Merge branch 'features/bmt-search' into features/repository-filters

app/assets/javascripts/application.js.erb

@@ -286,3 +286,5 @@ $(window).scroll(function() {
     scroll_function();
   })
 })
+
+window.I18n = I18n

app/assets/javascripts/repositories/repository_datatable.js

@@ -1,7 +1,7 @@
 /*
   globals I18n _ SmartAnnotation FilePreviewModal animateSpinner DataTableHelpers
   HelperModule RepositoryDatatableRowEditor prepareRepositoryHeaderForExport
-  initAssignedTasksDropdown
+  initAssignedTasksDropdown initBMTFilter
 */
 
 //= require jquery-ui/widgets/sortable
@@ -268,6 +268,7 @@ var RepositoryDatatable = (function(global) {
     $.getJSON($(TABLE_ID).data('toolbar-url'), (data) => {
       $('#toolbarButtonsDatatable').remove();
       $(data.html).appendTo('div.toolbar');
+      initBMTFilter();
     });
 
     TABLE.ajax.reload(null, false);
@@ -406,6 +407,10 @@ var RepositoryDatatable = (function(global) {
         url: $(TABLE_ID).data('source'),
         data: function(d) {
           d.archived = $('.repository-show').hasClass('archived');
+
+          if ($('[data-external-ids]').length) {
+            d.external_ids = $('[data-external-ids]').attr('data-external-ids').split(',');
+          }
         },
         global: false,
         type: 'POST'
@@ -551,6 +556,7 @@ var RepositoryDatatable = (function(global) {
         // Append buttons to inner toolbar in the table
         $.getJSON($(TABLE_ID).data('toolbar-url'), (data) => {
           $(data.html).appendTo('div.toolbar');
+          initBMTFilter();
         });
 
         $('div.toolbar-filter-buttons').prependTo('div.filter-container');
@@ -577,6 +583,7 @@ var RepositoryDatatable = (function(global) {
         });
 
         initAssignedTasksDropdown(TABLE_ID);
+
       }
     });
 

app/assets/javascripts/repository_columns/index.js

@@ -253,31 +253,12 @@ var RepositoryColumns = (function() {
     });
   }
 
-  function getColumnTypeText(el, colId) {
-    var colType = '';
-    switch (colId) {
-      case 'row-id':
-        colType = 'RepositoryNumberValue';
-        break;
-      case 'row-name':
-        colType = 'RepositoryTextValue';
-        break;
-      case 'added-on':
-        colType = 'RepositoryDateTimeValue';
-        break;
-      case 'added-by':
-        colType = 'RepositoryListValue';
-        break;
-      case 'archived-on':
-        colType = 'RepositoryDateTimeValue';
-        break;
-      case 'archived-by':
-        colType = 'RepositoryListValue';
-        break;
-      default:
-        colType = $(el).attr('data-type');
-    }
-    return I18n.t('libraries.manange_modal_column.select.' + colType.split(/(?=[A-Z])/).join('_').toLowerCase());
+  function getColumnTypeText(el) {
+    let colType = $(el).attr('data-type');
+    if (!colType) return '';
+
+    return I18n.t('libraries.manange_modal_column.select.' + colType.split(/(?=[A-Z])/).join('_')
+      .toLowerCase());
   }
 
   // loads the columns names in the manage columns modal index

app/assets/stylesheets/repositories.scss

@@ -135,13 +135,12 @@
     flex-wrap: nowrap;
     height: 6em;
     left: var(--repository-sidebar-margin);
-    overflow: hidden;
     padding: 1em 2em 0;
     position: fixed;
     top: calc(4em + var(--navbar-height));
     transition: .4s $timing-function-sharp;
     width: calc(100% - var(--repository-sidebar-margin));
-    z-index: 90;
+    z-index: 99;
 
     .filter-container {
       flex-shrink: 0;

app/assets/stylesheets/repository/bmt_filters.scss

@@ -0,0 +1,168 @@
+// scss-lint:disable SelectorDepth
+// scss-lint:disable NestingDepth
+
+.bmt-filters-button.active-filters {
+  position: relative;
+
+  &::after {
+    background: $brand-accent;
+    border-radius: 50%;
+    content: "";
+    display: block;
+    height: 8px;
+    position: absolute;
+    right: .3em;
+    top: .3em;
+    width: 8px;
+  }
+}
+
+#bmtFilterContainer {
+  min-width: 422px;
+  z-index: 100;
+
+  .sci-input-container {
+    margin-bottom: .5em;
+  }
+
+  .dropdown-selector-container {
+    width: 100%;
+  }
+
+  .field-suboption {
+    align-items: center;
+    display: flex;
+    margin-top: .5em;
+
+    .sci-checkbox-container {
+      margin-right: .25em;
+    }
+
+    .distance-attribute {
+      align-items: center;
+      display: flex;
+      flex-shrink: 0;
+      margin-bottom: .5em;
+      margin-top: 1.5em;
+
+      input[type=radio] {
+        margin: 0 .25em 0 .5em;
+      }
+    }
+  }
+
+  label {
+    font-weight: normal;
+  }
+
+  .form-group {
+    display: block;
+    width: 100%;
+
+    .form-control,
+    .form-select {
+      margin-bottom: 1.2em;
+      width: 100%;
+    }
+  }
+
+  .checkbox-label {
+    vertical-align: text-bottom;
+  }
+
+  .filter-list-notice {
+    color: $color-silver-chalice;
+    padding: 1em;
+  }
+
+  .header {
+    align-items: center;
+    border-bottom: $border-tertiary;
+    display: flex;
+    padding: 0 1em;
+
+    .title {
+      @include font-h2;
+    }
+
+    .clear-filters-btn {
+      margin-left: auto;
+    }
+  }
+
+  .filter-container {
+    border-bottom: $border-tertiary;
+    padding: 1em 3.5em 1em 1em;
+
+
+    .filter-title {
+      @include font-small;
+    }
+  }
+
+  .filter-element {
+    align-items: center;
+    display: flex;
+    position: relative;
+  }
+
+  .filter-remove {
+    cursor: pointer;
+    padding: 0;
+    position: absolute;
+    right: -2.5em;
+    top: -2px;
+  }
+
+  .filters-list {
+    border-top: $border-tertiary;
+    max-height: calc(100vh - 300px);
+    overflow-y: auto;
+  }
+
+  .footer {
+    align-items: center;
+    border-top: $border-tertiary;
+    display: flex;
+    padding: 5px 1em 0;
+
+    .add-filter {
+      margin-right: auto;
+    }
+  }
+
+  .saved-filters-container {
+    .title {
+      cursor: pointer;
+    }
+
+    &.open {
+      .fa-caret-down {
+        @include rotate(-180deg);
+      }
+    }
+  }
+
+  .saved-filters-list {
+    max-height: calc(100vh - 300px);
+    overflow-y: auto;
+    padding: 0 1em;
+  }
+
+  .saved-filters-element {
+    align-items: center;
+    cursor: pointer;
+    display: flex;
+    justify-content: space-between;
+    min-width: 200px;
+
+    i {
+      color: $color-silver-chalice;
+    }
+
+  }
+
+  .saved-filters-element:hover i {
+    color: $color-black;
+  }
+}

app/assets/stylesheets/repository/repository_table.scss

@@ -4,10 +4,28 @@
 @import "constants";
 
 .repository-table {
+  position: relative;
+
   .dataTables_filter {
     float: right;
   }
 
+  .repository-table-error {
+    background: $color-white;
+    display: none;
+    height: 200px;
+    padding: 1em;
+    position: absolute;
+    text-align: center;
+    top: 176px;
+    width: 100%;
+    z-index: 1;
+
+    &.active {
+      display: block;
+    }
+  }
+
   // hack only for firefox
   @-moz-document url-prefix() {
     input.form-control[type="file"] {

app/controllers/bio_eddie_assets_controller.rb

@@ -56,18 +56,22 @@ class BioEddieAssetsController < ApplicationController
   end
 
   def bmt_request
-    return render_404 unless ENV['BIOMOLECULE_TOOLKIT_BASE_URL']
+    return render_404 unless Rails.application.config.x.biomolecule_toolkit_base_url
 
-    uri = URI.parse(ENV['BIOMOLECULE_TOOLKIT_BASE_URL'])
-    uri.path = request.original_fullpath.remove('/biomolecule_toolkit')
+    uri = URI.parse(Rails.application.config.x.biomolecule_toolkit_base_url)
+    uri.path = File.join(uri.path, request.original_fullpath.remove('/biomolecule_toolkit'))
 
