@abi-software/map-side-bar 2.4.0-alpha-1 → 2.4.0-isan-0

package/src/components/SidebarContent.vue

@@ -1,730 +1,710 @@
-<template>
-  <el-card :body-style="bodyStyle" class="content-card">
-    <template #header>
-      <div class="header">
-        <el-input
-          class="search-input"
-          placeholder="Search"
-          v-model="searchInput"
-          @keyup="searchEvent"
-          clearable
-          @clear="clearSearchClicked"
-        ></el-input>
-        <el-select
-          v-model="mode"
-          class="data-type-select"
-          placeholder="Search over..."
-          @change="onSelectValueChange"
-        >
-          <el-option
-            v-for="item in selectOptions"
-            :key="item.value"
-            :label="item.label"
-            :value="item.value"
-          />
-        </el-select>
-      </div>
-    </template>
-    <SearchFilters
-      class="filters"
-      ref="filtersRef"
-      :entry="filterEntry"
-      :envVars="envVars"
-      @filterResults="filterUpdate"
-      @numberPerPage="numberPerPageUpdate"
-      @loading="filtersLoading"
-      @cascaderReady="cascaderReady"
-    ></SearchFilters>
-    <SearchHistory
-      ref="searchHistory"
-      @search="searchHistorySearch"
-    ></SearchHistory>
-      pmr hits: {{ pmrNumberOfHits }}
-    <div class="content scrollbar" v-loading="loadingCards" ref="content">
-      <div class="error-feedback" v-if="results.length === 0 && !loadingCards">
-        No results found - Please change your search / filter criteria.
-      </div>
-      <div v-for="(result, i) in results" :key="i" class="step-item">
-        <DatasetCard
-          v-if="result.dataSource === 'SPARC'"
-          class="dataset-card"
-          :entry="result"
-          :envVars="envVars"
-          @mouseenter="hoverChanged(result)"
-          @mouseleave="hoverChanged(undefined)"
-        ></DatasetCard>
-        <PMRDatasetCard
-          v-else-if="result.dataSource === 'PMR'"
-          class="dataset-card"
-          :entry="result"
-          :envVars="envVars"
-          @mouseenter="hoverChanged(result)"
-          @mouseleave="hoverChanged(undefined)"
-        ></PMRDatasetCard>
-        <flatmap-dataset-card
-          v-else-if="result.dataSource === 'Flatmap'"
-          class="dataset-card"
-          :entry="result"
-          :envVars="envVars"
-          @mouseenter="hoverChanged(result)"
-          @mouseleave="hoverChanged(undefined)"
-        ></flatmap-dataset-card>
-      </div>
-      <el-pagination
-        class="pagination"
-        v-model:current-page="page"
-        hide-on-single-page
-        large
-        layout="prev, pager, next"
-        :page-size="numberPerPage"
-        :total="numberOfHits"
-        @current-change="pageChange"
-      ></el-pagination>
-    </div>
-  </el-card>
-</template>
-
-<script>
-/* eslint-disable no-alert, no-console */
-import {
-  ElButton as Button,
-  ElCard as Card,
-  ElDrawer as Drawer,
-  ElIcon as Icon,
-  ElInput as Input,
-  ElPagination as Pagination,
-} from 'element-plus'
-import SearchFilters from './SearchFilters.vue'
-import SearchHistory from './SearchHistory.vue'
-import EventBus from './EventBus.js'
-
-import DatasetCard from "./DatasetCard.vue";
-import PMRDatasetCard from "./PMRDatasetCard.vue";
-import FlatmapDatasetCard from './FlatmapDatasetCard.vue';
-
-import allPaths from './allPaths.js'
-
-import { AlgoliaClient } from '../algolia/algolia.js'
-import { getFilters, facetPropPathMapping } from '../algolia/utils.js'
-import FlatmapQueries from '../flatmapQueries/flatmapQueries.js'
-import mixedPageCalculation from '../mixins/mixedPageCalculation.vue'
-
-// TODO: to update API URL
-const API_URL = "/data/pmr-sample.json";
-const RatioOfPMRResults = 0.2; // Ratio of PMR results to Sparc results
-
-// handleErrors: A custom fetch error handler to recieve messages from the server
-//    even when an error is found
-var handleErrors = async function (response) {
-  if (!response.ok) {
-    let parse = await response.json()
-    if (parse) {
-      throw new Error(parse.message)
-    } else {
-      throw new Error(response)
-    }
-  }
-  return response
-}
-
-var initial_state = {
-  searchInput: '',
-  lastSearch: '',
-  results: [],
-  pmrNumberOfHits: 0,
-  sparcNumberOfHits: 0,
-  variableRatio: RatioOfPMRResults,
-  filter: [],
-  loadingCards: false,
-  numberPerPage: 10,
-  page: 1,
-  pmrResultsOnlyFlag: false,
-  hasSearched: false,
-  contextCardEnabled: false,
-  pmrResults: [],
-  mode: 'Sparc Datasets',
-  allPaths: allPaths.values,
-  selectOptions: [
-    { value: "Sparc Datasets", label: "Sparc Datasets" },
-    { value: "PMR", label: "PMR" },
-    { value: "Flatmap", label: "Flatmap"}
-  ],
-};
-
-
-
-export default {
-  components: {
-    SearchFilters,
-    DatasetCard,
-    PMRDatasetCard,
-    FlatmapDatasetCard,
-    SearchHistory,
-    Button,
-    Card,
-    Drawer,
-    Icon,
-    Input,
-    Pagination
-  },
-  name: 'SideBarContent',
-  mixins: [mixedPageCalculation],
-  props: {
-    visible: {
-      type: Boolean,
-      default: false,
-    },
-    isDrawer: {
-      type: Boolean,
-      default: true,
-    },
-    entry: {
-      type: Object,
-      default: () => initial_state,
-    },
-    envVars: {
-      type: Object,
-      default: () => {},
-    },
-  },
