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feat(fastani): Re-enable FastANI calculator.
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
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| // The row used when displaying the genomes selected for query / reference | ||
| export interface FastAniQueryRow { | ||
| name: string, | ||
| isRep: boolean | null, | ||
| domain: string | null, | ||
| phylum: string | null, | ||
| class: string | null, | ||
| order: string | null, | ||
| family: string | null, | ||
| genus: string | null, | ||
| species: string | null | ||
| } | ||
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| export enum FastAniInputGroup { | ||
| query, | ||
| reference, | ||
| both | ||
| } | ||
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| export interface FastAniAddGenomesFromUserInput { | ||
| genomes: FastAniQueryRow[], | ||
| group: FastAniInputGroup | ||
| } |
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| <template> | ||
| <v-dialog | ||
| v-model="modalVisible" | ||
| width="700" | ||
| > | ||
| <template v-slot:activator="{ on, attrs }"> | ||
| <v-btn | ||
| class="white--text" | ||
| color="#5a6855" | ||
| depressed | ||
| small | ||
| v-bind="attrs" | ||
| @click="onAddGenomesFromTaxonClick" | ||
| v-on="on" | ||
| > | ||
| <v-icon left> | ||
| {{ addGenomesSvg }} | ||
| </v-icon> | ||
| Add genomes from taxon | ||
| </v-btn> | ||
| </template> | ||
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| <v-card> | ||
| <v-card-title class="text-h5 white--text" style="background-color: #5a6855"> | ||
| <v-icon dark left> | ||
| {{ addGenomesSvg }} | ||
| </v-icon> | ||
| Add genomes from taxon | ||
| </v-card-title> | ||
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| <v-card-text class="py-1"> | ||
| <v-row no-gutters> | ||
| <TaxonSearchAutocomplete | ||
| v-model="selectedTaxon" | ||
| :disabled="formDisabled" | ||
| class="ml-2 mt-3" | ||
| label="Taxon" | ||
| /> | ||
| </v-row> | ||
| <v-row class="mt-2" no-gutters> | ||
| <v-select | ||
| v-model="selectedGroup" | ||
| :items="groupOptions" | ||
| class="ml-2 mt-3" | ||
| clearable | ||
| dense | ||
| hide-details | ||
| label="Add genomes to" | ||
| outlined | ||
| > | ||
| </v-select> | ||
| </v-row> | ||
| <v-row no-gutters> | ||
| <v-checkbox | ||
| v-model="spReps" | ||
| :disabled="formDisabled" | ||
| class="ml-2" | ||
| label="Only include species representatives" | ||
| ></v-checkbox> | ||
| </v-row> | ||
| </v-card-text> | ||
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| <v-divider></v-divider> | ||
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| <v-card-actions> | ||
| <v-chip> | ||
| <template v-if="getTaxonSearching"> | ||
| Loading... | ||
| </template> | ||
| <template v-else> | ||
| {{ nGenomesInTaxon }} genomes to add | ||
| </template> | ||
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| </v-chip> | ||
| <v-spacer></v-spacer> | ||
| <v-btn | ||
| :disabled="formDisabled" | ||
| color="primary" | ||
| text | ||
| @click="emitGenomeIds" | ||
| > | ||
| Save | ||
| </v-btn> | ||
| <v-btn | ||
| color="primary" | ||
| text | ||
| @click="modalVisible = false" | ||
| > | ||
| Close | ||
| </v-btn> | ||
| </v-card-actions> | ||
| </v-card> | ||
| </v-dialog> | ||
| </template> | ||
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| <script lang="ts"> | ||
| import Vue from "vue"; | ||
| import TaxonSearchAutocomplete from "~/components/shared/TaxonSearchAutocomplete.vue"; | ||
| import {mdiPlusThick} from "@mdi/js"; | ||