     Net::HTTP.start(uri.host, uri.port, use_ssl: uri.scheme == 'https') do |http|
       api_request = "Net::HTTP::#{request.request_method.capitalize}".constantize.new(uri)
-      api_request['x-api-key'] = ENV['BIOMOLECULE_TOOLKIT_API_KEY'] if ENV['BIOMOLECULE_TOOLKIT_API_KEY']
+      if Rails.application.config.x.biomolecule_toolkit_api_key
+        api_request['x-api-key'] = Rails.application.config.x.biomolecule_toolkit_api_key
+      end
       api_request['Content-Type'] = 'application/json'
       request_body = request.body.read
+
       api_request.body = request_body if request_body.present?
       api_response = http.request(api_request)
+
       render body: api_response.body, content_type: api_response.content_type, status: api_response.code
     end
   end

app/controllers/bmt_filters_controller.rb

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+class BmtFiltersController < ApplicationController
+  before_action :check_manage_permission, except: :index
+
+  def index
+    render json: BmtFilter.all, each_serializer: BmtFilterSerializer
+  end
+
+  def create
+    filter = BmtFilter.new(
+      name: filters_params[:name],
+      filters: JSON.parse(filters_params[:filters])
+    )
+    filter.created_by = current_user
+    if filter.save
+      render json: filter, serializer: BmtFilterSerializer
+    else
+      render json: filter.errors.full_messages, status: :unprocessable_entity
+    end
+  end
+
+  def destroy
+    filter = BmtFilter.find(params[:id])
+    render json: { status: filter.destroy }
+  end
+
+  private
+
+  def filters_params
+    params.require(:bmt_filter).permit(:name, :filters)
+  end
+
+  def check_manage_permission
+    render_403 && return unless can_manage_bmt_filters?(@current_team)
+  end
+end

app/controllers/repositories_controller.rb

@@ -27,7 +27,7 @@ class RepositoriesController < ApplicationController
   def index
     respond_to do |format|
       format.html do
-        render 'empty_index' if Repository.accessible_by_teams(current_team).blank?
+        render 'empty_index' if @repositories.blank?
       end
       format.json do
         render json: prepare_repositories_datatable(@repositories, current_team, params)

app/helpers/repository_datatable_helper.rb

@@ -5,18 +5,11 @@ module RepositoryDatatableHelper
 
   def prepare_row_columns(repository_rows, repository, columns_mappings, team, options = {})
     repository_rows.map do |record|
-      row = {
-        'DT_RowId': record.id,
-        'DT_RowAttr': { 'data-state': row_style(record) },
-        '1': assigned_row(record),
-        '2': record.code,
-        '3': escape_input(record.name),
-        '4': I18n.l(record.created_at, format: :full),
-        '5': escape_input(record.created_by.full_name),
-        '6': (record.archived_on ? I18n.l(record.archived_on, format: :full) : ''),
-        '7': escape_input(record.archived_by&.full_name),
-        'recordInfoUrl': Rails.application.routes.url_helpers.repository_repository_row_path(repository, record)
-      }
+      row = public_send("#{repository.class.name.underscore}_default_columns", record)
+
+      row['DT_RowId'] = record.id
+      row['DT_RowAttr'] = { 'data-state': row_style(record) }
+      row['recordInfoUrl'] = Rails.application.routes.url_helpers.repository_repository_row_path(repository, record)
 
       unless options[:view_mode]
         row['recordUpdateUrl'] =
@@ -84,20 +77,39 @@ module RepositoryDatatableHelper
       can_manage_repository_rows?(repository)
   end
 
-  def default_table_order_as_js_array
-    Constants::REPOSITORY_TABLE_DEFAULT_STATE['order'].to_json
+  def repository_default_columns(record)
+    {
+      '1': assigned_row(record),
+      '2': record.code,
+      '3': escape_input(record.name),
+      '4': I18n.l(record.created_at, format: :full),
+      '5': escape_input(record.created_by.full_name),
+      '6': (record.archived_on ? I18n.l(record.archived_on, format: :full) : ''),
+      '7': escape_input(record.archived_by&.full_name)
+    }
   end
 
-  def default_table_columns
-    Constants::REPOSITORY_TABLE_DEFAULT_STATE['columns'].to_json
+  def linked_repository_default_columns(record)
+    {
+      '1': assigned_row(record),
+      '2': escape_input(record.external_id),
+      '3': record.code,
+      '4': escape_input(record.name),
+      '5': I18n.l(record.created_at, format: :full),
+      '6': escape_input(record.created_by.full_name),
+      '7': (record.archived_on ? I18n.l(record.archived_on, format: :full) : ''),
+      '8': escape_input(record.archived_by&.full_name)
+    }
   end
 
-  def default_snapshot_table_order_as_js_array
-    Constants::REPOSITORY_SNAPSHOT_TABLE_DEFAULT_STATE['order'].to_json
-  end
-
-  def default_snapshot_table_columns
-    Constants::REPOSITORY_SNAPSHOT_TABLE_DEFAULT_STATE['columns'].to_json
+  def bmt_repository_default_columns(record)
+    {
+      '1': assigned_row(record),
+      '2': escape_input(record.external_id),
+      '3': record.code,
+      '4': escape_input(record.name),
+      '5': I18n.l(record.created_at, format: :full)
+    }
   end
 
   def display_cell_value(cell, team)

app/javascript/.eslintrc.json

@@ -16,6 +16,7 @@
       "jsx": true
     }
   },
+  "ignorePatterns": ["*.vue", "**/mixins/*.js"],
   "rules": {
     "import/extensions": "off",
     "import/no-unresolved": "off",

app/javascript/packs/vue/bmt_filter.js

@@ -0,0 +1,82 @@
+import TurbolinksAdapter from 'vue-turbolinks';
+import Vue from 'vue/dist/vue.esm';
+import FilterContainer from '../../vue/bmt_filter/container.vue';
+
+Vue.use(TurbolinksAdapter);
+Vue.prototype.i18n = window.I18n;
+
+window.initBMTFilter = () => {
+  const bmtFilterContainer = new Vue({
+    el: '#bmtFilterContainer',
+    data: () => {
+      return {
+        bmtApiBaseUrl: $('#bmtFilterContainer').data('bmt-api-base-url'),
+        canManageFilters: $('#bmtFilterContainer').data('can-manage-filters'),
+        savedFilters: [],
+        filters: []
+      };
+    },
+    created() {
+      this.dataTableElement = $($('#bmtFilterContainer').data('datatable-id'));
+    },
+    components: {
+      'filter-container': FilterContainer
+    },
+    methods: {
+      updateFilters(filters) {
+        this.filters = filters;
+      },
+      getFilters() {
+        return this.filters;
+      },
+      updateExternalIds(ids) {
+        this.dataTableElement.attr('data-external-ids', ids.join(','));
+        this.closeFilters();
+        this.reloadDataTable();
+      },
+      clearFilters() {
+        this.clearSearchError();
+        this.dataTableElement.removeAttr('data-external-ids');
+      },
+      closeFilters() {
+        $(this.$el).closest('.dropdown').removeClass('open');
+      },
+      reloadDataTable() {
+        this.clearSearchError();
+        this.dataTableElement.DataTable().ajax.reload();
+      },
+      handleSearchError(error) {
+        $('.repository-table-error').addClass('active').html(error);
+      },
+      clearSearchError() {
+        $('.repository-table-error').removeClass('active').html('');
+      }
+    }
+  });
+
+  // prevent closing of dropdown
+  $('#bmtFilterContainer').on('click', (e) => e.stopPropagation());
+
+  // close saved filters dropdown
+  $('#bmtFiltersDropdownButton').on('hidden.bs.dropdown', (e) => {
+    $('.saved-filters-container').removeClass('open');
+  });
+
+  $("#saveBmtFilterForm" )
+    .off()
+    .on('ajax:before', function() {
+      $('#bmt_filter_filters').val(JSON.stringify(bmtFilterContainer.getFilters()));
+    })
+    .on('ajax:success', function(e, result) {
+      bmtFilterContainer.savedFilters.push(result.data);
+      $('#modalSaveBmtFilter').modal('hide');
+    });
+
+  $.get($('#bmtFilterContainer').data('saved-filters-url'), function(result) {
+    bmtFilterContainer.savedFilters = result.data;
+  })
+};
+
+$('.repository-show').on('click', '.open-save-bmt-modal', () => {
+  $('#modalSaveBmtFilter').modal('show');
+})