-  data: function () {
-    return {
-      ...this.entry,
-      bodyStyle: {
-        flex: '1 1 auto',
-        'flex-flow': 'column',
-        display: 'flex',
-      },
-      cascaderIsReady: false,
-    }
-  },
-  computed: {
-    // This computed property populates filter data's entry object with $data from this sidebar
-    filterEntry: function () {
-      return {
-        numberOfHits: this.numberOfHits,
-        filterFacets: this.filter,
-      }
-    },
-    // npp_SPARC: Number per page for SPARC datasets
-    npp_SPARC: function () {
-      return Math.round(this.numberPerPage * (1 - RatioOfPMRResults))
-    },
-    // npp_PMR: Number per page for PMR datasets
-    npp_PMR: function () {
-      return Math.round(this.numberPerPage * RatioOfPMRResults)
-    },
-    numberOfHits: function () {
-      return this.sparcNumberOfHits + this.pmrNumberOfHits
-    },
-    
-  },
-  methods: {
-    hoverChanged: function (data) {
-      this.$emit('hover-changed', data)
-    },
-    resetSearch: function () {
-      this.pmrNumberOfHits = 0
-      this.sparcNumberOfHits = 0
-      this.page = 1
-      this.calculateVariableRatio()
-      this.discoverIds = []
-      this._dois = []
-      this.results = []
-      this.loadingCards = false
-    },
-    // openSearch: Resets the results, populates dataset cards and filters. Will use Algolia and SciCrunch data uness pmr mode is set
-    openSearch: function(filter, search = '', resetSearch = true) {
-      if (resetSearch) {
-        this.resetSearch();
-        this.openAlgoliaSearch(filter, search);
-      } else {
-        this.searchAlgolia(filter, search);
-      }
-      this.openPMRSearch(filter, search)
-    },
-
-    // openPMRSearch: Resets the results, populates dataset cards and filters with PMR data.
-    openPMRSearch: function (filter, search = '') {
-      this.flatmapQueries.updateOffset(this.calculatePMROffest())
-      this.flatmapQueries.updateLimit(this.PMRLimit(this.pmrResultsOnlyFlag))
-      this.flatmapQueries.pmrSearch(filter, search).then((data) => {
-        data.forEach((result) => {
-          this.results.push(result)
-        })
-        this.pmrNumberOfHits = this.flatmapQueries.numberOfHits
-      })
-    },
-
-    // openAlgoliaSearch: Resets the results, populates dataset cards and filters with Algloia and SciCrunch data.
-    openAlgoliaSearch: function (filter, search = '') {
-      this.searchInput = search
-      //Proceed normally if cascader is ready
-      if (this.cascaderIsReady) {
-        this.filter =
-          this.$refs.filtersRef.getHierarchicalValidatedFilters(filter)
-        //Facets provided but cannot find at least one valid
-        //facet. Tell the users the search is invalid and reset
-        //facets check boxes.
-        if (
-          filter &&
-          filter.length > 0 &&
-          this.filter &&
-          this.filter.length === 0
-        ) {
-          this.$refs.filtersRef.checkShowAllBoxes()
-          this.resetSearch()
-        } else if (this.filter) {
-          this.searchAlgolia(this.filter, search)
-          this.$refs.filtersRef.setCascader(this.filter)
-        }
-      } else {
-        //cascader is not ready, perform search if no filter is set,
-        //otherwise waith for cascader to be ready
-        this.filter = filter
-        if (!filter || filter.length == 0) {
-          this.searchAlgolia(this.filter, search)
-        }
-      }
-    },
-    addFilter: function (filter) {
-      if (this.cascaderIsReady) {
-        this.resetSearch()
-        if (filter) {
-          if (this.$refs.filtersRef.addFilter(filter))
-            this.$refs.filtersRef.initiateSearch()
-        }
-      } else {
-        if (Array.isArray(this.filter)) {
-          this.filter.push(filter)
-        } else {
-          this.filter = [filter]
-        }
-      }
-    },
-    cascaderReady: function () {
-      this.cascaderIsReady = true
-      this.openSearch(this.filter, this.searchInput)
-    },
-    clearSearchClicked: function () {
-      this.searchInput = ''
-      this.resetSearch()
-      this.openSearch(this.filter, this.searchInput)
-      this.$refs.searchHistory.selectValue = 'Full search history'
-    },
-    searchEvent: function (event = false) {
-      if (event.keyCode === 13 || event instanceof MouseEvent) {
-        this.openSearch(this.filter, this.searchInput)
-        this.$refs.searchHistory.selectValue = 'Full search history'
-        this.$refs.searchHistory.addSearchToHistory(
-          this.filters,
-          this.searchInput
-        )
-      }
-    },
-    updatePMROnlyFlag: function (filters) {
-      const pmrSearchObject = filters.find((tmp) => tmp.facet === 'PMR');
-      if (pmrSearchObject) {
-        this.pmrResultsOnlyFlag = true
-      } else {
-        this.pmrResultsOnlyFlag = false
-      }
-    },
-    filterUpdate: function (filters) {
-      this.filters = [...filters]
-
-      // Check if PMR is in the filters
-      this.updatePMROnlyFlag(filters)
-      
-      // Note that we cannot use the openSearch function as that modifies filters
-      this.resetSearch()
-      this.searchAlgolia(filters, this.searchInput)
-      this.openPMRSearch(filters, this.searchInput)
-      this.$emit('search-changed', {
-        value: filters,
-        type: 'filter-update',
-      })
-    },
