@abi-software/flatmapvuer 1.1.4 → 1.2.0-beta.1

package/src/components/AnnotationTool.vue

@@ -1,501 +0,0 @@
-<template>
-  <el-main class="main">
-    <div class="block">
-      <el-row class="info-field">
-        <div class="title">Feature Annotations</div>
-      </el-row>
-      <template v-if="annotationEntry">
-        <el-row
-          v-for="(key, label) in displayPair"
-          v-show="annotationEntry[key]"
-          class="dialog-text"
-          :key="key"
-        >
-          <strong>{{ label }}: </strong>&nbsp;{{ annotationEntry[key] }}
-        </el-row>
-        <template v-if="prevSubs.length > 0">
-          <div
-            v-show="showSubmissions"
-            class="hide"
-            @click="showSubmissions = false"
-          >
-            Hide previous submissions
-            <el-icon><el-icon-arrow-up /></el-icon>
-          </div>
-          <div
-            v-show="!showSubmissions"
-            class="hide"
-            @click="showSubmissions = true"
-          >
-            Show previous {{ prevSubs.length }} submission(s)
-            <el-icon><el-icon-arrow-down /></el-icon>
-          </div>
-          <template v-if="showSubmissions">
-            <el-row class="dialog-spacer"></el-row>
-            <el-row class="dialog-text">
-              <strong class="sub-title">Previous submissions:</strong>
-            </el-row>
-            <div class="entry" v-for="(sub, index) in prevSubs" :key="index">
-              <el-row class="dialog-text">
-                <strong>{{ formatTime(sub.created) }}</strong>
-                {{ sub.creator.name }}
-              </el-row>
-              <el-row class="dialog-text">
-                <strong>Evidence: </strong>
-                <el-row
-                  v-for="evidence in sub.body.evidence"
-                  :key="evidence"
-                  class="dialog-text"
-                >
-                  <a :href="evidence" target="_blank"> {{ evidence }}</a>
-                </el-row>
-              </el-row>
-              <el-row class="dialog-text">
-                <strong>Comment: </strong> {{ sub.body.comment }}
-              </el-row>
-            </div>
-          </template>
-        </template>
-        <template v-if="authenticated">
-          <template v-if="isEditable">
-            <el-row class="dialog-spacer"></el-row>
-            <el-row v-if="!editing">
-              <el-icon class="standard-icon">
-                <el-icon-edit @click="editing = true" />
-              </el-icon>
-              <el-icon
-                class="standard-icon"
-                v-if="isDeleted"
-              >
-                <el-icon-delete @click="submit"/>
-              </el-icon>
-              <el-icon
-                class="standard-icon"
-                v-else-if="isPositionUpdated"
-              >
-                <el-icon-finished @click="submit" />
-              </el-icon>
-            </el-row>
-            <template v-else>
-              <el-row class="dialog-text">
-                <strong class="sub-title">Suggest changes:</strong>
-              </el-row>
-              <template v-if="!isDeleted">
-                <el-row class="dialog-text">
-                  <strong>Evidence:</strong>
-                </el-row>
-                <el-row v-for="(value, index) in evidence" :key="value">
-                  <el-col :span="20">
-                    {{ evidence[index] }}
-                  </el-col>
-                  <el-col :span="4">
-                    <el-icon class="standard-icon">
-                      <el-icon-close @click="removeEvidence(index)" />
-                    </el-icon>
-                  </el-col>
-                </el-row>
-                <el-row>
-                  <el-input
-                    size="small"
-                    placeholder="Enter"
-                    v-model="newEvidence"
-                    @change="evidenceEntered($event)"
-                  >
-                    <template #prepend>
-                      <el-select
-                        :teleported="false"
-                        v-model="evidencePrefix"
-                        placeholder="Select"
-                        class="select-box"
-                        popper-class="flatmap_dropdown"
-                      >
-                        <el-option
-                          v-for="item in evidencePrefixes"
-                          :key="item"
-                          :label="item"
-                          :value="item"
-                        >
-                          <el-row>
