mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #11799 from assuntad23/feature/6965/change-datatype-and-dbkey
Feature/6965/change datatype and dbkey
This commit is contained in:
Marius van den Beek
@@ -0,0 +1,124 @@
|
||||
<template>
|
||||
<div>
|
||||
<h4>{{ l("Edit Collection Attributes") }}</h4>
|
||||
<b-alert show variant="info" dismissible>
|
||||
{{ l("This will create a new collection in your History. Your quota usage will not increase.") }}
|
||||
</b-alert>
|
||||
<div v-if="jobError">
|
||||
<b-alert show variant="danger" dismissible>
|
||||
{{ errorMessage }}
|
||||
</b-alert>
|
||||
</div>
|
||||
<b-tabs content-class="mt-3">
|
||||
<b-tab>
|
||||
<template v-slot:title> <font-awesome-icon icon="table" /> {{ l("Database/Build") }}</template>
|
||||
<GenomeProvider v-slot="{ item, loading }">
|
||||
<div v-if="loading"><b-spinner label="Loading Genomes..."></b-spinner></div>
|
||||
<div v-else>
|
||||
<database-edit-tab
|
||||
v-if="item && databaseKeyFromElements"
|
||||
:database-key-from-elements="databaseKeyFromElements"
|
||||
:genomes="item"
|
||||
@clicked-save="clickedSave"
|
||||
/>
|
||||
</div>
|
||||
</GenomeProvider>
|
||||
</b-tab>
|
||||
<SuitableConvertersProvider :id="collection_id" v-slot="{ item }">
|
||||
<b-tab v-if="item && item.length">
|
||||
<template v-slot:title> <font-awesome-icon icon="cog" /> {{ l("Convert") }}</template>
|
||||
<suitable-converters-tab :suitable-converters="item" @clicked-convert="clickedConvert" />
|
||||
</b-tab>
|
||||
</SuitableConvertersProvider>
|
||||
</b-tabs>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
<script>
|
||||
import Vue from "vue";
|
||||
import BootstrapVue from "bootstrap-vue";
|
||||
import axios from "axios";
|
||||
import { prependPath } from "utils/redirect";
|
||||
import _l from "utils/localization";
|
||||
import { errorMessageAsString } from "utils/simple-error";
|
||||
import DatabaseEditTab from "./DatabaseEditTab";
|
||||
import SuitableConvertersTab from "./SuitableConvertersTab";
|
||||
import { GenomeProvider, SuitableConvertersProvider } from "../../providers";
|
||||
import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
|
||||
import { library } from "@fortawesome/fontawesome-svg-core";
|
||||
import { faDatabase, faTable, faBars, faUser, faCog } from "@fortawesome/free-solid-svg-icons";
|
||||
|
||||
library.add(faDatabase, faTable, faBars, faUser, faCog);
|
||||
|
||||
Vue.use(BootstrapVue);
|
||||
export default {
|
||||
created() {
|
||||
this.getCollectionDataAndAttributes();
|
||||
},
|
||||
components: {
|
||||
DatabaseEditTab,
|
||||
SuitableConvertersTab,
|
||||
FontAwesomeIcon,
|
||||
GenomeProvider,
|
||||
SuitableConvertersProvider,
|
||||
},
|
||||
data: function () {
|
||||
return {
|
||||
attributes_data: {},
|
||||
errorMessage: null,
|
||||
jobError: null,
|
||||
};
|
||||
},
|
||||
props: {
|
||||
collection_id: {
|
||||
type: String,
|
||||
required: true,
|
||||
},
|
||||
},
|
||||
computed: {
|
||||
databaseKeyFromElements: function () {
|
||||
return this.attributes_data.dbkey;
|
||||
},
|
||||
},
|
||||
methods: {
|
||||
l(str) {
|
||||
// _l conflicts private methods of Vue internals, expose as l instead
|
||||
return _l(str);
|
||||
},
|
||||
getCollectionDataAndAttributes: async function () {