-    searchAlgolia(filters, query = '') {
-      
-      // Remove loading if we dont expect any results
-      if (this.SPARCLimit() === 0) {
-        this.loadingCards = false
-        return
-      }
-      
-      // Algolia search
-
-      this.loadingCards = true
-      this.algoliaClient
-        .anatomyInSearch(getFilters(filters), query)
-        .then((r) => {
-          // Send result anatomy to the scaffold and flatmap
-          EventBus.emit('anatomy-in-datasets', r.forFlatmap)
-          EventBus.emit('number-of-datasets-for-anatomies', r.forScaffold)
-        })
-      this.algoliaClient
-        .search(getFilters(filters), query, this.calculateSPARCOffest(), this.SPARCLimit(this.pmrResultsOnlyFlag) )
-        .then((searchData) => {
-          this.sparcNumberOfHits = searchData.total
-          this.discoverIds = searchData.discoverIds
-          this._dois = searchData.dois
-          searchData.items.forEach((item) => {
-            item.detailsReady = false
-            this.results.push(item)
-          })
-          // add the items to the results
-          this.results.concat(searchData.items)
-          this.loadingCards = false
-          this.scrollToTop()
-          this.$emit('search-changed', {
-            value: this.searchInput,
-            type: 'query-update',
-          })
-          if (this._abortController) this._abortController.abort()
-          this._abortController = new AbortController()
-          const signal = this._abortController.signal
-          //Search ongoing, let the current flow progress
-          this.perItemSearch(signal, { count: 0 })
-        })
-    },
-    filtersLoading: function (val) {
-      this.loadingCards = val
-    },
-    numberPerPageUpdate: function (val) {
-      this.numberPerPage = val
-      this.pageChange(1)
-    },
-    pageChange: function (page) {
-      this.page = page
-      this.results = []
-      this.calculateVariableRatio()
-      this.openSearch(this.filter, this.searchInput, false)
-    },
-    handleMissingData: function (doi) {
-      let i = this.results.findIndex((res) => res.doi === doi)
-      if (this.results[i]) this.results[i].detailsReady = true
-    },
-    perItemSearch: function (signal, data) {
-      //Maximum 10 downloads at once to prevent long waiting time
-      //between unfinished search and new search
-      const maxDownloads = 10
-      if (maxDownloads > data.count) {
-        const doi = this._dois.shift()
-        if (doi) {
-          data.count++
-          this.callSciCrunch(this.envVars.API_LOCATION, { dois: [doi] }, signal)
-            .then((result) => {
-              if (result.numberOfHits === 0) this.handleMissingData(doi)
-              else this.resultsProcessing(result)
-              this.$refs.content.style['overflow-y'] = 'scroll'
-              data.count--
-              //Async::Download finished, get the next one
-              this.perItemSearch(signal, data)
-            })
-            .catch((result) => {
-              if (result.name !== 'AbortError') {
-                this.handleMissingData(doi)
-                data.count--
-                //Async::Download not aborted, get the next one
-                this.perItemSearch(signal, data)
-              }
-            })
-          //Check and make another request until it gets to max downloads
-          this.perItemSearch(signal, data)
-        }
-      }
-    },
-    scrollToTop: function () {
-      if (this.$refs.content) {
-        this.$refs.content.scroll({ top: 0, behavior: 'smooth' })
-      }
-    },
-    resetPageNavigation: function () {
-      this.page = 1
-    },
-    resultsProcessing: function (data) {
-      this.lastSearch = this.searchInput
-
-      if (data.results.length === 0) {
-        return
-      }
-      data.results.forEach((element) => {
-        // match the scicrunch result with algolia result
-        let i = this.results.findIndex((res) =>
-          element.doi ? element.doi.includes(res.doi) : false
-        )
-        // Assign scicrunch results to the object
-        Object.assign(this.results[i], element)
-        // Assign the attributes that need some processing
-        Object.assign(this.results[i], {
-          numberSamples: element.sampleSize ? parseInt(element.sampleSize) : 0,
-          numberSubjects: element.subjectSize
-            ? parseInt(element.subjectSize)
-            : 0,
-          updated:
-            (element.updated && element.updated.length) > 0
-              ? element.updated[0].timestamp.split('T')[0]
-              : '',
-          url: element.uri[0],
-          datasetId: element.dataset_identifier,
-          datasetRevision: element.dataset_revision,
-          datasetVersion: element.dataset_version,
-          organs:
-            element.organs && element.organs.length > 0
-              ? [...new Set(element.organs.map((v) => v.name))]
-              : undefined,
-          species: element.organisms
-            ? element.organisms[0].species
-              ? [
-                  ...new Set(
-                    element.organisms.map((v) =>
-                      v.species ? v.species.name : null
-                    )
-                  ),
-                ]
-              : undefined
-            : undefined, // This processing only includes each gender once into 'sexes'