-                            <el-col :span="12">{{ item }}</el-col>
-                          </el-row>
-                        </el-option>
-                      </el-select>
-                    </template>
-                  </el-input>
-                </el-row>
-              </template>
-              <el-row>
-                <strong>Comment:</strong>
-              </el-row>
-              <el-row class="dialog-text">
-                <el-input
-                  type="textarea"
-                  :autosize="{ minRows: 2, maxRows: 4 }"
-                  placeholder="Enter"
-                  v-model="comment"
-                />
-              </el-row>
-              <el-row class="dialog-text">
-                <el-button class="button" type="primary" plain @click="submit">
-                  Submit
-                </el-button>
-              </el-row>
-            </template>
-            <el-row class="dialog-text" v-if="errorMessage">
-              <strong class="sub-title"> {{ errorMessage }} </strong>
-            </el-row>
-          </template>
-        </template>
-      </template>
-    </div>
-  </el-main>
-</template>
-
-<script>
-import {
-  ArrowUp as ElIconArrowUp,
-  ArrowDown as ElIconArrowDown,
-  Edit as ElIconEdit,
-  Close as ElIconClose,
-  Delete as ElIconDelete,
-  Finished as ElIconFinished,
-} from '@element-plus/icons-vue'
-/* eslint-disable no-alert, no-console */
-import {
-  ElButton as Button,
-  ElCol as Col,
-  ElInput as Input,
-  ElMain as Main,
-  ElRow as Row,
-  ElSelect as Select,
-} from 'element-plus'
-
-export default {
-  name: 'AnnotationTool',
-  components: {
-    Button,
-    Col,
-    Input,
-    Main,
-    Row,
-    Select,
-    ElIconArrowUp,
-    ElIconArrowDown,
-    ElIconEdit,
-    ElIconClose,
-  },
-  props: {
-    annotationEntry: {
-      type: Object,
-    },
-  },
-  inject: ['flatmapAPI', '$annotator', 'userApiKey'],
-  data: function () {
-    return {
-      displayPair: {
-        'Feature ID': 'featureId',
-        Tooltip: 'label',
-        Models: 'models',
-        Name: 'name',
-        Resource: 'resourceId',
-      },
-      editing: false,
-      evidencePrefixes: ['DOI:', 'PMID:'],
-      evidencePrefix: 'DOI:',
-      evidence: [],
-      authenticated: false,
-      newEvidence: '',
-      comment: '',
-      prevSubs: [],
-      showSubmissions: true,
-      errorMessage: '',
-      creator: undefined
-    }
-  },
-  computed: {
-    isEditable: function () {
-      return (
-        this.annotationEntry['resourceId'] &&
-        this.annotationEntry['featureId']
-      )
-    },
-    isPositionUpdated: function () {
-      return (
-        this.annotationEntry['resourceId'] &&
-        this.annotationEntry['type'] === 'updated' &&
-        this.annotationEntry['positionUpdated']
-      )
-    },
-    isDeleted: function () {
-      return (
-        this.annotationEntry['resourceId'] &&
-        this.annotationEntry['type'] === 'deleted'
-      )
-    }
-  },
-  methods: {
-    evidenceEntered: function (value) {
-      if (value) {
-        this.evidence.push(this.evidencePrefix + value)
-        this.newEvidence = ''
-      }
-    },
-    formatTime: function (dateString) {
-      const options = {
-        year: 'numeric',
-        month: 'long',
-        day: 'numeric',
-        hour: 'numeric',
-        minute: 'numeric',
-        second: 'numeric',
-      }
-      return new Date(dateString).toLocaleDateString(undefined, options)
-    },
-    updatePrevSubmissions: function () {
-      if (this.$annotator && this.authenticated) {
-        if (
-          this.annotationEntry['resourceId'] &&
-          this.annotationEntry['featureId']
-        ) {
-          this.$annotator
-            .itemAnnotations(
-              this.userApiKey,
-              this.annotationEntry['resourceId'],
-              this.annotationEntry['featureId']
-            )
-            .then((value) => {
-              this.prevSubs = value
-            })
-            .catch((reason) => {
-              console.log(reason) // Error!
-            })
-        }
-      }
-    },
-    submit: function () {
-      // User can either update/delete annotation directly 
-      // or provide extra comments for update/delete action
-      if (
-        this.annotationEntry['type'] === 'updated' &&
-        this.annotationEntry['positionUpdated']
-      ) {
-        this.comment = this.comment ?
-          `Position Updated: ${this.comment}` :
-          'Position Updated'
-      } else if (this.annotationEntry['type'] === 'deleted') {
-        this.comment = this.comment ?