|
||||
let attributesGet = this.$store.getters.getCollectionAttributes(this.collection_id);
|
||||
if (attributesGet == null) {
|
||||
await this.$store.dispatch("fetchCollectionAttributes", this.collection_id);
|
||||
attributesGet = this.$store.getters.getCollectionAttributes(this.collection_id);
|
||||
}
|
||||
this.attributes_data = attributesGet;
|
||||
},
|
||||
clickedSave: function (attribute, newValue) {
|
||||
const url = prependPath("/api/dataset_collections/" + this.collection_id);
|
||||
const data = {};
|
||||
if (attribute == "dbkey") {
|
||||
data["dbkey"] = newValue.id;
|
||||
} else if (attribute == "file_ext") {
|
||||
data["file_ext"] = newValue.id;
|
||||
}
|
||||
axios.put(url, data).catch(this.handleError);
|
||||
},
|
||||
clickedConvert: function (selectedConverter) {
|
||||
const url = prependPath(`/api/tools/${selectedConverter.tool_id}/convert`);
|
||||
const data = {
|
||||
src: "hdca",
|
||||
id: this.collection_id,
|
||||
source_type: selectedConverter.original_type,
|
||||
target_type: selectedConverter.target_type,
|
||||
};
|
||||
axios.post(url, data).catch(this.handleError);
|
||||
},
|
||||
handleError: function (err) {
|
||||
this.errorMessage = errorMessageAsString(err, "History import failed.");
|
||||
if (err?.data?.stderr) {
|
||||
this.jobError = err.data;
|
||||
}
|
||||
},
|
||||
},
|
||||
};
|
||||
</script>
|
||||
@@ -0,0 +1,59 @@
|
||||
<template>
|
||||
<div>
|
||||
<div class="alert alert-secondary" role="alert">
|
||||
<div class="float-left">Change Database/Build of all elements in collection</div>
|
||||
<div class="text-right">
|
||||
<button
|
||||
class="save-collection-edit btn btn-primary"
|
||||
@click="clickedSave"
|
||||
:disabled="selectedGenome.id == databaseKeyFromElements"
|
||||
>
|
||||
{{ l("Save") }}
|
||||
</button>
|
||||
</div>
|
||||
</div>
|
||||
<b>{{ l("Database/Build") }}: </b>
|
||||
<multiselect
|
||||
v-model="selectedGenome"
|
||||
deselect-label="Can't remove this value"
|
||||
track-by="id"
|
||||
label="text"
|
||||
:options="genomes"
|
||||
:searchable="true"
|
||||
:allow-empty="false"
|
||||
>
|
||||
{{ selectedGenome.text }}
|
||||
</multiselect>
|
||||
</div>
|
||||
</template>
|
||||
<script>
|
||||
import Multiselect from "vue-multiselect";
|
||||
|
||||
export default {
|
||||
created() {
|
||||
this.selectedGenome = this.genomes.find((element) => element.id == this.databaseKeyFromElements);
|
||||
},
|
||||
components: { Multiselect },
|
||||
data: function () {
|
||||
return {
|
||||
selectedGenome: {},
|
||||
};
|
||||
},
|
||||
props: {
|
||||
genomes: {
|
||||
type: Array,
|
||||
required: true,
|
||||
},
|
||||
databaseKeyFromElements: {
|
||||
type: String,
|
||||
required: true,
|
||||
},
|
||||
},
|
||||
methods: {
|
||||
clickedSave: function () {
|
||||
this.$emit("clicked-save", "dbkey", this.selectedGenome);
|
||||
this.selectedGenome = this.genomes.find((element) => element.id == this.databaseKeyFromElements);
|
||||
},
|
||||
},
|
||||
};
|
||||
</script>
|
||||
@@ -0,0 +1,51 @@
|
||||
<template>
|
||||
<div>
|
||||
<div class="alert alert-secondary" role="alert">
|
||||
<div class="float-left">Convert all datasets to new format</div>
|
||||
<div class="text-right">
|
||||
<button
|
||||
class="run-tool-collection-edit btn btn-primary"