-          scaffolds: element['abi-scaffold-metadata-file'],
-          thumbnails: element['abi-thumbnail']
-            ? element['abi-thumbnail']
-            : element['abi-scaffold-thumbnail'],
-          scaffoldViews: element['abi-scaffold-view-file'],
-          videos: element.video,
-          plots: element['abi-plot'],
-          images: element['common-images'],
-          contextualInformation:
-            element['abi-contextual-information'].length > 0
-              ? element['abi-contextual-information']
-              : undefined,
-          segmentation: element['mbf-segmentation'],
-          simulation: element['abi-simulation-file'],
-          additionalLinks: element.additionalLinks,
-          detailsReady: true,
-        })
-        this.results[i] = this.results[i]
-      })
-    },
-    createfilterParams: function (params) {
-      let p = new URLSearchParams()
-      //Check if field is array or value
-      for (const key in params) {
-        if (Array.isArray(params[key])) {
-          params[key].forEach((e) => {
-            p.append(key, e)
-          })
-        } else {
-          p.append(key, params[key])
-        }
-      }
-      return p.toString()
-    },
-    callSciCrunch: function (apiLocation, params = {}, signal) {
-      return new Promise((resolve, reject) => {
-        // Add parameters if we are sent them
-        let fullEndpoint =
-          this.envVars.API_LOCATION +
-          this.searchEndpoint +
-          '?' +
-          this.createfilterParams(params)
-        fetch(fullEndpoint, { signal })
-          .then(handleErrors)
-          .then((response) => response.json())
-          .then((data) => resolve(data))
-          .catch((data) => reject(data))
-      })
-    },
-    getAlgoliaFacets: async function () {
-      let facets = await this.algoliaClient.getAlgoliaFacets(
-        facetPropPathMapping
-      )
-      return facets
-    },
-    searchHistorySearch: function (item) {
-      this.searchInput = item.search
-      this.filters = item.filters
-      this.openSearch(item.filters, item.search)
-    },
-    onSelectValueChange: function (val) {
-      this.mode = val
-      this.openSearch(this.filter, this.searchInput, val)
-    },
-  },
-  mounted: function () {
-    // initialise algolia
-    this.algoliaClient = new AlgoliaClient(
-      this.envVars.ALGOLIA_ID,
-      this.envVars.ALGOLIA_KEY,
-      this.envVars.PENNSIEVE_API_LOCATION
-    )
-    this.algoliaClient.initIndex(this.envVars.ALGOLIA_INDEX)
-
-    // initialise flatmap queries
-    this.flatmapQueries = new FlatmapQueries()
-    this.flatmapQueries.initialise(this.envVars.FLATMAP_API_LOCATION)
-
-    // open search
-    this.openSearch(this.filter, this.searchInput, this.mode )
-  },
-  created: function () {
-    //Create non-reactive local variables
-    this.searchEndpoint = 'dataset_info/using_multiple_dois/'
-  },
-}
-</script>
-
-<style lang="scss" scoped>
-.dataset-card {
-  position: relative;
-
-  &::before {
-    content: "";
-    display: block;
-    width: calc(100% - 15px);
-    height: 100%;
-    position: absolute;
-    top: 7px;
-    left: 7px;
-    border-style: solid;
-    border-radius: 5px;
-    border-color: transparent;
-  }
-
-  &:hover {
-    &::before {
-      border-color: var(--el-color-primary);
-    }
-  }
-}
-
-.content-card {
-  height: 100%;
-  flex-flow: column;
-  display: flex;
-}
-
-.data-type-select {
-  width: 90px;
-  margin-left: 10px;
-}
-
-.button {
-  background-color: $app-primary-color;
-  border: $app-primary-color;
-  color: white;
-}
-
-.step-item {
-  font-size: 14px;
-  margin-bottom: 18px;
-  text-align: left;
-}
-
-.search-input {
-  width: 298px !important;
-  height: 40px;
-  padding-right: 14px;
-  align-items: left;
-}
-
-.header {
-  border: solid 1px #292b66;
-  background-color: #292b66;
-  text-align: left;
-
-  .el-button {
-    &:hover,
-    &:focus {
-      background: $app-primary-color;
-      box-shadow: -3px 2px 4px #00000040;
-      color: #fff;
-    }
-  }
-}
-
-.pagination {
-  padding-bottom: 16px;
-  background-color: white;
-  padding-left: 95px;
-  font-weight: bold;
-}
-
-.pagination :deep(button) {
-  background-color: white !important;
-}
-.pagination :deep(li) {
-  background-color: white !important;
-}
-.pagination :deep(li.is-active) {
-  color: $app-primary-color;
-}
-
-.error-feedback {
-  font-family: Asap;
-  font-size: 14px;
-  font-style: italic;
-  padding-top: 15px;
-}
-
-.content-card :deep(.el-card__header) {
-  background-color: #292b66;
-  padding: 1rem;
-}
-
-.content-card :deep(.el-card__body) {
-  background-color: #f7faff;
-  overflow-y: hidden;
-  padding: 1rem;
-}
-
-.content {
-  // width: 515px;
-  flex: 1 1 auto;
-  box-shadow: 0 2px 12px 0 rgba(0, 0, 0, 0.06);
-  border: solid 1px #e4e7ed;
-  background-color: #ffffff;
-  overflow-y: scroll;
-  scrollbar-width: thin;
-}
-
-.content :deep(.el-loading-spinner .path) {
-  stroke: $app-primary-color;
-}
-
-.content :deep(.step-item:first-child .seperator-path) {
-  display: none;
-}
-
-.content :deep(.step-item:not(:first-child) .seperator-path) {
-  width: 455px;
-  height: 0px;
-  border: solid 1px #e4e7ed;
-  background-color: #e4e7ed;
-}
-
-.scrollbar::-webkit-scrollbar-track {
-  border-radius: 10px;
-  background-color: #f5f5f5;
-}
-
-.scrollbar::-webkit-scrollbar {