-          `Feature Deleted: ${this.comment}` :
-          'Feature Deleted'
-      }
-
-      if (this.evidence.length > 0 || this.comment) {
-        if (
-          this.annotationEntry['resourceId'] &&
-          this.annotationEntry['featureId']
-        ) {
-          const evidenceURLs = []
-          this.evidence.forEach((evidence) => {
-            if (evidence.includes('DOI:')) {
-              const link = evidence.replace('DOI:', 'https://doi.org/')
-              evidenceURLs.push(new URL(link))
-            } else if (evidence.includes('PMID:')) {
-              const link = evidence.replace(
-                'PMID:',
-                'https://pubmed.ncbi.nlm.nih.gov/'
-              )
-              evidenceURLs.push(new URL(link))
-            }
-          })
-          const userAnnotation = {
-            resource: this.annotationEntry['resourceId'],
-            item: Object.assign({id: this.annotationEntry['featureId']},
-                    Object.fromEntries(
-                      Object.entries(this.annotationEntry)
-                            .filter(([key]) => ['label', 'models'].includes(key)))),
-            body: {
-              evidence: evidenceURLs,
-              comment: this.comment,
-            },
-            feature: this.annotationEntry['feature']
-          }
-          Object.assign(userAnnotation.body, this.annotationEntry['body'])
-          if (this.annotationEntry['type'] === 'deleted') {
-            userAnnotation.feature = undefined
-          }
-          if (this.creator) userAnnotation.creator = this.creator
-          this.$annotator
-            .addAnnotation(this.userApiKey, userAnnotation)
-            .then(() => {
-              this.$emit('annotation', userAnnotation)
-              this.errorMessage = ''
-              this.resetSubmission()
-              this.updatePrevSubmissions()
-            })
-            .catch(() => {
-              this.errorMessage =
-                'There is a problem with the submission, please try again later'
-            })
-        }
-      }
-    },
-    removeEvidence: function (index) {
-      this.evidence.splice(index, 1)
-    },
-    resetSubmission: function () {
-      this.editing = false
-      this.evidence = []
-      this.newFeature = ''
-      this.comment = ''
-    },
-  },
-  watch: {
-    annotationEntry: {
-      handler: function (newVal, oldVal) {
-        if (newVal !== oldVal) {
-          this.resetSubmission()
-          this.updatePrevSubmissions()
-        }
-      },
-      immediate: false,
-      deep: false,
-    },
-  },
-  mounted: function () {
-    this.$annotator.authenticate(this.userApiKey).then((userData) => {
-      if (userData.name && userData.email) {
-        this.creator = userData
-        if (!userData.orcid) this.creator.orcid = '0000-0000-0000-0000'
-        this.authenticated = true
-        this.updatePrevSubmissions()
-      } else {
-        this.errorMessage = ''
-      }
-    })
-  },
-}
-</script>
-
-<style lang="scss" scoped>
-
-.info-field {
-  display: flex;
-}
-
-.block {
-  margin-bottom: 0.5em;
-
-  .main > &:first-of-type {
-    margin-right: 0.5em;
-  }
-}
-
-.button {
-  padding-top: 5px;
-  padding-bottom: 5px;
-}
-
-.standard-icon {
-  color: $app-primary-color;
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-.dialog-text {
-  color: rgb(48, 49, 51);
-  font-size: 14px;
-  font-weight: normal;
-  line-height: 20px;
-}
-
-.main {
-  font-size: 14px;
-  text-align: left;
-  line-height: 1.5em;
-  font-family: Asap, sans-serif, Helvetica;
-  font-weight: 400;
-  /* outline: thin red solid; */
-  padding: 1em !important;
-  overflow-x: hidden;
-  overflow-y: auto;
-  min-width: 300px; // .maplibregl-popup max-width
-  max-height: 400px;
-  scrollbar-width: thin;
-
-  &::-webkit-scrollbar {
-    width: 4px;
-  }
-
-  &::-webkit-scrollbar-thumb {
-    border-radius: 10px;
-    box-shadow: inset 0 0 6px #c0c4cc;
-  }
-}
-
-.title {
-  font-size: 18px;
-  font-weight: 500;
-  font-weight: bold;
-  padding-bottom: 8px;
-  color: rgb(131, 0, 191);