|
||||
@click="clickedConvert"
|
||||
:disabled="selectedConverter == {}"
|
||||
>
|
||||
{{ l("Convert Collection") }}
|
||||
</button>
|
||||
</div>
|
||||
</div>
|
||||
<b>{{ l("Converter Tool: ") }}</b>
|
||||
<multiselect
|
||||
v-model="selectedConverter"
|
||||
deselect-label="Can't remove this value"
|
||||
track-by="name"
|
||||
label="name"
|
||||
:options="suitableConverters"
|
||||
:searchable="true"
|
||||
:allow-empty="true"
|
||||
>
|
||||
</multiselect>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
<script>
|
||||
import Multiselect from "vue-multiselect";
|
||||
export default {
|
||||
components: { Multiselect },
|
||||
data: function () {
|
||||
return {
|
||||
selectedConverter: {},
|
||||
};
|
||||
},
|
||||
props: {
|
||||
suitableConverters: {
|
||||
type: Array,
|
||||
required: true,
|
||||
},
|
||||
},
|
||||
methods: {
|
||||
clickedConvert: function () {
|
||||
this.$emit("clicked-convert", this.selectedConverter);
|
||||
this.selectedConverter = {};
|
||||
},
|
||||
},
|
||||
};
|
||||
</script>
|
||||
@@ -1,45 +1,87 @@
|
||||
<template>
|
||||
<b-button-group>
|
||||
<IconButton
|
||||
icon="info-circle"
|
||||
v-if="hasJob"
|
||||
key="dataset-details"
|
||||
title="View Dataset Collection Details"
|
||||
@click.stop.prevent="backboneRoute(collectionDetailsPath)"
|
||||
variant="link"
|
||||
class="px-1"
|
||||
>
|
||||
</IconButton>
|
||||
<b-dropdown right no-caret variant="link" size="sm" boundary="window" toggle-class="p-0">
|
||||
<template v-slot:button-content>
|
||||
<IconButton icon="trash" title="Delete Colletion" variant="link" class="px-1" />
|
||||
</template>
|
||||
<b-dropdown-item @click.stop="$emit('delete')">
|
||||
<span v-localize>Delete Collection Only </span>
|
||||
</b-dropdown-item>
|
||||
<b-dropdown-item @click.stop="$emit('delete', { recursive: true })">
|
||||
<span v-localize>Delete Contained Datasets</span>
|
||||
</b-dropdown-item>
|
||||
<b-dropdown-item @click.stop="$emit('delete', { recursive: true, purge: true })">
|
||||
<span v-localize>Purge Contained Datasets</span>
|
||||
</b-dropdown-item>
|
||||
</b-dropdown>
|
||||
</b-button-group>
|
||||
<div class="collection-menu">
|
||||
<b-button-group>
|
||||
<IconButton
|
||||
icon="info-circle"
|
||||
v-if="hasJob"
|
||||
key="dataset-details"
|
||||
title="View Dataset Collection Details"
|
||||
@click.stop.prevent="backboneRoute(collectionDetailsPath)"
|
||||
variant="link"
|
||||
class="px-1"
|
||||
>
|
||||
</IconButton>
|
||||
<IconButton
|
||||
v-if="notIn(STATES.DISCARDED)"
|
||||
icon="pen"
|
||||
:title="editButtonTitle"
|
||||
:disabled="dsc.deleted || isIn(STATES.UPLOAD, STATES.NEW)"
|
||||
@click.stop="backboneRoute('collection/edit/' + dsc.hdca_id)"
|
||||
variant="link"
|
||||
class="px-1 dsc-edit-view"
|
||||
/>
|
||||
<b-dropdown v-if="notIn(STATES.DISCARDED)" no-caret right variant="link" size="sm" boundary="window">
|
||||
<template v-slot:button-content>
|
||||
<Icon icon="trash" variant="link" />
|
||||
<span class="sr-only">Delete Collection</span>
|
||||
</template>
|
||||
|
||||
<b-dropdown-item @click.stop="$emit('delete')">
|
||||
<span v-localize>Delete Collection Only </span>
|
||||
</b-dropdown-item>
|
||||
|
||||
<b-dropdown-item @click.stop="$emit('delete', { recursive: true })">