-  width: 12px;
-  right: -12px;
-  background-color: #f5f5f5;
-}
-
-.scrollbar::-webkit-scrollbar-thumb {
-  border-radius: 4px;
-  box-shadow: 0 2px 4px 0 rgba(0, 0, 0, 0.06);
-  background-color: #979797;
-}
-
-:deep(.el-input__suffix) {
-  padding-right: 0px;
-}
-
-:deep(.my-drawer) {
-  background: rgba(0, 0, 0, 0);
-  box-shadow: none;
-}
-</style>
+<template>
+  <el-card :body-style="bodyStyle" class="content-card">
+    <template #header>
+      <div class="header">
+        <el-input
+          class="search-input"
+          placeholder="Search"
+          v-model="searchInput"
+          @keyup="searchEvent"
+          clearable
+          @clear="clearSearchClicked"
+        ></el-input>
+        <el-button
+          type="primary"
+          class="button"
+          @click="searchEvent"
+          size="large"
+        >
+          Search
+        </el-button>
+      </div>
+    </template>
+    <SearchFilters
+      class="filters"
+      ref="filtersRef"
+      :entry="filterEntry"
+      :envVars="envVars"
+      @filterResults="filterUpdate"
+      @numberPerPage="numberPerPageUpdate"
+      @loading="filtersLoading"
+      @cascaderReady="cascaderReady"
+    ></SearchFilters>
+    <SearchHistory
+      ref="searchHistory"
+      @search="searchHistorySearch"
+    ></SearchHistory>
+      pmr hits: {{ pmrNumberOfHits }}
+    <div class="content scrollbar" v-loading="loadingCards" ref="content">
+      <div class="error-feedback" v-if="results.length === 0 && !loadingCards">
+        No results found - Please change your search / filter criteria.
+      </div>
+      <div v-for="(result, i) in results" :key="result.doi || i" class="step-item">
+        <DatasetCard
+          v-if="result.dataSource === 'SPARC'"
+          class="dataset-card"
+          :entry="result"
+          :envVars="envVars"
+          @mouseenter="hoverChanged(result)"
+          @mouseleave="hoverChanged(undefined)"
+        ></DatasetCard>
+        <PMRDatasetCard
+          v-else-if="result.dataSource === 'PMR'"
+          class="dataset-card"
+          :entry="result"
+          :envVars="envVars"
+          @flatmap-clicked="onFlatmapClicked"
+          @simulation-clicked="onSimulationClicked"
+          @mouseenter="hoverChanged(result)"
+          @mouseleave="hoverChanged(undefined)"
+        ></PMRDatasetCard>
+      </div>
+      <el-pagination
+        class="pagination"
+        v-model:current-page="page"
+        hide-on-single-page
+        large
+        layout="prev, pager, next"
+        :page-size="numberPerPage"
+        :total="numberOfHits"
+        @current-change="pageChange"
+      ></el-pagination>
+    </div>
+  </el-card>
+</template>
+
+<script>
+/* eslint-disable no-alert, no-console */
+import {
+  ElButton as Button,
+  ElCard as Card,
+  ElDrawer as Drawer,
+  ElIcon as Icon,
+  ElInput as Input,
+  ElPagination as Pagination,
+} from 'element-plus'
+import SearchFilters from './SearchFilters.vue'
+import SearchHistory from './SearchHistory.vue'
+import EventBus from './EventBus.js'
+
+import DatasetCard from "./DatasetCard.vue";
+import PMRDatasetCard from "./PMRDatasetCard.vue";
+
+import { AlgoliaClient } from '../algolia/algolia.js'
+import { getFilters, facetPropPathMapping } from '../algolia/utils.js'
+import FlatmapQueries from '../flatmapQueries/flatmapQueries.js'
+import mixedPageCalculation from '../mixins/mixedPageCalculation.vue'
+
+const RatioOfPMRResults = 0.2; // Ratio of PMR results to Sparc results
+
+// handleErrors: A custom fetch error handler to recieve messages from the server
+//    even when an error is found
+var handleErrors = async function (response) {
+  if (!response.ok) {
+    let parse = await response.json()
+    if (parse) {
+      throw new Error(parse.message)
+    } else {
+      throw new Error(response)
+    }
+  }
+  return response
+}
+
+var initial_state = {
+  searchInput: '',
+  lastSearch: '',
+  results: [],
+  pmrNumberOfHits: 0,
+  sparcNumberOfHits: 0,
+  filter: [],
+  loadingCards: false,
+  numberPerPage: 10,
+  page: 1,
+  pmrResultsOnlyFlag: false,
+  hasSearched: false,
+  contextCardEnabled: false,
+  pmrResults: [],
+  RatioOfPMRResults: RatioOfPMRResults,
+};
+
+
+
+export default {
+  components: {
+    SearchFilters,
+    DatasetCard,
+    PMRDatasetCard,
+    SearchHistory,
+    Button,
+    Card,
+    Drawer,
+    Icon,
+    Input,
+    Pagination
+  },
+  name: 'SideBarContent',
+  mixins: [mixedPageCalculation],
+  props: {
+    visible: {
+      type: Boolean,
+      default: false,
+    },
+    isDrawer: {
+      type: Boolean,
+      default: true,
+    },
+    entry: {
+      type: Object,
+      default: () => initial_state,
+    },
+    envVars: {
+      type: Object,
+      default: () => {},
+    },
+  },
+  data: function () {
+    return {
+      ...this.entry,
+      bodyStyle: {
+        flex: '1 1 auto',
+        'flex-flow': 'column',
+        display: 'flex',
+      },
+      cascaderIsReady: false,
+    }
+  },
+  computed: {
+    // This computed property populates filter data's entry object with $data from this sidebar
+    filterEntry: function () {
+      return {
+        numberOfHits: this.numberOfHits,
+        filterFacets: this.filter,
+      }
+    },
+    // npp_SPARC: Number per page for SPARC datasets
+    npp_SPARC: function () {