-}
-
-.sub-title {
-  font-size: 16px;
-}
-
-.dialog-spacer {
-  border-bottom: 1px solid #e4e7ed;
-  margin-bottom: 10px;
-}
-
-.submit {
-  color: $app-primary-color;
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-.entry ~ .entry {
-  border-top: 1px solid #e4e7ed;
-  margin-top: 10px;
-}
-
-.hide {
-  color: $app-primary-color;
-  cursor: pointer;
-  margin-right: 6px;
-  margin-top: 3px;
-}
-
-:deep(.el-input__inner),
-:deep(.el-textarea__inner) {
-  font-family: Asap, sans-serif;
-}
-
-.select-box {
-  width: 80px;
-  background-color: var(--white);
-  font-weight: 500;
-  color: rgb(48, 49, 51);
-  :deep(.el-input__inner) {
-    height: 30px;
-    color: rgb(48, 49, 51);
-  }
-  :deep(.el-input__icon) {
-    line-height: 30px;
-  }
-}
-
-:deep(.flatmap_dropdown) {
-  min-width: 80px !important;
-  .el-select-dropdown__item {
-    white-space: nowrap;
-    text-align: left;
-    &.selected {
-      color: $app-primary-color;
-      font-weight: normal;
-    }
-  }
-}
-</style>

package/src/components/ConnectionDialog.vue

@@ -1,134 +0,0 @@
-<template>
-  <div class="dialog-container">
-    <el-row>
-      <el-col>
-        <span class="dialog-title">Visualise connection</span>
-        <el-row v-if="inDrawing">
-          <span class="dialog-subtitle">Finalise drawing</span>
-          <el-button-group>
-            <el-button
-              type="primary"
-              plain
-              @click="$emit('confirmDrawn', true)"
-            >
-              Confirm
-            </el-button>
-            <el-button type="primary" plain @click="$emit('cancelDrawn', true)">
-              Cancel
-            </el-button>
-          </el-button-group>
-        </el-row>
-        <el-row v-else>
-          <el-button
-            type="primary"
-            plain
-            @click="$emit('dialogDisplay', false)"
-          >
-            Close
-          </el-button>
-        </el-row>
-      </el-col>
-    </el-row>
-    <el-row v-if="hasConnection">
-      <el-col>
-        <b><span>Related Features</span></b>
-        <el-row v-for="(value, key) in connectionEntry" :key="key">
-          <el-card :shadow="shadowDisplay(key)" @click="handleTooltip(key)">
-            <span>{{ capitalise(value.label) }}</span>
-          </el-card>
-        </el-row>
-      </el-col>
-    </el-row>
-  </div>
-</template>
-
-<script>
-/* eslint-disable no-alert, no-console */
-import {
-  ElRow as Row,
-  ElCol as Col,
-  ElCard as Card,
-  ElButton as Button,
-  ElButtonGroup as ButtonGroup,
-} from "element-plus";
-
-export default {
-  name: "ConnectionDialog",
-  components: {
-    Row,
-    Col,
-    ButtonGroup,
-    Button,
-    Card,
-  },
-  props: {
-    connectionEntry: {
-      type: Object,
-    },
-    inDrawing: {
-      type: Boolean,
-      default: false,
-    },
-    hasConnection: {
-      type: Boolean,
-      default: false,
-    },
-  },
-  data: function () {
-    return {
-      tooltipId: undefined,
-    };
-  },
-  methods: {
-    shadowDisplay: function (value) {
-      return this.tooltipId === value ? "always" : "hover";
-    },
-    capitalise: function (label) {
-      return label[0].toUpperCase() + label.slice(1);
-    },
-    handleTooltip: function (value) {
-      this.tooltipId = this.tooltipId === value ? undefined : value;
-      this.$emit("featureTooltip", this.tooltipId);
-    },
-  },
-};
-</script>
-
-<style lang="scss" scoped>
-.dialog-container {
-  width: 200px;
-  height: fit-content;
-  text-align: justify;
-  border-radius: 4px;
-  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
-  pointer-events: auto;
-  background: #fff;
-  border: 1px solid $app-primary-color;
-  display: flex;
-  flex-direction: column;
-  padding: 0.8em;
-}
-
-.dialog-title {
-  font-size: 18px;
-  font-weight: bold;
-  color: rgb(131, 0, 191);
-}
-
-.dialog-subtitle {
-  margin-top: 5px;
-  font-size: 15px;
-  color: rgb(131, 0, 191);
-}
-
-.el-button {
-  margin: 5px 0px;
-}
-
-:deep(.el-card) {
-  width: 100%;
-  --el-card-padding: 8px;
-  border: 0;
-  cursor: pointer;
-}
-</style>