|
||||
<span v-localize>Delete Contained Datasets</span>
|
||||
</b-dropdown-item>
|
||||
|
||||
<b-dropdown-item @click.stop="$emit('delete', { recursive: true, purge: true })">
|
||||
<span v-localize>Purge Contained Datasets</span>
|
||||
</b-dropdown-item>
|
||||
</b-dropdown>
|
||||
</b-button-group>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
<script>
|
||||
import { DatasetCollection } from "../../model/DatasetCollection";
|
||||
import { DatasetCollection } from "../../model";
|
||||
import { legacyNavigationMixin } from "components/plugins/legacyNavigation";
|
||||
import Vue from "vue";
|
||||
import BootstrapVue from "bootstrap-vue";
|
||||
import IconButton from "components/IconButton";
|
||||
|
||||
Vue.use(BootstrapVue);
|
||||
export default {
|
||||
mixins: [legacyNavigationMixin],
|
||||
data() {
|
||||
return {
|
||||
deleteSelected: null,
|
||||
deleteCollectionModalShow: false,
|
||||
};
|
||||
},
|
||||
components: {
|
||||
IconButton,
|
||||
},
|
||||
mixins: [legacyNavigationMixin],
|
||||
inject: ["STATES"],
|
||||
props: {
|
||||
dsc: { type: DatasetCollection, required: true },
|
||||
},
|
||||
computed: {
|
||||
editButtonTitle() {
|
||||
if (this.dsc.deleted) {
|
||||
return "Collection must not be deleted to edit";
|
||||
}
|
||||
if (this.dsc.purged) {
|
||||
return "Cannot edit attributes of collections removed from disk";
|
||||
}
|
||||
const unreadyStates = new Set([this.STATES.UPLOAD, this.STATES.NEW]);
|
||||
if (unreadyStates.has(this.dsc.state)) {
|
||||
return "This collection is not yet editable";
|
||||
}
|
||||
return "Edit attributes";
|
||||
},
|
||||
deleteCollectionButtonTitle() {
|
||||
return "Delete Collection";
|
||||
},
|
||||
hasJob() {
|
||||
return this.dsc?.job_source_type == "Job";
|
||||
},
|
||||
@@ -47,5 +89,22 @@ export default {
|
||||
return `jobs/${this.dsc.job_source_id}/view`;
|
||||
},
|
||||
},
|
||||
methods: {
|
||||
runDelete: function (kind) {
|
||||
if (kind) {
|
||||
this.$emit("delete", kind);
|
||||
} else {
|
||||
this.$emit("delete");
|
||||
}
|
||||
},
|
||||
notIn(...states) {
|
||||
const badStates = new Set(states);
|
||||
return !badStates.has(this.dsc.state);
|
||||
},
|
||||
isIn(...states) {
|
||||
const goodStates = new Set(states);
|
||||
return goodStates.has(this.dsc.state);
|
||||
},
|
||||
},
|
||||
};
|
||||
</script>
|
||||
|
||||
@@ -2,6 +2,8 @@
|
||||
export {
|
||||
// DatasetProvider,
|
||||
DatasetCollectionContentProvider,
|
||||
GenomeProvider,
|
||||
SuitableConvertersProvider,
|
||||
JobProvider,
|
||||
} from "./storeProviders";
|
||||
|
||||
|
||||
@@ -80,6 +80,38 @@ export const DatasetCollectionProvider = {
|
||||
},
|
||||
};
|
||||
|
||||
export const GenomeProvider = {
|
||||
mixins: [SimpleProviderMixin],
|
||||
async mounted() {
|
||||
await this.load();
|
||||
},
|
||||
methods: {
|
||||
...mapCacheActions(["fetchUploadGenomes"]),
|
||||
async load() {
|
||||
this.loading = true;
|
||||
let genomes = this.getUploadGenomes();
|
||||
if (genomes == null || genomes.length == 0) {
|
||||
await this.fetchUploadGenomes();
|
||||
genomes = this.getUploadGenomes();
|
||||
}
|
||||
this.item = genomes;
|
||||
this.loading = false;
|
||||
},
|
||||
},
|
||||
computed: {
|
||||
...mapGetters(["getUploadGenomes"]),