+      return Math.round(this.numberPerPage * (1 - RatioOfPMRResults))
+    },
+    // npp_PMR: Number per page for PMR datasets
+    npp_PMR: function () {
+      return Math.round(this.numberPerPage * RatioOfPMRResults)
+    },
+    numberOfHits: function () {
+      return this.sparcNumberOfHits + this.pmrNumberOfHits
+    },
+
+  },
+  methods: {
+    hoverChanged: function (data) {
+      this.$emit('hover-changed', data)
+    },
+    onFlatmapClicked: function (data) {
+      this.$emit('flatmap-clicked', data);
+    },
+    onSimulationClicked: function (payload) {
+      this.$emit('simulation-clicked', payload)
+    },
+    // resetSearch: Resets the results, and page, and variable results ratio
+    //     Does not: reset filters, search input, or search history
+    resetSearch: function () {
+      this.pmrNumberOfHits = 0
+      this.sparcNumberOfHits = 0
+      this.page = 1
+      this.calculateVariableRatio()
+      this.discoverIds = []
+      this._dois = []
+      this.results = []
+      this.loadingCards = false
+    },
+    // openSearch: Resets the results, populates dataset cards and filters. Will use Algolia and SciCrunch data uness pmr mode is set
+    openSearch: function(filter, search = '', resetSearch = true) {
+      if (resetSearch) {
+        this.resetSearch();
+        this.openAlgoliaSearch(filter, search);
+      } else {
+        this.searchAlgolia(filter, search);
+      }
+      this.openPMRSearch(filter, search)
+    },
+
+    // openPMRSearch: Resets the results, populates dataset cards and filters with PMR data.
+    openPMRSearch: function (filter, search = '') {
+      this.flatmapQueries.updateOffset(this.calculatePMROffest())
+      this.flatmapQueries.updateLimit(this.PMRLimit(this.pmrResultsOnlyFlag))
+      this.flatmapQueries.pmrSearch(filter, search).then((data) => {
+        data.forEach((result) => {
+          this.results.push(result)
+        })
+        this.pmrNumberOfHits = this.flatmapQueries.numberOfHits
+      })
+    },
+
+    // openAlgoliaSearch: Resets the results, populates dataset cards and filters with Algloia and SciCrunch data.
+    openAlgoliaSearch: function (filter, search = '') {
+      this.searchInput = search
+      //Proceed normally if cascader is ready
+      if (this.cascaderIsReady) {
+        this.filter =
+          this.$refs.filtersRef.getHierarchicalValidatedFilters(filter)
+        //Facets provided but cannot find at least one valid
+        //facet. Tell the users the search is invalid and reset
+        //facets check boxes.
+        if (
+          filter &&
+          filter.length > 0 &&
+          this.filter &&
+          this.filter.length === 0
+        ) {
+          this.$refs.filtersRef.checkShowAllBoxes()
+          this.resetSearch()
+        } else if (this.filter) {
+          this.searchAlgolia(this.filter, search)
+          this.$refs.filtersRef.setCascader(this.filter)
+        }
+      } else {
+        //cascader is not ready, perform search if no filter is set,
+        //otherwise waith for cascader to be ready
+        this.filter = filter
+        if (!filter || filter.length == 0) {
+          this.searchAlgolia(this.filter, search)
+        }
+      }
+    },
+    addFilter: function (filter) {
+      if (this.cascaderIsReady) {
+        this.resetSearch()
+        if (filter) {
+          if (this.$refs.filtersRef.addFilter(filter))
+            this.$refs.filtersRef.initiateSearch()
+        }
+      } else {
+        if (Array.isArray(this.filter)) {
+          this.filter.push(filter)
+        } else {
+          this.filter = [filter]
+        }
+      }
+    },
+    cascaderReady: function () {
+      this.cascaderIsReady = true
+      this.openSearch(this.filter, this.searchInput)
+    },
+    clearSearchClicked: function () {
+      this.searchInput = ''
+      this.resetSearch()
+      this.openSearch(this.filter, this.searchInput)
+      this.$refs.searchHistory.selectValue = 'Full search history'
+    },
+    searchEvent: function (event = false) {
+      if (event.keyCode === 13 || event instanceof MouseEvent) {
+        this.openSearch(this.filter, this.searchInput)
+        this.$refs.searchHistory.selectValue = 'Full search history'
+        this.$refs.searchHistory.addSearchToHistory(
+          this.filter,
+          this.searchInput
+        )
+      }
+    },
+    updatePMROnlyFlag: function (filters) {
+      const pmrSearchObject = filters.find((tmp) => tmp.facet === 'PMR');
+      if (pmrSearchObject) {
+        this.pmrResultsOnlyFlag = true
+      } else {
+        this.pmrResultsOnlyFlag = false
+      }
+    },
+    filterUpdate: function (filters) {
+      this.filter = [...filters]
+
+      // Check if PMR is in the filters
+      this.updatePMROnlyFlag(filters)
+
+      // Note that we cannot use the openSearch function as that modifies filters
+      this.resetSearch()
+      this.searchAlgolia(filters, this.searchInput)
+      this.openPMRSearch(filters, this.searchInput)
+      this.$emit('search-changed', {
+        value: filters,
+        type: 'filter-update',
+      })
+    },
+    searchAlgolia(filters, query = '') {
+
+      // Remove loading if we dont expect any results
+      if (this.SPARCLimit() === 0) {
+        this.loadingCards = false
+        return
+      }
+
+      // Algolia search
