-
Notifications
You must be signed in to change notification settings - Fork 22
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Started Project VCF functionality * Sample mapping CRUD and ui * Added vcfs table and some CRUD * Added permissions tab * Added import vcf and finetuned permissions * Started export functionality and UI * Bugfix mapping/export dialogs * Added mapping for export and some TRs * Completed the VCF export and functionality * Added french TR and minor ui fix * Removed old interface --------- Co-authored-by: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>
- Loading branch information
Showing
14 changed files
with
1,327 additions
and
34 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
281 changes: 281 additions & 0 deletions
281
opal-ui/src/components/project/AddVcfMappingTableDialog.vue
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,281 @@ | ||
| <template> | ||
| <template> | ||
| <q-dialog v-model="showDialog" persistent @hide="onHide"> | ||
| <q-card class="dialog-sm"> | ||
| <q-card-section> | ||
| <div class="text-h6">{{ dialogTitle }}</div> | ||
| </q-card-section> | ||
|
|
||
| <q-separator /> | ||
|
|
||
| <q-card-section v-if="tables.length < 1"> | ||
| <q-banner inline-actions rounded class="bg-orange text-white">{{ | ||
| $t('vcf_store.no_mapping_tables') | ||
| }}</q-banner> | ||
| </q-card-section> | ||
|
|
||
| <q-card-section v-else> | ||
| <q-select | ||
| v-model="selectedTable" | ||
| :options="filterOptions" | ||
| :label="$t('table')" | ||
| :hint="$t('vcf_store.mapping_table_hint')" | ||
| class="q-mb-md" | ||
| dense | ||
| emit-value | ||
| map-options | ||
| use-input | ||
| use-chips | ||
| hide-selection | ||
| input-debounce="0" | ||
| @update:model-value="onSelectTable" | ||
| @filter="onFilterFn" | ||
| > | ||
| <template v-slot:option="scope"> | ||
| <q-item v-show="!!!scope.opt.value" class="text-help" dense clickable disable :label="scope.opt.group"> | ||
| <q-item-section class="q-pa-none"> | ||
| {{ scope.opt.label }} | ||
| </q-item-section> | ||
| </q-item> | ||
| <q-item v-show="!!scope.opt.value" dense clickable v-close-popup @click="onSelectTable(scope.opt.value)"> | ||
| <q-item-section class="q-pl-md"> | ||
| {{ scope.opt.label }} | ||
| </q-item-section> | ||
| </q-item> | ||
| </template> | ||
| </q-select> | ||
|
|
||
| <q-select | ||
| v-model="selectedParticipantIdVariable" | ||
| dense | ||
| class="q-mb-md" | ||
| :label="$t('vcf_store.participant_id')" | ||
| :hint="$t('vcf_store.participant_id_hint')" | ||
| :options="participantIdOptions" | ||
| emit-value | ||
| map-options | ||
| @update:model-value="newMapping.participantIdVariable = $event.name" | ||
| /> | ||
|
|
||
| <q-select | ||
| v-model="selectedRoleVariable" | ||
| dense | ||
| class="q-mb-md" | ||
| :label="$t('vcf_store.participant_id')" | ||
| :hint="$t('vcf_store.participant_id_hint')" | ||
| :options="roleOptions" | ||
| emit-value | ||
| map-options | ||
| @update:model-value="newMapping.sampleRoleVariable = $event.name" | ||
| /> | ||
| </q-card-section> | ||
|
|
||
| <q-separator /> | ||
|
|
||
| <q-card-actions align="right" class="bg-grey-3"> | ||
| <q-btn flat :label="$t('cancel')" color="secondary" v-close-popup /> | ||
| <q-btn flat :label="submitCaption" color="primary" :disable="!canAdd" @click="onAdd" v-close-popup /> | ||
| </q-card-actions> | ||
| </q-card> | ||
| </q-dialog> | ||
| </template> | ||
| </template> | ||
|
|
||
| <script lang="ts"> | ||
| export default defineComponent({ | ||