|
||||
},
|
||||
};
|
||||
|
||||
export const SuitableConvertersProvider = {
|
||||
mixins: [SimpleProviderMixin],
|
||||
computed: {
|
||||
url() {
|
||||
return prependPath(`/api/dataset_collections/${this.id}/suitable_converters`);
|
||||
},
|
||||
},
|
||||
};
|
||||
|
||||
export const DatasetCollectionContentProvider = {
|
||||
mixins: [SimpleProviderMixin],
|
||||
computed: {
|
||||
|
||||
@@ -31,6 +31,7 @@ import TrsImport from "components/Workflow/TrsImport.vue";
|
||||
import TrsSearch from "components/Workflow/TrsSearch.vue";
|
||||
import InteractiveTools from "components/InteractiveTools/InteractiveTools.vue";
|
||||
import WorkflowList from "components/Workflow/WorkflowList.vue";
|
||||
import CollectionEditView from "components/Collections/common/CollectionEditView.vue";
|
||||
import HistoryImport from "components/HistoryImport.vue";
|
||||
import { HistoryExport } from "components/HistoryExport/index";
|
||||
import HistoryView from "components/HistoryView.vue";
|
||||
@@ -98,6 +99,7 @@ export const getAnalysisRouter = (Galaxy) => {
|
||||
"(/)jobs(/)(:job_id)(/)view": "show_job",
|
||||
"(/)custom_builds": "show_custom_builds",
|
||||
"(/)datasets/edit": "show_dataset_edit_attributes",
|
||||
"(/)collection(/)edit(/)(:collection_id)": "show_collection_edit_attributes",
|
||||
"(/)datasets/error": "show_dataset_error",
|
||||
"(/)datasets(/)(:dataset_id)/details": "show_dataset_details",
|
||||
"(/)interactivetool_entry_points(/)list": "show_interactivetool_list",
|
||||
@@ -388,6 +390,10 @@ export const getAnalysisRouter = (Galaxy) => {
|
||||
}
|
||||
},
|
||||
|
||||
show_collection_edit_attributes: function (collection_id) {
|
||||
this._display_vue_helper(CollectionEditView, { collection_id: collection_id });
|
||||
},
|
||||
|
||||
show_dataset_error: function (params) {
|
||||
const datasetId = params.dataset_id;
|
||||
this._display_vue_helper(DatasetError, { datasetId: datasetId });
|
||||
|
||||
@@ -0,0 +1,32 @@
|
||||
export const state = {
|
||||
collectionAttributes: {},
|
||||
};
|
||||
import Vue from "vue";
|
||||
import { prependPath } from "utils/redirect";
|
||||
import axios from "axios";
|
||||
|
||||
const getters = {
|
||||
getCollectionAttributes: (state) => (collectionId) => {
|
||||
return state.collectionAttributes[collectionId] || null;
|
||||
},
|
||||
};
|
||||
|
||||
const actions = {
|
||||
fetchCollectionAttributes: async ({ commit }, collectionId) => {
|
||||
const { data } = await axios.get(prependPath("api/dataset_collections/" + collectionId + "/attributes"));
|
||||
commit("saveCollectionAttributes", { collectionId, collectionAttributes: data });
|
||||
},
|
||||
};
|
||||
|
||||
const mutations = {
|
||||
saveCollectionAttributes: (state, { collectionId, collectionAttributes }) => {
|
||||
Vue.set(state.collectionAttributes, collectionId, collectionAttributes);
|
||||
},
|
||||
};
|
||||
|
||||
export const collectionAttributesStore = {
|
||||
state,
|
||||
getters,
|
||||
actions,
|
||||
mutations,
|
||||
};
|
||||
@@ -0,0 +1,34 @@
|
||||
export const state = {
|
||||
uploadDatatypes: [],
|
||||
};
|
||||
import UploadUtils from "mvc/upload/upload-utils";
|
||||
|
||||
const getters = {
|
||||
getUploadDatatypes: (state) => () => {
|
||||
return state.uploadDatatypes;
