tasks/new_matrix/components/rows/batchView.vue b/app/javascript/vue/tasks/new_matrix/components/rows/batchView.vue
@@ -45,7 +45,7 @@
           klass: classType
         }
         CreateRowBatchLoad(object).then((response) => {
-          this.$store.dispatch(ActionNames.GetMatrixObservationRows, this.matrixId)
+          this.$store.dispatch(ActionNames.GetMatrixObservationRows, { per: 500 })
         })
       }
     }