app/javascript/vue/bmt_filter/container.vue

@@ -0,0 +1,171 @@
+<template>
+  <div class="filters-container">
+    <div class="header">
+      <div id="savedFiltersContainer" class="dropdown saved-filters-container" @click="toggleSavedFilters">
+        <div class="title" id="savedFilterDropdown">
+          {{ i18n.t('repositories.show.bmt_search.title') }}
+          <i v-if="savedFilters.length" class="fas fa-caret-down"></i>
+        </div>
+        <div v-if="savedFilters.length" class="dropdown-menu saved-filters-list">
+          <SavedFilterElement
+            v-for="(savedFilter, index) in savedFilters"
+            :key="savedFilter.id"
+            :savedFilter.sync="savedFilters[index]"
+            :canManageFilters="canManageFilters"
+            @savedFilter:load="loadFilters"
+            @savedFilter:delete="savedFilters.splice(index, 1)"
+          />
+        </div>
+      </div>
+      <button class="btn btn-light clear-filters-btn" @click="closeSavedFilters() && clearFilters()">
+        <i class="fas fa-times-circle"></i>
+        {{ i18n.t('repositories.show.bmt_search.clear_all') }}
+      </button>
+    </div>
+    <div class="filters-list" @click="closeSavedFilters">
+      <div v-if="filters.length == 0" class="filter-list-notice">
+        {{ i18n.t('repositories.show.bmt_search.no_filters') }}
+      </div>
+      <FilterElement
+        v-for="(filter, index) in filters"
+        :key="filter.id"
+        :filter.sync="filters[index]"
+        :additionalDataAttributes="additionalDataAttributes"
+        @filter:delete="filters.splice(index, 1)"
+        @filter:update="updateFilter"
+      />
+    </div>
+    <div class="footer" @click="closeSavedFilters">
+      <button class="btn btn-secondary add-filter" @click="addFilter">
+        <i class="fas fa-plus"></i>
+        {{ i18n.t('repositories.show.bmt_search.add_filter') }}
+      </button>
+      <button @click="fetchCIDs" class="btn btn-primary">
+        {{ i18n.t('repositories.show.bmt_search.apply') }}
+      </button>
+    </div>
+  </div>
+</template>
+
+ <script>
+  import FilterElement from 'vue/bmt_filter/filter.vue'
+  import SavedFilterElement from 'vue/bmt_filter/saved_filter.vue'
+
+  export default {
+    name: 'FilterContainer',
+    data() {
+      return {
+        filters: [],
+        additionalDataAttributes: []
+      }
+    },
+    props: {
+      container: Object,
+      savedFilters: Array,
+      bmtApiBaseUrl: String,
+      canManageFilters: Boolean
+    },
+    created() {
+      this.fetchAdditionalDataAttributes();
+    },
+    components: { FilterElement, SavedFilterElement },
+    computed: {
+      searchJSON() {
+        let mergedFilters = this.filters.map(f => f.data).filter(f => f.type !== 'additionalDataFilter');
+        let additionalDataFilters = this.filters.map(f => f.data).filter(f => f.type === 'additionalDataFilter');
+
+        mergedFilters.push(
+          {
+            'type': 'additionalDataFilter',
+            'dataList': additionalDataFilters.map(f => {
+              return { 'attribute': f.attribute, 'value': f.value }
+            })
+          }
+        );
+
+        return {
+          'filters': mergedFilters,
+          'resultAttributeNames': ['Cid']
+        }
+      }
+    },
+    watch: {
+      filters() {
+        $('.open-save-bmt-modal').toggleClass('hidden', !this.filters.length)
+        $('.bmt-filters-button').toggleClass('active-filters', !!this.filters.length)
+      }
+    },
+    methods: {
+      addFilter() {
+        const id = this.filters.length ? this.filters[this.filters.length - 1].id + 1 : 1
+        this.filters.push({ id: id, data: { type: "fullSequenceFilter" } });
+      },
+      updateFilter(filter) {
+        this.filters.find((f) => f.id === filter.id).data = filter.data;
+        this.$emit('filters:update', this.searchJSON.filters);
+      },
+      clearFilters() {
+        this.filters = [];
+        this.$emit('filters:clear');
+      },
+      fetchCIDs() {
+        $.ajax({
+          type: 'POST',
+          url: this.bmtApiBaseUrl + '/macromolecule/search',
+          data: JSON.stringify(this.searchJSON),
+          contentType: 'application/json; charset=utf-8',
+          dataType: 'json',
+          success: (data) => {
+            this.$emit('cids:update', data.map(i => i.Cid))
+          },
+          error: ()=> {
+            this.$emit('cids:update', [])
+            this.$emit('cids:error', this.i18n.t('repositories.show.error_searching'));
+          }
+        });
+      },
+      closeSavedFilters() {
+        $('.saved-filters-container').removeClass('open');
+        return true;
+      },
+      toggleSavedFilters() {
+        $('.saved-filters-container').toggleClass('open');
+      },
+      fetchAdditionalDataAttributes() {
+        $.get(this.bmtApiBaseUrl + '/admin/macromolecules/attributes', (data) => {
+          this.additionalDataAttributes = data
+        });
+      },
+      loadFilters(filters) {
+        this.clearFilters();
+
+        let id = 1;
+
+        filters.forEach(filter => {
+          // extract additional filters
+          if(filter.type === 'additionalDataFilter') {
+            filter.dataList.forEach(additionalDataFilter => {
+              this.filters.push(
+                {
+                  'id': id++,
+                  'data': {
+                    'type': 'additionalDataFilter',
+                    'attribute': additionalDataFilter.attribute,
+                    'value': additionalDataFilter.value
+                  }
+                }
+              )
+            });
+          } else {
+            this.filters.push(
+              {
+                'id': id++,
+                'data': filter
+              }
+            );
+          }
+        });
+      }
+    }
+  }
+ </script>

app/javascript/vue/bmt_filter/filter.vue

@@ -0,0 +1,90 @@
+<template>
+  <div class="filter-container">
+    <b class='filter-title'>Filter</b>  
+    <div class="filter-element">
+      <div class="form-group filter-action">
+      
+        <div class="sci-input-container">
+          <DropdownSelector
+            :options="prepareTypesOptions()"
+            :selectorId="`bmtFilter${this.filter.id}`"
+            @dropdown:changed="updateFilter"
+          />
+        </div>
+        <component
+          :is="type"
+          @filter:updateData="updateFilter"
+          :additionalDataAttributes="additionalDataAttributes"
+          :currentData="filter.data" />
+      </div>
+      <div class="filter-remove">
+        <button class="btn btn-light icon-btn" @click="$emit('filter:delete')">
+          <i class="fas fa-times-circle"></i>
+        </button>
+      </div>
+      <hr>
+    </div>
+</div>
+</template>
+
+<script>
+  import additionalDataFilter from 'vue/bmt_filter/filters/additionalDataFilter.vue'
+  import entityTypeFilter from 'vue/bmt_filter/filters/entityTypeFilter.vue'
+  import monomerTypeFilter from 'vue/bmt_filter/filters/monomerTypeFilter.vue'
+  import subsequenceFilter from 'vue/bmt_filter/filters/subsequenceFilter.vue'
+  import variantSequenceFilter from 'vue/bmt_filter/filters/variantSequenceFilter.vue'
+  import fullSequenceFilter from 'vue/bmt_filter/filters/fullSequenceFilter.vue'
+  import monomerSubstructureSearchFilter from 'vue/bmt_filter/filters/monomerSubstructureSearchFilter.vue'
+  import DropdownSelector from 'vue/shared/dropdown_selector.vue'
+
+  export default {
+    props: {
+      filter: Object,
+      additionalDataAttributes: Array
+    },
+    data() {
+      return {
+        type: this.filter.data.type,
+        types: [
+          'additionalDataFilter',
+          'entityTypeFilter',
+          'monomerTypeFilter',
+          'subsequenceFilter',
+          'variantSequenceFilter',
+          'fullSequenceFilter',
+          'monomerSubstructureSearchFilter'
+        ],
+        additionaDataAttributes: []
+      }
+    },
+    components: {
+      additionalDataFilter,
+      entityTypeFilter,
+      monomerTypeFilter,
+      subsequenceFilter,
+      variantSequenceFilter,
+      fullSequenceFilter,
+      monomerSubstructureSearchFilter,
+      DropdownSelector
+    },
+    methods: {
+      prepareTypesOptions() {
+        return this.types.map(option => {
+          return {label: this.i18n.t(`repositories.show.bmt_search.filters.types.${option}.name`), value: option}
+        })
+      },
+      updateFilter(value) {
+        this.type = value;
+        this.$emit(
+          'filter:update',
+          {
+            id: this.filter.id,
+            data: {
+              type: value
+            }
+          }
+        );
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/additionalDataFilter.vue