| name: 'AddVcfMappingTableDialog', | ||
| }); | ||
| </script> | ||
|
|
||
| <script setup lang="ts"> | ||
| import { VCFSamplesMappingDto } from 'src/models/Plugins'; | ||
| import { TableDto, VariableDto, CategoryDto } from 'src/models/Magma'; | ||
| import { notifyError } from 'src/utils/notify'; | ||
| interface DialogProps { | ||
| modelValue: boolean; | ||
| project: string; | ||
| mapping?: VCFSamplesMappingDto; | ||
| } | ||
| type SelectOption = { label: string; value: TableDto | undefined }; | ||
| const props = defineProps<DialogProps>(); | ||
| const emit = defineEmits(['update:modelValue', 'update']); | ||
| const projectsStore = useProjectsStore(); | ||
| const datasourceStore = useDatasourceStore(); | ||
| const tables = ref([] as TableDto[]); | ||
| const { t } = useI18n(); | ||
| const showDialog = ref(props.modelValue); | ||
| const newMapping = ref({} as VCFSamplesMappingDto); | ||
| const selectedTable = ref<TableDto | null>(null); | ||
| const selectedParticipantIdVariable = ref<VariableDto | null>(null); | ||
| const selectedRoleVariable = ref<VariableDto | null>(null); | ||
| let mappingOptions = [] as SelectOption[]; | ||
| const filterOptions = ref([] as SelectOption[]); | ||
| const participantIdOptions = ref([] as { label: string; value: VariableDto }[]); | ||
| const roleOptions = ref([] as { label: string; value: VariableDto }[]); | ||
| const editMode = computed(() => !!props.mapping && !!props.mapping.projectName); | ||
| const submitCaption = computed(() => (editMode.value ? t('update') : t('add'))); | ||
| const dialogTitle = computed(() => (editMode.value ? t('vcf_store.edit_mapping') : t('vcf_store.add_mapping'))); | ||
| const canAdd = computed(() => !!selectedTable.value && !!selectedParticipantIdVariable.value && !!selectedRoleVariable.value); | ||
| function initMappingOptions() { | ||
| if (tables.value.length > 0) { | ||
| let lastGroup = ''; | ||
| tables.value.forEach((table) => { | ||
| const tableRef = `${table.datasourceName}.${table.name}`; | ||
| if (!!!selectedTable.value && newMapping.value.tableReference === tableRef) { | ||
| selectedTable.value = table; | ||
| } | ||
| if (!!table.datasourceName && table.datasourceName !== lastGroup) { | ||
| lastGroup = table.datasourceName; | ||
| mappingOptions.push({ label: lastGroup } as SelectOption); | ||
| } | ||
| mappingOptions.push({ label: table.name, value: table }); | ||
| }); | ||
| filterOptions.value = [...mappingOptions]; | ||
| if (!!selectedTable.value) { | ||
| getVariables(); | ||
| } | ||
| } | ||
| } | ||
| function initializeVariableOptions(variables: VariableDto[]) { | ||
| let roleVariableSuggestion: VariableDto | undefined = undefined; | ||
| let participantIdVariableSuggestion: VariableDto | undefined = undefined; | ||
| roleOptions.value = []; | ||
| participantIdOptions.value = []; | ||
| (variables || []).forEach((variable) => { | ||
| const variableName = variable.name; | ||
| let roleCategory = null; | ||
| const categories: CategoryDto[] = variable.categories || []; | ||
| if (!!!roleVariableSuggestion) { | ||
| if (categories.length > 0) { | ||
| roleCategory = categories.find((category: CategoryDto) => { | ||
| const categoryName = category.name.toLowerCase(); | ||
| return ['control', 'sample'].includes(categoryName); | ||
| }); | ||
| } | ||
| if (!!newMapping.value.sampleRoleVariable) { | ||
| if (variableName === newMapping.value.sampleRoleVariable) { | ||
| roleVariableSuggestion = variable; | ||
| } | ||