+
+      this.loadingCards = true
+      this.algoliaClient
+        .anatomyInSearch(getFilters(filters), query)
+        .then((r) => {
+          // Send result anatomy to the scaffold and flatmap
+          EventBus.emit('anatomy-in-datasets', r.forFlatmap)
+          EventBus.emit('number-of-datasets-for-anatomies', r.forScaffold)
+        })
+      this.algoliaClient
+        .search(getFilters(filters), query, this.calculateSPARCOffest(), this.SPARCLimit(this.pmrResultsOnlyFlag) )
+        .then((searchData) => {
+          this.sparcNumberOfHits = searchData.total
+          this.discoverIds = searchData.discoverIds
+          this._dois = searchData.dois
+          searchData.items.forEach((item) => {
+            item.detailsReady = false
+            this.results.push(item)
+          })
+          // add the items to the results
+          this.results.concat(searchData.items)
+          this.loadingCards = false
+          this.scrollToTop()
+          this.$emit('search-changed', {
+            value: this.searchInput,
+            type: 'query-update',
+          })
+          if (this._abortController) this._abortController.abort()
+          this._abortController = new AbortController()
+          const signal = this._abortController.signal
+          //Search ongoing, let the current flow progress
+          this.perItemSearch(signal, { count: 0 })
+        })
+    },
+    filtersLoading: function (val) {
+      this.loadingCards = val
+    },
+    numberPerPageUpdate: function (val) {
+      this.numberPerPage = val
+      this.pageChange(1)
+    },
+    pageChange: function (page) {
+      this.page = page
+      this.results = []
+      this.calculateVariableRatio()
+      this.openSearch(this.filter, this.searchInput, false)
+    },
+    handleMissingData: function (doi) {
+      let i = this.results.findIndex((res) => res.doi === doi)
+      if (this.results[i]) this.results[i].detailsReady = true
+    },
+    perItemSearch: function (signal, data) {
+      //Maximum 10 downloads at once to prevent long waiting time
+      //between unfinished search and new search
+      const maxDownloads = 10
+      if (maxDownloads > data.count) {
+        const doi = this._dois.shift()
+        if (doi) {
+          data.count++
+          this.callSciCrunch(this.envVars.API_LOCATION, { dois: [doi] }, signal)
+            .then((result) => {
+              if (result.numberOfHits === 0) this.handleMissingData(doi)
+              else this.resultsProcessing(result)
+              this.$refs.content.style['overflow-y'] = 'scroll'
+              data.count--
+              //Async::Download finished, get the next one
+              this.perItemSearch(signal, data)
+            })
+            .catch((result) => {
+              if (result.name !== 'AbortError') {
+                this.handleMissingData(doi)
+                data.count--
+                //Async::Download not aborted, get the next one
+                this.perItemSearch(signal, data)
+              }
+            })
+          //Check and make another request until it gets to max downloads
+          this.perItemSearch(signal, data)
+        }
+      }
+    },
+    scrollToTop: function () {
+      if (this.$refs.content) {
+        this.$refs.content.scroll({ top: 0, behavior: 'smooth' })
+      }
+    },
+    resetPageNavigation: function () {
+      this.page = 1
+    },
+    resultsProcessing: function (data) {
+      this.lastSearch = this.searchInput
+
+      if (data.results.length === 0) {
+        return
+      }
+      data.results.forEach((element) => {
+        // match the scicrunch result with algolia result
+        let i = this.results.findIndex((res) =>
+          element.doi ? element.doi.includes(res.doi) : false
+        )
+        // Assign scicrunch results to the object
+        Object.assign(this.results[i], element)
+        // Assign the attributes that need some processing
+        Object.assign(this.results[i], {
+          numberSamples: element.sampleSize ? parseInt(element.sampleSize) : 0,
+          numberSubjects: element.subjectSize
+            ? parseInt(element.subjectSize)
+            : 0,
+          updated:
+            (element.updated && element.updated.length) > 0
+              ? element.updated[0].timestamp.split('T')[0]
+              : '',
+          url: element.uri[0],
+          datasetId: element.dataset_identifier,
+          datasetRevision: element.dataset_revision,
+          datasetVersion: element.dataset_version,
+          organs:
+            element.organs && element.organs.length > 0
+              ? [...new Set(element.organs.map((v) => v.name))]
+              : undefined,
+          species: element.organisms
+            ? element.organisms[0].species
+              ? [
+                  ...new Set(
+                    element.organisms.map((v) =>
+                      v.species ? v.species.name : null
+                    )
+                  ),
+                ]
+              : undefined
+            : undefined, // This processing only includes each gender once into 'sexes'
+          scaffolds: element['abi-scaffold-metadata-file'],
+          thumbnails: element['abi-thumbnail']
+            ? element['abi-thumbnail']
+            : element['abi-scaffold-thumbnail'],
+          scaffoldViews: element['abi-scaffold-view-file'],