|
||||
},
|
||||
};
|
||||
|
||||
const actions = {
|
||||
fetchUploadDatatypes: async ({ commit }) => {
|
||||
try {
|
||||
const data = await UploadUtils.getUploadDatatypes(false, UploadUtils.AUTO_EXTENSION);
|
||||
commit("saveUploadDatatypes", { datatypes: data });
|
||||
} catch (err) {
|
||||
console.log("Error: unable to load datatypes", err);
|
||||
}
|
||||
},
|
||||
};
|
||||
|
||||
const mutations = {
|
||||
saveUploadDatatypes: (state, { datatypes }) => {
|
||||
state.uploadDatatypes = datatypes;
|
||||
},
|
||||
};
|
||||
|
||||
export const datatypeStore = {
|
||||
state,
|
||||
getters,
|
||||
actions,
|
||||
mutations,
|
||||
};
|
||||
@@ -0,0 +1,34 @@
|
||||
export const state = {
|
||||
uploadGenomes: [],
|
||||
};
|
||||
import UploadUtils from "mvc/upload/upload-utils";
|
||||
|
||||
const getters = {
|
||||
getUploadGenomes: (state) => () => {
|
||||
return state.uploadGenomes;
|
||||
},
|
||||
};
|
||||
|
||||
const actions = {
|
||||
fetchUploadGenomes: async ({ commit }) => {
|
||||
try {
|
||||
const data = await UploadUtils.getUploadGenomes(UploadUtils.DEFAULT_GENOME);
|
||||
commit("saveUploadGenomes", { genomes: data });
|
||||
} catch (err) {
|
||||
console.log("Error: unable to load genomes", err);
|
||||
}
|
||||
},
|
||||
};
|
||||
|
||||
const mutations = {
|
||||
saveUploadGenomes: (state, { genomes }) => {
|
||||
state.uploadGenomes = genomes;
|
||||
},
|
||||
};
|
||||
|
||||
export const genomeStore = {
|
||||
state,
|
||||
getters,
|
||||
actions,
|
||||
mutations,
|
||||
};
|
||||
@@ -22,6 +22,9 @@ import { toolStore } from "./toolStore";
|
||||
import { datasetPathDestinationStore } from "./datasetPathDestinationStore";
|
||||
import { datasetExtFilesStore } from "./datasetExtFilesStore";
|
||||
import { jobStore } from "./jobStore";
|
||||
import { collectionAttributesStore } from "./collectionAttributesStore";
|
||||
import { genomeStore } from "./genomeStore";
|
||||
import { datatypeStore } from "./datatypeStore";
|
||||
import { panelStore } from "./panelStore";
|
||||
|
||||
// beta features
|
||||
@@ -57,6 +60,9 @@ export function createStore() {
|
||||
workflows: workflowStore,
|
||||
informationStore: jobStore,
|
||||
tools: toolStore,
|
||||
collectionAttributesStore: collectionAttributesStore,
|
||||
genomeStore: genomeStore,
|
||||
datatypeStore: datatypeStore,
|
||||
},
|
||||
};
|
||||
|
||||
|
||||
@@ -76,6 +76,25 @@ def validate(dataset_instance):
|
||||
return datatype_validation
|
||||
|
||||
|
||||
def get_params_and_input_name(converter, deps, target_context=None):
|
||||
# Generate parameter dictionary
|
||||
params = {}
|
||||
# determine input parameter name and add to params
|
||||
input_name = 'input1'
|
||||
for key, value in converter.inputs.items():
|
||||
if deps and value.name in deps:
|
||||
params[value.name] = deps[value.name]
|
||||
elif value.type == 'data':
|
||||
input_name = key
|
||||
|
||||
# add potentially required/common internal tool parameters e.g. '__job_resource'
|
||||
if target_context:
|
||||
for key, value in target_context.items():
|
||||
if key.startswith('__'):
|
||||
params[key] = value
|
||||
return params, input_name
|
||||
|
||||
|
||||
class DataMeta(abc.ABCMeta):
|
||||
"""
|
||||
Metaclass for Data class. Sets up metadata spec.