@@ -0,0 +1,39 @@
+<template>
+  <div class="filter-form">
+    <div class="sci-input-container">
+      <select @change="updateFilterData" v-model="attribute" class="sci-input-field">
+        <option
+          v-for="attribute in additionalDataAttributes"
+          :key="attribute.name" :value="attribute.name">
+            {{ attribute.name }}
+        </option>
+      </select>
+    </div>
+    <div class="sci-input-container">
+      <input
+        @input="updateFilterData"
+        class="sci-input-field"
+        type="text"
+        name="value"
+        v-model="value"
+      />
+    </div>
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'additionalDataFilter',
+    mixins: [FilterMixin],
+    props: {
+      additionalDataAttributes: Array
+    },
+    data() {
+      return {
+        attribute: null,
+        value: null
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/entityTypeFilter.vue

@@ -0,0 +1,25 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="entityType"
+      v-model="entityType"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.entityTypeFilter.placeholder')"
+    />
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'entityTypeFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        entityType: ""
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/fullSequenceFilter.vue

@@ -0,0 +1,42 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="sequence"
+      v-model="sequence"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.fullSequenceFilter.placeholder')"
+    />
+    <div>
+      <label class="field-suboption">
+        <div class="sci-checkbox-container">
+          <input
+            @change="updateFilterData"
+            class="sci-checkbox"
+            type="checkbox"
+            v-model="derivativesIncluded"
+          />
+          <label class="sci-checkbox-label"></label>
+        </div>
+        <span class="checkbox-label">
+          {{ i18n.t('repositories.show.bmt_search.filters.types.fullSequenceFilter.derivatives_included') }}
+        </span>
+      </label>
+    </div>
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'fullsequenceFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        sequence: "",
+        derivativesIncluded: false
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/monomerSubstructureSearchFilter.vue

@@ -0,0 +1,25 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="structure"
+      v-model="structure"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.monomerSubstructureSearchFilter.placeholder')"
+    />
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'monomerSubstructureSearchFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        structure: ""
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/monomerTypeFilter.vue

@@ -0,0 +1,25 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="monomerType"
+      v-model="monomerType"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.monomerTypeFilter.placeholder')"
+    />
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'monomerTypeFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        monomerType: ""
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/subsequenceFilter.vue

@@ -0,0 +1,42 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="sequence"
+      v-model="sequence"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.subsequenceFilter.placeholder')"
+    />
+    <div>
+      <label class="field-suboption">
+        <div class="sci-checkbox-container">
+          <input
+            @change="updateFilterData"
+            class="sci-checkbox"
+            type="checkbox"
+            v-model="derivativesIncluded"
+          />
+          <label class="sci-checkbox-label"></label>
+        </div>
+        <span class="checkbox-label">
+          {{ i18n.t('repositories.show.bmt_search.filters.types.subsequenceFilter.derivatives_included') }}
+        </span>
+      </label>
+    </div>
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'subsequenceFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        sequence: "",
+        derivativesIncluded: false
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/filters/variantSequenceFilter.vue

@@ -0,0 +1,53 @@
+<template>
+  <div class="sci-input-container">
+    <input
+      @input="updateFilterData"
+      class="sci-input-field"
+      type="text"
+      name="sequence"
+      v-model="sequence"
+      :placeholder="i18n.t('repositories.show.bmt_search.filters.types.variantSequenceFilter.placeholder')"
+    />
+    <div>
+      <label class="field-suboption">
+        <div class="sci-input-container">
+            <label for="distance">{{ i18n.t('repositories.show.bmt_search.filters.types.variantSequenceFilter.distance') }}</label>
+            <input class="sci-input-field" @input="updateFilterData" type="text" v-model="distance" />
+        </div>
+        <label class="distance-attribute">
+          <input
+            @change="updateFilterData"
+            type="radio"
+            v-model="distanceType"
+            value="EXACT"
+          />
+          <span>{{ i18n.t('repositories.show.bmt_search.filters.types.variantSequenceFilter.exact') }}</span>
+        </label>
+        <label class="distance-attribute">
+          <input
+            @change="updateFilterData"
+            type="radio"
+            v-model="distanceType"
+            value="MAX"
+          />
+          <span>{{ i18n.t('repositories.show.bmt_search.filters.types.variantSequenceFilter.maximum') }}</span>
+        </label>
+      </label>
+    </div>
+  </div>
+</template>
+
+<script>
+  import FilterMixin from 'vue/bmt_filter/mixins/filter.js'
+  export default {
+    name: 'variantSequenceFilter',
+    mixins: [FilterMixin],
+    data() {
+      return {
+        sequence: "",
+        distance: null,
+        distanceType: "EXACT"
+      }
+    }
+  }
+</script>

app/javascript/vue/bmt_filter/mixins/filter.js

@@ -0,0 +1,19 @@
+export default {
+  props: {
+    currentData: Object
+  },
+  data() {
+    return {
+      type: this.$options.name
+    }
+  },
+  created() {
+    // load existing filter data
+    Object.keys(this.currentData).forEach((key) => { this[key] = this.currentData[key] });
+  },
+  methods: {
+    updateFilterData() {
+      this.$emit('filter:updateData', this.$data);
+    }
+  }
+}

app/javascript/vue/bmt_filter/saved_filter.vue

@@ -0,0 +1,34 @@
+<template>
+  <div class="saved-filters-element">
+    <span @click="loadFilters">{{ savedFilter.attributes.name }}</span>
+    <button v-if="canManageFilters" class="btn btn-light icon-btn" @click="deleteFilter">
+      <i class="fas fa-trash"></i>
+    </button>
+  </div>
+</template>
+
+<script>
+  export default {
+    name: 'SavedFilterElement',
+    props: {
+      savedFilter: Object,
+      canManageFilters: Boolean
+    },
+    methods: {
+      loadFilters() {
+        this.$emit('savedFilter:load', this.savedFilter.attributes.filters)
+      },
+      deleteFilter() {
+        let filter = this
+        $.ajax({
+          url: this.savedFilter.attributes.delete_url,
+          type: 'DELETE',
+          dataType: 'json',
+          success: function() {
+            filter.$emit('savedFilter:delete')
+          }
+        });
+      }
+    }
+  }
+</script>

app/javascript/vue/shared/dropdown_selector.vue

@@ -0,0 +1,59 @@
+<template>
+  <div class="dropdown-selector">
+    <select :id="this.selectorId">
+      <option
+        v-for="option in this.options"
+        :key="option.label" :value="option.value">
+          {{ option.label }}
+      </option>
+    </select>
+  </div>
+</template>
+
+<script>
+  export default {
+    name: 'DropdownSelector',
+    props: {
+      options: Array,
+      selectorId: String,
+      noEmptyOption: {
+        type: Boolean,
+        default: true
+      },
+      singleSelect: {
+        type: Boolean,
+        default: true
+      },
+      closeOnSelect: {
+        type: Boolean,
+        default: true
+      },
+      selectAppearance: {
+        type: String,
+        default: 'simple'
+      },
+      onChange: Function
+
+    },
+    mounted: function() {
+      dropdownSelector.init(`#${this.selectorId}`, {
+        noEmptyOption: this.noEmptyOption,
+        singleSelect: this.singleSelect,
+        closeOnSelect: this.closeOnSelect,
+        selectAppearance: this.selectAppearance,
+        onChange: () => {
+          if (this.onChange) this.onChange();
+          this.selectChanged(dropdownSelector.getValues(`#${this.selectorId}`))
+        }
+      });
+    },
+    methods: {
+      selectChanged(value) {
+        this.$emit(
+          'dropdown:changed',
+          value
+        );
+      }
+    }
+  }
+</script>

app/models/bmt_filter.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+class BmtFilter < ApplicationRecord
+
+  attr_accessor :delete_url
+
+  belongs_to :created_by,
+             foreign_key: :created_by_id,
+             class_name: 'User',
+             optional: true
+
+  validates :name, :filters, presence: true
+end

app/models/bmt_repository.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+class BmtRepository < LinkedRepository
+  before_create :enforce_singleton
+
+  def default_table_state
+    state = Constants::REPOSITORY_TABLE_DEFAULT_STATE.deep_dup
+    state['order'] = [[3, 'asc']]
+    state
+  end
+
+  def default_sortable_columns
+    [
+      'assigned',
+      'repository_rows.external_id',
+      'repository_rows.id',
+      'repository_rows.name',
+      'repository_rows.created_at'
+    ]
+  end
+
+  def default_search_fileds
+    super - ['users.full_name']
+  end
+
+  private
+
+  def enforce_singleton
+    raise ActiveRecord::RecordNotSaved, I18n.t('repositories.bmt_singleton_error') if self.class.any?
+  end
+end