| } else if (!!roleCategory || variableName.match(/role/i) != null) { | ||
| roleVariableSuggestion = variable; | ||
| } | ||
| } | ||
| if (!!!participantIdVariableSuggestion ) { | ||
| if (!!newMapping.value.participantIdVariable) { | ||
| if (variableName === newMapping.value.participantIdVariable) { | ||
| participantIdVariableSuggestion = variable; | ||
| } | ||
| } | ||
| else if (variableName.match(/participant/i) != null) { | ||
| participantIdVariableSuggestion = variable; | ||
| } | ||
| } | ||
| roleOptions.value.push({ label: variableName, value: variable }); | ||
| participantIdOptions.value.push({ label: variableName, value: variable }); | ||
| }); | ||
| if (!!participantIdVariableSuggestion) { | ||
| selectedParticipantIdVariable.value = participantIdVariableSuggestion; | ||
| newMapping.value.participantIdVariable = participantIdVariableSuggestion.name; | ||
| } | ||
| if (!!roleVariableSuggestion) { | ||
| selectedRoleVariable.value = roleVariableSuggestion; | ||
| newMapping.value.sampleRoleVariable = roleVariableSuggestion.name; | ||
| } | ||
| } | ||
| async function getVariables() { | ||
| if (selectedTable.value && selectedTable.value.datasourceName && selectedTable.value.name) { | ||
| datasourceStore | ||
| .getTableVariables(selectedTable.value.datasourceName, selectedTable.value.name) | ||
| .then((variables) => { | ||
| initializeVariableOptions(variables); | ||
| }); | ||
| } | ||
| } | ||
| // eslint-disable-next-line @typescript-eslint/no-explicit-any | ||
| function onFilterFn(val: string, update: any) { | ||
| update(() => { | ||
| if (val.trim().length === 0) { | ||
| filterOptions.value = [...mappingOptions]; | ||
| } else { | ||
| const needle = val.toLowerCase(); | ||
| filterOptions.value = [ | ||
| ...mappingOptions.filter((v: SelectOption) => 'label' in v && v.label.toLowerCase().indexOf(needle) > -1), | ||
| ]; | ||
| } | ||
| }); | ||
| } | ||
| // Handlers | ||
| watch( | ||
| () => props.modelValue, | ||
| (value) => { | ||
| if (value) { | ||
| datasourceStore.getAllTables('Sample').then((response) => { | ||
| tables.value = response; | ||
| if (props.mapping && props.mapping.projectName) { | ||
| newMapping.value = { ...props.mapping }; | ||
| } else { | ||
| newMapping.value = { projectName: props.project } as VCFSamplesMappingDto; | ||
| } | ||
| initMappingOptions(); | ||
| }); | ||
| showDialog.value = true; | ||
| } | ||
| } | ||
| ); | ||
| function onSelectTable(table: TableDto | null) { | ||
| selectedTable.value = table; | ||
| if (!!table) { | ||
| newMapping.value.tableReference = `${table.datasourceName}.${table.name}`; | ||
| getVariables(); | ||
| } else { | ||
| selectedParticipantIdVariable.value = null; | ||
| selectedRoleVariable.value = null; | ||
| participantIdOptions.value = []; | ||
| roleOptions.value = []; | ||
| } | ||
| } | ||
| function onHide() { | ||
| mappingOptions = []; | ||
| newMapping.value = {} as VCFSamplesMappingDto; | ||
| selectedTable.value = null; | ||
| selectedParticipantIdVariable.value = null; | ||
| selectedRoleVariable.value = null; | ||
| filterOptions.value = []; | ||
| roleOptions.value = []; | ||
| participantIdOptions.value = []; | ||
| emit('update:modelValue', false); | ||
| } | ||
| async function onAdd() { | ||
| try { | ||
| await projectsStore.addVcfSamplesMapping(props.project, newMapping.value); | ||
| emit('update'); | ||
| onHide(); | ||
| } catch (error) { | ||
| notifyError(error); | ||
| } | ||
| } | ||
| </script> |
Oops, something went wrong.