|
||||
@@ -620,20 +639,9 @@ class Data(metaclass=DataMeta):
|
||||
|
||||
if converter is None:
|
||||
raise Exception(f"A converter does not exist for {original_dataset.ext} to {target_type}.")
|
||||
# Generate parameter dictionary
|
||||
params = {}
|
||||
# determine input parameter name and add to params
|
||||
input_name = 'input1'
|
||||
for key, value in converter.inputs.items():
|
||||
if deps and value.name in deps:
|
||||
params[value.name] = deps[value.name]
|
||||
elif value.type == 'data':
|
||||
input_name = key
|
||||
# add potentially required/common internal tool parameters e.g. '__job_resource'
|
||||
if target_context:
|
||||
for key, value in target_context.items():
|
||||
if key.startswith('__'):
|
||||
params[key] = value
|
||||
|
||||
params, input_name = get_params_and_input_name(converter, deps, target_context)
|
||||
|
||||
params[input_name] = original_dataset
|
||||
# Make the target datatype available to the converter
|
||||
params['__target_datatype__'] = target_type
|
||||
|
||||
@@ -3,6 +3,7 @@ import logging
|
||||
from sqlalchemy.orm import joinedload, Query
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.datatypes.registry import Registry
|
||||
from galaxy.exceptions import (
|
||||
ItemAccessibilityException,
|
||||
MessageException,
|
||||
@@ -218,6 +219,38 @@ class DatasetCollectionManager:
|
||||
dataset_collection.collection_type = collection_type
|
||||
return dataset_collection
|
||||
|
||||
def get_converters_for_collection(self, trans, id, datatypes_registry: Registry, instance_type="history"):
|
||||
dataset_collection_instance = self.get_dataset_collection_instance(
|
||||
trans,
|
||||
id=id,
|
||||
instance_type=instance_type,
|
||||
check_ownership=True
|
||||
)
|
||||
dbkeys_and_extensions = dataset_collection_instance.dataset_dbkeys_and_extensions_summary
|
||||
suitable_converters = set()
|
||||
first_extension = True
|
||||
most_recent_datatype = None
|
||||
# TODO error checking
|
||||
for datatype in dbkeys_and_extensions[1]:
|
||||
new_converters = datatypes_registry.get_converters_by_datatype(datatype)
|
||||
set_of_new_converters = set()
|
||||
for tgt_type, tgt_val in new_converters.items():
|
||||
converter = (tgt_type, tgt_val)
|
||||
set_of_new_converters.add(converter)
|
||||
if (first_extension is True):
|
||||
suitable_converters = set_of_new_converters
|
||||
most_recent_datatype = datatype
|
||||
first_extension = False
|
||||
else:
|
||||
suitable_converters = suitable_converters.intersection(set_of_new_converters)
|
||||
if suitable_converters:
|
||||
most_recent_datatype = datatype
|
||||
suitable_tool_ids = list()
|
||||
for tool in suitable_converters:
|
||||
tool_info = {"tool_id": tool[1].id, "name": tool[1].name, "target_type": tool[0], "original_type": most_recent_datatype}
|
||||
suitable_tool_ids.append(tool_info)
|
||||
return suitable_tool_ids
|
||||
|
||||
def _element_identifiers_to_elements(self,
|
||||
trans,
|
||||
collection_type_description,
|
||||
|
||||
@@ -5,6 +5,7 @@ HistoryDatasetCollectionAssociations (HDCAs) are datasets contained or created i
|
||||
history.