app/models/linked_repository.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+class LinkedRepository < Repository
+  def default_table_state
+    state = Constants::REPOSITORY_TABLE_DEFAULT_STATE.deep_dup
+    state['order'] = [[3, 'asc']]
+    state['ColReorder'] << state['ColReorder'].length
+    state['columns'].insert(1, Constants::REPOSITORY_TABLE_STATE_CUSTOM_COLUMN_TEMPLATE)
+    state
+  end
+
+  def default_sortable_columns
+    [
+      'assigned',
+      'repository_rows.external_id',
+      'repository_rows.id',
+      'repository_rows.name',
+      'repository_rows.created_at',
+      'users.full_name',
+      'repository_rows.archived_on',
+      'archived_bies_repository_rows.full_name'
+    ]
+  end
+
+  def default_search_fileds
+    super << 'repository_rows.external_id'
+  end
+end

app/models/repository.rb

@@ -97,8 +97,24 @@ class Repository < RepositoryBase
     end
   end
 
-  def default_columns_count
-    Constants::REPOSITORY_TABLE_DEFAULT_STATE['columns'].length
+  def default_table_state
+    Constants::REPOSITORY_TABLE_DEFAULT_STATE
+  end
+
+  def default_sortable_columns
+    [
+      'assigned',
+      'repository_rows.id',
+      'repository_rows.name',
+      'repository_rows.created_at',
+      'users.full_name',
+      'repository_rows.archived_on',
+      'archived_bies_repository_rows.full_name'
+    ]
+  end
+
+  def default_search_fileds
+    ['repository_rows.name', RepositoryRow::PREFIXED_ID_SQL, 'users.full_name']
   end
 
   def i_shared?(team)

app/models/repository_base.rb

@@ -1,6 +1,9 @@
 # frozen_string_literal: true
 
 class RepositoryBase < ApplicationRecord
+  require 'sti_preload'
+
+  include StiPreload
   include Discard::Model
 
   self.table_name = 'repositories'
@@ -32,6 +35,22 @@ class RepositoryBase < ApplicationRecord
     cell_includes
   end
 
+  def default_table_state
+    raise NotImplementedError
+  end
+
+  def default_table_columns
+    default_table_state['columns'].to_json
+  end
+
+  def default_columns_count
+    default_table_state['columns'].length
+  end
+
+  def default_table_order_as_js_array
+    default_table_state['order'].to_json
+  end
+
   def destroy_discarded(discarded_by_id = nil)
     self.discarded_by_id = discarded_by_id
     destroy

app/models/repository_column.rb

@@ -55,7 +55,7 @@ class RepositoryColumn < ApplicationRecord
     # Calculate old_column_index - this can only be done before
     # record is deleted when we still have its index
     old_column_index = (
-      Constants::REPOSITORY_TABLE_DEFAULT_STATE['columns'].length +
+      repository.default_columns_count +
       repository.repository_columns
                 .order(id: :asc)
                 .pluck(:id)

app/models/repository_snapshot.rb

@@ -45,8 +45,8 @@ class RepositorySnapshot < RepositoryBase
     repository_snapshot.reload
   end
 
-  def default_columns_count
-    Constants::REPOSITORY_SNAPSHOT_TABLE_DEFAULT_STATE['columns'].length
+  def default_table_state
+    Constants::REPOSITORY_SNAPSHOT_TABLE_DEFAULT_STATE
   end
 
   def assigned_rows(my_module)

app/permissions/repository.rb

@@ -32,6 +32,8 @@ Canaid::Permissions.register_for(Repository) do
 
   # repository: archive, restore
   can :archive_repository do |user, repository|
+    next false if repository.is_a?(BmtRepository)
+
     !repository.shared_with?(user.current_team) && user.is_admin_of_team?(repository.team)
   end
 
@@ -52,6 +54,8 @@ Canaid::Permissions.register_for(Repository) do
 
   # repository: create/import record
   can :create_repository_rows do |user, repository|
+    next false if repository.is_a?(BmtRepository)
+
     if repository.shared_with?(user.current_team)
       repository.shared_with_write?(user.current_team) && user.is_normal_user_or_admin_of_team?(user.current_team)
     elsif user.teams.include?(repository.team)

app/permissions/team.rb

@@ -36,6 +36,10 @@ Canaid::Permissions.register_for(Team) do
     user.is_normal_user_or_admin_of_team?(team)
   end
 
+  can :manage_bmt_filters do |user, team|
+    user.is_normal_user_or_admin_of_team?(team)
+  end
+
   # repository: create, copy
   can :create_repositories do |user, team|
     within_limits = Repository.within_global_limits?

app/serializers/bmt_filter_serializer.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+class BmtFilterSerializer < ActiveModel::Serializer
+  include Rails.application.routes.url_helpers
+
+  attributes :name, :filters, :delete_url
+
+  def delete_url
+    bmt_filter_path(object.id)
+  end
+end

app/services/biomolecule_toolkit_client.rb

@@ -2,55 +2,67 @@
 
 class BiomoleculeToolkitClient
   MACROMOLECULES_PATH = '/api/macromolecules'
+  MACROMOLECULES_ATTRIBUTES_PATH = '/api/admin/attributes/MACROMOLECULE'
 
   class BiomoleculeToolkitClientException < StandardError; end
 
   def initialize
-    @host = Rails.configuration.x.biomolecule_toolkit_host
-    @http = Net::HTTP.new(
-      Rails.configuration.x.biomolecule_toolkit_host,
-      Rails.application.config.x.biomolecule_toolkit_port
-    )
+    @uri = URI.parse(Rails.application.config.x.biomolecule_toolkit_base_url)
+    @http = Net::HTTP.new(@uri.host, @uri.port)
+    @http.use_ssl = (@uri.scheme == 'https')
   end
 
   def healthy?
-    request = Net::HTTP::Get.new('/api/health')
+    request = Net::HTTP::Get.new(build_request_path('/api/health'))
     process_request(request)&.dig('status') == 'UP'
   end
 
+  def list_attributes
+    request = Net::HTTP::Get.new(build_request_path(MACROMOLECULES_ATTRIBUTES_PATH))
+    process_request(request)
+  end
+
   def list
-    request = Net::HTTP::Get.new(MACROMOLECULES_PATH)
+    request = Net::HTTP::Get.new(build_request_path(MACROMOLECULES_PATH))
     process_request(request)
   end
 
   def create(params:)
-    request = Net::HTTP::Post.new(MACROMOLECULES_PATH, 'Content-Type': 'application/json')
+    request = Net::HTTP::Post.new(build_request_path(MACROMOLECULES_PATH))
     request.body = params
     process_request(request)
   end
 
   def get(cid:)
-    request = Net::HTTP::Get.new("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}")
+    request = Net::HTTP::Get.new(build_request_path("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}"))
     process_request(request)
   end
 
   def update(cid:, params:)
-    request = Net::HTTP::Put.new("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}", 'Content-Type': 'application/json')
+    request = Net::HTTP::Put.new(build_request_path("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}"))
     request.body = params
     process_request(request)
   end
 
   def delete
-    request = Net::HTTP::Delete.new("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}")
+    request = Net::HTTP::Delete.new(build_request_path("#{MACROMOLECULES_PATH}/#{CGI.escape(cid)}"))
     process_request(request)
   end
 
   private
 
+  def build_request_path(sub_path)
+    File.join(@uri.path, sub_path)
+  end
+
   def process_request(request)
+    if Rails.application.config.x.biomolecule_toolkit_api_key
+      request['x-api-key'] = Rails.application.config.x.biomolecule_toolkit_api_key
+    end
+    request['Content-Type'] = 'application/json'
     response = @http.request(request)
 
-    case response.class
+    case response
     when Net::HTTPOK
       JSON.parse(response.body)
     when Net::HTTPNoContent

app/services/repository_datatable_service.rb

@@ -75,16 +75,14 @@ class RepositoryDatatableService
         repository_rows.count
       end
 
-    if search_value.present?
-      matched_by_user = repository_rows.joins(:created_by).where_attributes_like('users.full_name', search_value)
+    repository_rows = repository_rows.where(external_id: @params[:external_ids]) if @params[:external_ids]
 
-      repository_row_matches =  repository_rows
-                                .where_attributes_like(
-                                  ['repository_rows.name', RepositoryRow::PREFIXED_ID_SQL],
-                                  search_value
-                                )
+    if search_value.present?
+      if @repository.default_search_fileds.include?('users.full_name')
+        repository_rows = repository_rows.joins(:created_by)
+      end
+      repository_row_matches = repository_rows.where_attributes_like(@repository.default_search_fileds, search_value)
       results = repository_rows.where(id: repository_row_matches)
-      results = results.or(repository_rows.where(id: matched_by_user))
 
       data_types = @repository.repository_columns.pluck(:data_type).uniq
 
@@ -114,15 +112,7 @@ class RepositoryDatatableService
   end
 
   def build_sortable_columns
-    array = [
-      'assigned',
-      'repository_rows.id',
-      'repository_rows.name',
-      'repository_rows.created_at',
-      'users.full_name',
-      'repository_rows.archived_on',
-      'archived_bies_repository_rows.full_name',
-    ]
+    array = @repository.default_sortable_columns
     @repository.repository_columns.count.times do
       array << 'repository_cell.value'
     end

app/services/repository_table_state_column_update_service.rb

@@ -9,7 +9,7 @@ class RepositoryTableStateColumnUpdateService
   def update_states_with_new_column(repository)
     raise ArgumentError, 'repository is empty' if repository.blank?
 