| import {isDefined, maybeToLocaleString} from "~/assets/ts/common"; | ||
| import {FastAniAddGenomesFromUserInput, FastAniInputGroup, FastAniQueryRow} from "~/assets/models/fastani"; | ||
| import {TaxonGenomesDetailRow} from "~/assets/api/taxon"; | ||
| export default Vue.extend({ | ||
| components: {TaxonSearchAutocomplete}, | ||
| data: () => ({ | ||
| // Icons | ||
| addGenomesSvg: mdiPlusThick, | ||
| // Modal data | ||
| modalVisible: false, | ||
| // Form data | ||
| groupOptions: ['Query genomes', 'Reference genomes', 'Query & Reference genomes'], | ||
| selectedTaxon: '', | ||
| selectedGroup: 'Query genomes', | ||
| spReps: true, | ||
| // API calls | ||
| getTaxonSearching: false, | ||
| // API return data | ||
| apiSearchResult: [] as FastAniQueryRow[], | ||
| }), | ||
| watch: { | ||
| // If the taxon changes, we need to load those genomes | ||
| selectedTaxon(after: string, before: string) { | ||
| if (after && after.length > 0 && after != before) { | ||
| this.getGenomesFromTaxon(); | ||
| } | ||
| }, | ||
| // If the user toggles the species representatives checkbox, we need to reload the genomes | ||
| spReps(after: boolean, before: boolean) { | ||
| if (after !== before && this.selectedTaxon.length > 3) { | ||
| this.getGenomesFromTaxon(); | ||
| } | ||
| }, | ||
| }, | ||
| computed: { | ||
| nGenomesInTaxon(): string { | ||
| return maybeToLocaleString(this.apiSearchResult.length) as string; | ||
| }, | ||
| formDisabled(): boolean { | ||
| return this.getTaxonSearching; | ||
| }, | ||
| selectedGroupAsEnum(): FastAniInputGroup { | ||
| if (this.selectedGroup === 'Query genomes') { | ||
| return FastAniInputGroup.query; | ||
| } else if (this.selectedGroup === 'Reference genomes') { | ||
| return FastAniInputGroup.reference; | ||
| } else { | ||
| return FastAniInputGroup.both; | ||
| } | ||
| } | ||
| }, | ||
| methods: { | ||
| // Emit the chosen genome ids to the parent | ||
| emitGenomeIds() { | ||
| const output = { | ||
| genomes: this.apiSearchResult, | ||
| group: this.selectedGroupAsEnum, | ||
| } as FastAniAddGenomesFromUserInput; | ||
| this.$emit('input', output); | ||
| this.modalVisible = false; | ||
| }, | ||
| // Load the genomes associated with a taxon | ||
| getGenomesFromTaxon() { | ||
| if (isDefined(this.selectedTaxon) && this.selectedTaxon.length > 3) { | ||
| // Register the start of the search | ||
| this.getTaxonSearching = true; | ||
| // Make the API call | ||
| this.$api.taxon.getTaxonGenomesDetail(this.selectedTaxon, this.spReps).then(resp => { | ||
| const out: FastAniQueryRow[] = []; | ||
| for (let i = 0; i < resp.data.rows.length; i++) { | ||
| const curItem:TaxonGenomesDetailRow = resp.data.rows[i]; | ||
| out.push({ | ||
| name: curItem.gid, | ||
| isRep: curItem.gtdbIsRep, | ||
| domain: curItem.gtdbDomain, | ||
| phylum: curItem.gtdbPhylum, | ||
| class: curItem.gtdbClass, | ||
| order: curItem.gtdbOrder, | ||
| family: curItem.gtdbFamily, | ||
| genus: curItem.gtdbGenus, | ||
| species: curItem.gtdbSpecies | ||
| }) | ||
| } | ||
| this.apiSearchResult = out; | ||
| }) | ||
| .catch((err) => { | ||
| this.$accessor.api.defaultCatch(err); | ||
| }) | ||
| .finally(() => { | ||
| this.getTaxonSearching = false; | ||
| }) | ||
| } | ||
| }, | ||
| // Toggle the modal open | ||
| onAddGenomesFromTaxonClick() { | ||
| this.modalVisible = !this.modalVisible; | ||
| }, | ||
| }, | ||
| }) | ||
| </script> | ||
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| <style scoped> | ||
| </style> |
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