+          videos: element.video,
+          plots: element['abi-plot'],
+          images: element['common-images'],
+          contextualInformation:
+            element['abi-contextual-information'].length > 0
+              ? element['abi-contextual-information']
+              : undefined,
+          segmentation: element['mbf-segmentation'],
+          simulation: element['abi-simulation-file'],
+          additionalLinks: element.additionalLinks,
+          detailsReady: true,
+        })
+        this.results[i] = this.results[i]
+      })
+    },
+    createfilterParams: function (params) {
+      let p = new URLSearchParams()
+      //Check if field is array or value
+      for (const key in params) {
+        if (Array.isArray(params[key])) {
+          params[key].forEach((e) => {
+            p.append(key, e)
+          })
+        } else {
+          p.append(key, params[key])
+        }
+      }
+      return p.toString()
+    },
+    callSciCrunch: function (apiLocation, params = {}, signal) {
+      return new Promise((resolve, reject) => {
+        // Add parameters if we are sent them
+        let fullEndpoint =
+          this.envVars.API_LOCATION +
+          this.searchEndpoint +
+          '?' +
+          this.createfilterParams(params)
+        fetch(fullEndpoint, { signal })
+          .then(handleErrors)
+          .then((response) => response.json())
+          .then((data) => resolve(data))
+          .catch((data) => reject(data))
+      })
+    },
+    getAlgoliaFacets: async function () {
+      let facets = await this.algoliaClient.getAlgoliaFacets(
+        facetPropPathMapping
+      )
+      return facets
+    },
+    searchHistorySearch: function (item) {
+      this.searchInput = item.search
+      this.filters = item.filters
+      this.openSearch(item.filters, item.search)
+    },
+  },
+  mounted: function () {
+    // initialise algolia
+    this.algoliaClient = new AlgoliaClient(
+      this.envVars.ALGOLIA_ID,
+      this.envVars.ALGOLIA_KEY,
+      this.envVars.PENNSIEVE_API_LOCATION
+    )
+    this.algoliaClient.initIndex(this.envVars.ALGOLIA_INDEX)
+
+    // initialise flatmap queries
+    this.flatmapQueries = new FlatmapQueries()
+    this.flatmapQueries.initialise(this.envVars.FLATMAP_API_LOCATION)
+
+    // open search
+    this.openSearch(this.filter, this.searchInput, this.mode )
+  },
+  created: function () {
+    //Create non-reactive local variables
+    this.searchEndpoint = 'dataset_info/using_multiple_dois/'
+  },
+}
+</script>
+
+<style lang="scss" scoped>
+.dataset-card {
+  position: relative;
+
+  &::before {
+    content: "";
+    display: block;
+    width: calc(100% - 15px);
+    height: 100%;
+    position: absolute;
+    top: 7px;
+    left: 7px;
+    border-style: solid;
+    border-radius: 5px;
+    border-color: transparent;
+  }
+
+  &:hover {
+    &::before {
+      border-color: var(--el-color-primary);
+    }
+  }
+}
+
+.content-card {
+  height: 100%;
+  flex-flow: column;
+  display: flex;
+}
+
+.data-type-select {
+  width: 90px;
+  margin-left: 10px;
+}
+
+.button {
+  background-color: $app-primary-color;
+  border: $app-primary-color;
+  color: white;
+}
+
+.step-item {
+  font-size: 14px;
+  margin-bottom: 18px;
+  text-align: left;
+}
+
+.search-input {
+  width: 298px !important;
+  height: 40px;
+  padding-right: 14px;
+  align-items: left;
+}
+
+.header {
+  border: solid 1px #292b66;
+  background-color: #292b66;
+  text-align: left;
+
+  .el-button {
+    &:hover,
+    &:focus {
+      background: $app-primary-color;
+      box-shadow: -3px 2px 4px #00000040;
+      color: #fff;
+    }
+  }
+}
+
+.pagination {
+  padding-bottom: 16px;
+  background-color: white;
+  padding-left: 95px;
+  font-weight: bold;
+}
+
+.pagination :deep(button) {
+  background-color: white !important;
+}
+.pagination :deep(li) {
+  background-color: white !important;
+}
+.pagination :deep(li.is-active) {
+  color: $app-primary-color;
+}
+
+.error-feedback {
+  font-family: Asap;
+  font-size: 14px;
+  font-style: italic;
+  padding-top: 15px;
+}
+
+.content-card :deep(.el-card__header) {
+  background-color: #292b66;
+  padding: 1rem;
+}
+
+.content-card :deep(.el-card__body) {
+  background-color: #f7faff;
+  overflow-y: hidden;
+  padding: 1rem;
+}
+
+.content {
+  // width: 515px;
+  flex: 1 1 auto;
+  box-shadow: 0 2px 12px 0 rgba(0, 0, 0, 0.06);
+  border: solid 1px #e4e7ed;
+  background-color: #ffffff;
+  overflow-y: scroll;
+  scrollbar-width: thin;
+}
+
+.content :deep(.el-loading-spinner .path) {
+  stroke: $app-primary-color;
+}
+
+.content :deep(.step-item:first-child .seperator-path) {
+  display: none;
+}
+
+.content :deep(.step-item:not(:first-child) .seperator-path) {
+  width: 455px;
+  height: 0px;
+  border: solid 1px #e4e7ed;
+  background-color: #e4e7ed;
+}
+
+.scrollbar::-webkit-scrollbar-track {
+  border-radius: 10px;
+  background-color: #f5f5f5;
+}
+
+.scrollbar::-webkit-scrollbar {
+  width: 12px;
+  right: -12px;
+  background-color: #f5f5f5;
+}
+
+.scrollbar::-webkit-scrollbar-thumb {
+  border-radius: 4px;
+  box-shadow: 0 2px 4px 0 rgba(0, 0, 0, 0.06);
+  background-color: #979797;
+}
+
+:deep(.el-input__suffix) {
+  padding-right: 0px;
+}
+
+:deep(.my-drawer) {
+  background: rgba(0, 0, 0, 0);
+  box-shadow: none;
+}
+</style>