-    columns_num = Constants::REPOSITORY_TABLE_DEFAULT_STATE['columns'].length + repository.repository_columns.count
+    columns_num = repository.default_columns_count + repository.repository_columns.count
     RepositoryTableState.where(
       repository: repository
     ).find_each do |table_state|
@@ -49,7 +49,7 @@ class RepositoryTableStateColumnUpdateService
         if state.dig('order', 0, 0).to_i == old_column_index
           # Fallback to default order if user had table ordered by
           # the deleted column
-          state['order'] = Constants::REPOSITORY_TABLE_DEFAULT_STATE['order']
+          state['order'] = repository.default_table_state['order']
         elsif state.dig('order', 0, 0).to_i > old_column_index
           state['order'][0][0] -= 1
         end

app/services/repository_table_state_service.rb

@@ -26,7 +26,7 @@ class RepositoryTableStateService
 
   def update_state(state)
     saved_state = load_state
-    state['order'] = Constants::REPOSITORY_TABLE_DEFAULT_STATE['order'] if state.dig('order', 0, 0).to_i < 1
+    state['order'] = @repository.default_table_state['order'] if state.dig('order', 0, 0).to_i < 1
 
     return if saved_state.state.except('time') == state.except('time')
 
@@ -47,10 +47,10 @@ class RepositoryTableStateService
   private
 
   def generate_default_state
-    default_columns_num = Constants::REPOSITORY_TABLE_DEFAULT_STATE['columns'].length
+    default_columns_num = @repository.default_columns_count
 
     # This state should be strings-only
-    state = Constants::REPOSITORY_TABLE_DEFAULT_STATE.deep_dup
+    state = @repository.default_table_state.deep_dup
     @repository.repository_columns.each_with_index do |_, index|
       real_index = default_columns_num + index
       state['columns'][real_index] = Constants::REPOSITORY_TABLE_STATE_CUSTOM_COLUMN_TEMPLATE

app/views/my_modules/repositories/_full_view_snapshot_table.html.erb

@@ -5,8 +5,8 @@
        data-repository-name="<%= @repository_snapshot.name %>"
        data-repository-snapshot-created="<%= l(@repository_snapshot.created_at, format: :full) %>"
        data-assigned-items-count="<%= @repository_snapshot.repository_rows.count %>"
-       data-default-order="<%= default_snapshot_table_order_as_js_array %>"
-       data-default-table-columns="<%= default_snapshot_table_columns %>"
+       data-default-order="<%= @repository_snapshot.default_table_order_as_js_array %>"
+       data-default-table-columns="<%= @repository_snapshot.default_table_columns %>"
        data-load-state-url="<%= repository_load_table_state_path(@repository_snapshot) %>"
        data-export-url="<%= export_repository_snapshot_my_module_repository_snapshot_path(@my_module, @repository_snapshot) %>"
        data-versions-sidebar-url="<%= full_view_sidebar_my_module_repository_snapshots_path(@my_module, @repository_snapshot.parent_id) %>"

app/views/my_modules/repositories/_full_view_table.html.erb

@@ -2,8 +2,8 @@
        data-id="<%= @repository.id %>"
        data-type="live"
        data-source="<%= index_dt_my_module_repository_path(@my_module, @repository) %>"
-       data-default-order="<%= default_table_order_as_js_array %>"
-       data-default-table-columns="<%= default_table_columns %>"
+       data-default-order="<%= @repository.default_table_order_as_js_array %>"
+       data-default-table-columns="<%= @repository.default_table_columns %>"
        data-repository-name="<%= @repository.name %>"
        data-assigned-items-count="<%= @my_module.repository_rows_count(@repository) %>"
        data-load-state-url="<%= repository_load_table_state_path(@repository) %>"

app/views/repositories/_repository_table.html.erb

@@ -1,4 +1,5 @@
 <div class="repository-table">
+  <div class="repository-table-error"></div>
   <table id="repository-table-<%= repository.id %>" class="table"
     data-current-uri="<%= request.original_url %>"
     data-repository-id="<%= repository.id %>"
@@ -20,8 +21,8 @@
     data-columns-delete-text="<%= I18n.t('repositories.columns_delete') %>"
     data-available-columns="<%= repository_available_columns_path(repository) %>"
     data-columns-changed="<%= I18n.t('repositories.columns_changed') %>"
-    data-default-order="<%= default_table_order_as_js_array %>"
-    data-default-table-columns="<%= default_table_columns %>"
+    data-default-order="<%= @repository.default_table_order_as_js_array %>"
+    data-default-table-columns="<%= @repository.default_table_columns %>"
     data-editable="<%= can_manage_repository_rows?(repository) %>"
     data-snapshot-provisioning="<%= @snapshot_provisioning %>"
     data-status-url="<%= repository_status_path(@repository) %>">
@@ -32,12 +33,17 @@
             <span class="sci-checkbox-label"></span>
         </th>
         <th id="assigned" data-unmanageable="true"><%= t("repositories.table.assigned") %></th>
+        <% if @repository.is_a?(LinkedRepository) %>
+          <th id="row-external-id"><%= t('repositories.table.external_id') %></th>
+        <% end %>
         <th id="row-id"><%= t("repositories.table.id") %></th>
         <th id="row-name"><%= t("repositories.table.row_name") %></th>
         <th id="added-on" ><%= t("repositories.table.added_on") %></th>
-        <th id="added-by" ><%= t("repositories.table.added_by") %></th>
-        <th id="archived-on"><%= t("repositories.table.archived_on") %></th>
-        <th id="archived-by"><%= t("repositories.table.archived_by") %></th>
+        <% unless @repository.is_a?(BmtRepository) %>
+          <th id="added-by" ><%= t("repositories.table.added_by") %></th>
+          <th id="archived-on"><%= t("repositories.table.archived_on") %></th>
+          <th id="archived-by"><%= t("repositories.table.archived_by") %></th>
+        <% end %>
         <% repository.repository_columns.order(:id).each do |column| %>
           <th
             class="repository-column"

app/views/repositories/_save_bmt_filter_modal.html.erb

@@ -0,0 +1,26 @@
+<div class="modal fade" id="modalSaveBmtFilter" tabindex="-1" role="dialog" aria-labelledby="modal-import-records-label">
+  <div class="modal-dialog" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4 class="modal-title">
+          <%= t('repositories.show.bmt_search.save_filters') %>
+        </h4>
+      </div>
+      <%= form_with model: BmtFilter.new, method: :post, :html => { :id => "saveBmtFilterForm" } do |f| %>
+        <div class="modal-body">
+          <%= f.hidden_field :filters, class: "sci-input-field" %>
+          <div class="sci-input-container">
+            <%= f.label :name %>
+            <%= f.text_field :name, class: "sci-input-field" %>
+          </div>
+        </div>
+
+        <div class="modal-footer">
+          <button type="button" class="btn btn-default" data-dismiss="modal"><%= t('general.cancel')%></button>
+          <%= f.submit t('general.save'), class: "btn btn-success" %>
+        </div>
+      <% end %>
+    </div>
+  </div>
+</div>

app/views/repositories/_toolbar_buttons.html.erb

@@ -85,5 +85,44 @@
       </table>
     <% end %>
   </div>
-
-</div>
+  <% if @repository.is_a?(BmtRepository) %>
+    <div class="dropdown" id="bmtFiltersDropdownButton">
+        <button id="bmtFiltersDropdown"
+                class="btn btn-secondary bmt-filters-button"
+                type="button"
+                data-toggle="dropdown"
+                aria-haspopup="true"
+      >
+        <span class="fas fa-microscope"></span>
+        <%= t('repositories.show.bmt_search.bmt_filter') %>
+      </button>
+      <div
+        class="dropdown-menu bmt-filters-container"
+        id="bmtFilterContainer"
+        data-datatable-id="#repository-table-<%= @repository.id %>"
+        data-saved-filters-url="<%= bmt_filters_url %>"
+        data-can-manage-filters="<%= can_manage_bmt_filters?(current_team) %>"
+        data-bmt-api-base-url="<%= bmt_request_url(path: 'api') %>"
+      >
+        <filter-container
+          @filters:update="updateFilters"
+          @filters:clear="clearFilters"
+          @cids:update="updateExternalIds"
+          @cids:error="handleSearchError"
+          :can-manage-filters="canManageFilters"
+          :bmt-api-base-url="bmtApiBaseUrl"
+          :saved-filters.sync="savedFilters"
+          :filters.sync="filters" />
+      </div>
+    </div>
+    <% if can_manage_bmt_filters?(current_team) %>
+      <button
+        class="btn btn-light open-save-bmt-modal hidden"
+        type="button"
+        aria-haspopup="true"
+      >
+        <span class="fas fa-save"></span>
+        <%= t('repositories.show.bmt_search.save_filters') %>
+      </button>
+    <% end %>
+  <% end %>

app/views/repositories/show.html.erb

@@ -93,7 +93,7 @@
                   </a>
                 </li>
               <% end %>
-              <% if can_create_repositories?(current_team) && !@repository.shared_with?(current_team) %>
+              <% if !@repository.is_a?(BmtRepository) && can_create_repositories?(current_team) && !@repository.shared_with?(current_team) %>
                 <li data-view-mode="active">
                   <%= link_to t('repositories.index.options_dropdown.copy'),
                               team_repository_copy_modal_path(current_team, repository_id: @repository),
@@ -129,15 +129,17 @@
             </ul>
           <% end %>
         </div>
-          <%= render layout: "shared/view_switch", locals: {disabled: @repository.archived?} do %>
-            <li class="view-switch-archived" data-view-mode="active">
-              <i class="fas fa-archive button-icon"></i>
-              <%= t('repositories.show.show_archived_items') %>
-            </li>
-            <li class="view-switch-active" data-view-mode="archived">
-              <i class="fas fa-rocket button-icon"></i>
-              <%= t('repositories.show.show_active_items') %>
-            </li>
+          <% unless @repository.is_a?(BmtRepository) %>
+            <%= render layout: "shared/view_switch", locals: {disabled: @repository.archived?} do %>
+              <li class="view-switch-archived" data-view-mode="active">
+                <i class="fas fa-archive button-icon"></i>
+                <%= t('repositories.show.show_archived_items') %>
+              </li>
+              <li class="view-switch-active" data-view-mode="archived">
+                <i class="fas fa-rocket button-icon"></i>
+                <%= t('repositories.show.show_active_items') %>
+              </li>
+            <% end %>
           <% end %>
       </div>
       <div class="toolbar-delimiter"></div>
@@ -165,7 +167,11 @@
            locals: { repository: @repository } %>
 
 <%= render partial: 'repository_columns/manage_column_modal', locals: { my_module_page: false } %>
+<%= render partial: 'save_bmt_filter_modal' %>
 
+<% if @repository.is_a?(BmtRepository) %>
+  <%= javascript_pack_tag 'vue/bmt_filter' %>
+<% end %>
 <%= javascript_include_tag 'repositories/edit' %>
 <%= javascript_include_tag 'repositories/repository_datatable' %>
 <%= javascript_include_tag "repositories/show" %>
@@ -174,6 +180,8 @@
 <%= javascript_pack_tag 'pdfjs/pdf_js' %>
 <%= stylesheet_pack_tag 'pdfjs/pdf_js_styles' %>
 
+
+
 <script type="text/javascript" charset="utf-8">
   var formatJS = "<%= datetime_picker_format_date_only %>"
 </script>

config/initializers/biomolecule_toolkit_client.rb

@@ -1,4 +1,4 @@
 # frozen_string_literal: true
 
-Rails.application.config.x.biomolecule_toolkit_host = ENV['BIOMOLECULE_TOOLKIT_HOST']
-Rails.application.config.x.biomolecule_toolkit_port = ENV['BIOMOLECULE_TOOLKIT_PORT'] || 80
+Rails.application.config.x.biomolecule_toolkit_base_url = ENV['BIOMOLECULE_TOOLKIT_BASE_URL']
+Rails.application.config.x.biomolecule_toolkit_api_key = ENV['BIOMOLECULE_TOOLKIT_API_KEY']

config/initializers/extends.rb

@@ -392,6 +392,8 @@ class Extends
     change_user_role_on_experiment
     change_user_role_on_my_module
   )
+
+  STI_PRELOAD_CLASSES = %w(LinkedRepository BmtRepository)
 end
 
 # rubocop:enable Style/MutableConstant

config/locales/en.yml

@@ -1304,6 +1304,7 @@ en:
       i_shared: "Shared inventory (owned by your Team)"
       shared_edit: "Shared inventory (owned by %{team_name}). You can edit."
       shared_read: "Shared inventory (owned by %{team_name}). You can view."
+    bmt_singleton_error: "Only one BMT inventory can be present."
     index:
       head_title: "Inventories"
       title: "Inventories"
@@ -1387,9 +1388,49 @@ en:
       no_items_matched: "No items matched your search request"
       no_archived_items: "No archived items here"
       no_archived_items_matched: "No archived items matched your search request"
+      error_searching: "Error searching, please try again"
 
+      bmt_search:
+        bmt_filter: "Biomolecule filter"
+        save_filters: "Save filters"
+        title: "Filters"
+        clear_all: "Clear all"
+        add_filter: "Add filter"
+        apply: "Apply"
+        filter: "Filter"
+        no_filters: "No active filters."
+        filters:
+          types:
+            additionalDataFilter:
+              name: "Additional data"
+            entityTypeFilter:
+              name: "Entity type"
+              placeholder: "Enter entity type"
+            monomerTypeFilter:
+              name: "Monomer type"
+              placeholder: "Enter monomer type"
+            subsequenceFilter:
+              name: "Subsequence"
+              placeholder: "Enter subsequence"
+              derivatives_included: "Derivatives included"
+            variantSequenceFilter:
+              name: "Variant sequence"
+              placeholder: "Enter variant sequence"
+              derivatives_included: "Derivatives included"
+              distance: "Distance"
+              distance_type: "Distance type"
+              exact: "Exact"
+              maximum: "Maximum"
+            fullSequenceFilter:
+              name: "Full sequence"
+              placeholder: "Enter full sequence"
+              derivatives_included: "Derivatives included"
+            monomerSubstructureSearchFilter:
+              name: "Monomer substructure"
+              placeholder: "Enter substructure"
     table:
       id: 'ID'
+      external_id: 'External ID'
       assigned: "Assigned"
       assigned_search: 'Search...'
       assigned_tooltip: "%{tasks} tasks in 
%{experiments} experiments,
%{projects} projects"
@@ -2791,7 +2832,7 @@ en:
 
   bio_eddie:
     new_molecule: "New Molecule"
-    new_button: "Create Biomolecule"
+    new_button: "Biomolecule"
     molecule_name_placeholder: "Click here to enter Molecule name"
     no_molecules_found: "No Molecules Found"
     save_and_register: "Save & Register to Biomolecule Toolkit"

config/routes.rb

@@ -800,11 +800,14 @@ Rails.application.routes.draw do
     end
   end
 
+  resources :bmt_filters, only: %i(index create destroy)
+
   match '/marvin4js-license.cxl', to: 'bio_eddie_assets#license', via: :get
 
   match 'biomolecule_toolkit/*path', to: 'bio_eddie_assets#bmt_request',
                                      via: %i(get post put delete),
-                                     defaults: { format: 'json' }
+                                     defaults: { format: 'json' },
+                                     as: 'bmt_request'
 
   post 'global_activities', to: 'global_activities#index'
 

db/migrate/20210812095254_add_external_id_to_repositories.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require File.expand_path('app/helpers/database_helper')
+
+class AddExternalIdToRepositories < ActiveRecord::Migration[6.1]
+  include DatabaseHelper
+
+  def up
+    add_column :repository_rows, :external_id, :string, null: true
+    add_index :repository_rows, :external_id, unique: true, name: 'unique_index_repository_rows_on_external_id'
+    add_gin_index_without_tags(:repository_rows, :external_id)
+  end
+
+  def down
+    remove_index :repository_rows, name: 'index_repository_rows_on_external_id'
+    remove_index :repository_rows, :external_id, unique: true, name: 'unique_index_repository_rows_on_external_id'
+    remove_column :repository_rows, :external_id, :string, null: true
+  end
+end

db/migrate/20210825112050_create_bmt_filters.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+class CreateBmtFilters < ActiveRecord::Migration[6.1]
+  def change
+    create_table :bmt_filters do |t|
+      t.string :name, null: false
+      t.json :filters, null: false
+      t.references :created_by, index: true, foreign_key: { to_table: :users }
+      t.timestamps
+    end
+  end
+end

db/structure.sql

@@ -313,6 +313,39 @@ CREATE SEQUENCE public.assets_id_seq
 ALTER SEQUENCE public.assets_id_seq OWNED BY public.assets.id;
 
 
+--
+-- Name: bmt_filters; Type: TABLE; Schema: public; Owner: -
+--
+
+CREATE TABLE public.bmt_filters (
+    id bigint NOT NULL,
+    name character varying NOT NULL,
+    filters json NOT NULL,
+    created_by_id bigint,
+    created_at timestamp(6) without time zone NOT NULL,
+    updated_at timestamp(6) without time zone NOT NULL
+);
+
+
+--
+-- Name: bmt_filters_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE public.bmt_filters_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
+
+
+--
+-- Name: bmt_filters_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE public.bmt_filters_id_seq OWNED BY public.bmt_filters.id;
+
+
 --
 -- Name: checklist_items; Type: TABLE; Schema: public; Owner: -
 --
@@ -1877,7 +1910,8 @@ CREATE TABLE public.repository_rows (
     archived_on timestamp without time zone,
     restored_on timestamp without time zone,
     archived_by_id bigint,
-    restored_by_id bigint
+    restored_by_id bigint,
+    external_id character varying
 );
 
 
@@ -3155,6 +3189,13 @@ ALTER TABLE ONLY public.asset_text_data ALTER COLUMN id SET DEFAULT nextval('pub
 ALTER TABLE ONLY public.assets ALTER COLUMN id SET DEFAULT nextval('public.assets_id_seq'::regclass);
 
 
+--
+-- Name: bmt_filters id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.bmt_filters ALTER COLUMN id SET DEFAULT nextval('public.bmt_filters_id_seq'::regclass);
+
+
 --
 -- Name: checklist_items id; Type: DEFAULT; Schema: public; Owner: -
 --
@@ -3758,6 +3799,14 @@ ALTER TABLE ONLY public.assets
     ADD CONSTRAINT assets_pkey PRIMARY KEY (id);
 
 
+--
+-- Name: bmt_filters bmt_filters_pkey; Type: CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.bmt_filters
+    ADD CONSTRAINT bmt_filters_pkey PRIMARY KEY (id);
+
+
 --
 -- Name: checklist_items checklist_items_pkey; Type: CONSTRAINT; Schema: public; Owner: -
 --
@@ -4529,6 +4578,13 @@ CREATE INDEX index_assets_on_last_modified_by_id ON public.assets USING btree (l
 CREATE INDEX index_assets_on_team_id ON public.assets USING btree (team_id);
 
 
+--
+-- Name: index_bmt_filters_on_created_by_id; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_bmt_filters_on_created_by_id ON public.bmt_filters USING btree (created_by_id);
+
+
 --
 -- Name: index_checklist_items_on_checklist_id; Type: INDEX; Schema: public; Owner: -
 --
@@ -5502,6 +5558,13 @@ CREATE INDEX index_repository_number_values_on_last_modified_by_id ON public.rep
 CREATE INDEX index_repository_rows_on_archived_by_id ON public.repository_rows USING btree (archived_by_id);
 
 
+--
+-- Name: index_repository_rows_on_external_id; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE INDEX index_repository_rows_on_external_id ON public.repository_rows USING gin (public.trim_html_tags((external_id)::text) public.gin_trgm_ops);
+
+
 --
 -- Name: index_repository_rows_on_id_text; Type: INDEX; Schema: public; Owner: -
 --
@@ -6195,6 +6258,13 @@ CREATE INDEX index_wopi_actions_on_extension_and_action ON public.wopi_actions U
 CREATE INDEX index_zip_exports_on_user_id ON public.zip_exports USING btree (user_id);
 
 
+--
+-- Name: unique_index_repository_rows_on_external_id; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE UNIQUE INDEX unique_index_repository_rows_on_external_id ON public.repository_rows USING btree (external_id);
+
+
 --
 -- Name: comments fk_rails_03de2dc08c; Type: FK CONSTRAINT; Schema: public; Owner: -
 --
@@ -7339,6 +7409,14 @@ ALTER TABLE ONLY public.protocols
     ADD CONSTRAINT fk_rails_dcb4ab6aa9 FOREIGN KEY (parent_id) REFERENCES public.protocols(id);
 
 
+--
+-- Name: bmt_filters fk_rails_de5b654b84; Type: FK CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.bmt_filters
+    ADD CONSTRAINT fk_rails_de5b654b84 FOREIGN KEY (created_by_id) REFERENCES public.users(id);
+
+
 --
 -- Name: my_modules fk_rails_e21638fa54; Type: FK CONSTRAINT; Schema: public; Owner: -
 --
@@ -7700,7 +7778,10 @@ INSERT INTO "schema_migrations" (version) VALUES
 ('20210716124649'),
 ('20210720112050'),
 ('20210811103123'),
+('20210812095254'),
+('20210825112050'),
 ('20210906132120'),
 ('20211103115450');
+>>>>>>> features/bmt-search
 
 

lib/sti_preload.rb

@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+module StiPreload
+  unless Rails.application.config.eager_load
+    extend ActiveSupport::Concern
+
+    included do
+      cattr_accessor :preloaded, instance_accessor: false
+    end
+
+    class_methods do
+      def descendants
+        preload_sti unless preloaded
+        super
+      end
+
+      def preload_sti
+        Extends::STI_PRELOAD_CLASSES.each do |type|
+          logger.debug("Preloading STI type #{type}")
+          type.constantize
+        end
+
+        self.preloaded = true
+      end
+    end
+  end
+end

lib/tasks/biomolecule_toolkit.rake

@@ -0,0 +1,46 @@
+# frozen_string_literal: true
+
+namespace :biomolecule_toolkit do
+  desc 'Creates new BMT inventory and maps BMT macromolecules attributes to its columns'
+  task :init_repository, [:team_id] => :environment do |_, args|
+    raise StandardError, 'BMT repository already exists!' if BmtRepository.any?
+
+    bmt_client = BiomoleculeToolkitClient.new
+    attributes = bmt_client.list_attributes
+
+    team = Team.find(args[:team_id])
+    BmtRepository.transaction do
+      repository = BmtRepository.create!(name: 'Biomolecule registry', team: team, created_by: team.created_by)
+      attributes.each do |attribute|
+        repository.repository_columns.create!(name: attribute['name'],
+                                              data_type: 'RepositoryTextValue',
+                                              created_by: team.created_by)
+      end
+    end
+  end
+
+  desc 'Syncs BMT inventory columns with BMT macromolecules attributes'
+  task sync_repository: :environment do
+    raise StandardError, 'BMT repository does not exist!' if BmtRepository.none?
+
+    bmt_client = BiomoleculeToolkitClient.new
+    attributes = bmt_client.list_attributes
+
+    BmtRepository.transaction do
+      repository = BmtRepository.take
+      attributes.each do |attribute|
+        next if repository.repository_columns.find_by(name: attribute['name']).present?
+
+        repository.repository_columns.create!(name: attribute['name'],
+                                              data_type: 'RepositoryTextValue',
+                                              created_by: repository.created_by)
+      end
+
+      repository.repository_columns.each do |repository_column|
+        next if attributes.pluck('name').include?(repository_column.name)
+
+        repository_column.destroy!
+      end
+    end
+  end
+end

package.json

@@ -83,8 +83,8 @@
     "postcss-smart-import": "^0.7.6",
     "precss": "^2.0.0",
     "prop-types": "^15.7.2",
-    "rails-erb-loader": "^5.4.2",
     "react": "^16.8.6",
+    "rails-erb-loader": "^5.4.2",
     "react-bootstrap": "^0.31.5",
     "react-bootstrap-table": "^4.3.1",
     "react-bootstrap-timezone-picker": "^1.0.12",
@@ -113,10 +113,10 @@
     "tui-image-editor": "git://github.com/biosistemika/tui.image-editor",
     "twemoji": "^12.1.4",
     "typeface-lato": "^0.0.75",
+    "vue": "^2.6.11",
     "vue-loader": "^15.9.1",
     "vue-template-compiler": "^2.6.12",
     "vue-turbolinks": "^2.2.1",
-    "vue": "^2.6.11",
     "webpack": "^4.35.2",
     "webpack-cli": "^3.3.5",
     "webpack-manifest-plugin": "^1.3.2",

spec/controllers/repository_rows_controller_spec.rb

@@ -13,7 +13,7 @@ describe RepositoryRowsController, type: :controller do
     RepositoryTableState.create(
       repository: repository,
       user: user,
-      state: Constants::REPOSITORY_TABLE_DEFAULT_STATE
+      state: repository.default_teble_state
     )
   end
   let!(:repository_row) do