|
||||
"""
|
||||
import logging
|
||||
from typing import Dict
|
||||
|
||||
from galaxy import model
|
||||
from galaxy.managers import (
|
||||
@@ -39,6 +40,11 @@ def stream_dataset_collection(dataset_collection_instance, upstream_mod_zip=Fals
|
||||
return archive
|
||||
|
||||
|
||||
def set_collection_attributes(dataset_element, *payload):
|
||||
for attribute, value in payload:
|
||||
setattr(dataset_element, attribute[1], value[1])
|
||||
|
||||
|
||||
# TODO: to DatasetCollectionInstanceManager
|
||||
class HDCAManager(
|
||||
base.ModelManager,
|
||||
@@ -77,7 +83,9 @@ class HDCAManager(
|
||||
returned.append(processed)
|
||||
return returned
|
||||
|
||||
# TODO: un-stub
|
||||
def update_attributes(self, content, payload: Dict):
|
||||
# pre-requisite checked that attributes are valid
|
||||
self.map_datasets(content, fn=lambda item, *args: set_collection_attributes(item, payload.items()))
|
||||
|
||||
|
||||
# serializers
|
||||
|
||||
@@ -5530,6 +5530,7 @@ class HistoryDatasetCollectionAssociation(
|
||||
== HistoryDatasetCollectionAssociation.id), # type: ignore
|
||||
back_populates='hidden_beneath_collection_instance')
|
||||
|
||||
dict_dbkeysandextensions_visible_keys = ['dbkeys', 'extensions']
|
||||
editable_keys = ('name', 'deleted', 'visible')
|
||||
|
||||
def __init__(self, deleted=False, visible=True, **kwd):
|
||||
@@ -5566,6 +5567,24 @@ class HistoryDatasetCollectionAssociation(
|
||||
else:
|
||||
return None
|
||||
|
||||
@property
|
||||
def dataset_dbkeys_and_extensions_summary(self):
|
||||
if not hasattr(self, '_dataset_dbkeys_and_extensions_summary'):
|
||||
rows = self.collection._get_nested_collection_attributes(hda_attributes=('_metadata', 'extension'))
|
||||
extensions = set()
|
||||
dbkeys = set()
|
||||
for row in rows:
|
||||
if row is not None:
|
||||
dbkey_field = row._metadata.get('dbkey')
|
||||
if isinstance(dbkey_field, list):
|
||||
for dbkey in dbkey_field:
|
||||
dbkeys.add(dbkey)
|
||||
else:
|
||||
dbkeys.add(dbkey_field)
|
||||
extensions.add(row.extension)
|
||||
self._dataset_dbkeys_and_extensions_summary = (dbkeys, extensions)
|
||||
return self._dataset_dbkeys_and_extensions_summary
|
||||
|
||||
@property
|
||||
def job_source_id(self):
|
||||
return self.implicit_collection_jobs_id or self.job_id
|
||||
@@ -5620,16 +5639,23 @@ class HistoryDatasetCollectionAssociation(
|
||||
|
||||
def to_dict(self, view='collection'):
|
||||
original_dict_value = super().to_dict(view=view)
|
||||
dict_value = dict(
|
||||
hid=self.hid,
|
||||
history_id=self.history.id,
|
||||
history_content_type=self.history_content_type,
|
||||
visible=self.visible,
|
||||
deleted=self.deleted,
|
||||
job_source_id=self.job_source_id,
|
||||
job_source_type=self.job_source_type,
|
||||
**self._base_to_dict(view=view)
|
||||
)
|
||||
if (view == 'dbkeysandextensions'):
|
||||
(dbkeys, extensions) = self.dataset_dbkeys_and_extensions_summary
|
||||
dict_value = dict(
|
||||
dbkey=dbkeys.pop() if len(dbkeys) == 1 else "?",
|
||||
extension=extensions.pop() if len(extensions) == 1 else "auto"
|
||||
)
|
||||
else:
|
||||
dict_value = dict(
|
||||
hid=self.hid,
|
||||
history_id=self.history.id,
|
||||
history_content_type=self.history_content_type,
|
||||
visible=self.visible,
|
||||
deleted=self.deleted,
|
||||
job_source_id=self.job_source_id,
|
||||
job_source_type=self.job_source_type,
|
||||
**self._base_to_dict(view=view)
|
||||
)
|
||||
|
||||
dict_value.update(original_dict_value)
|
||||
|
||||
|
||||
@@ -269,6 +269,14 @@ history_panel:
|
||||
options_use_beta_history:
|
||||
type: xpath
|
||||
selector: '//a[text()="Use Beta History Panel"]'
|
||||
options_use_legacy_history:
|
||||
type: xpath
|
||||
selector: '//button[contains(span, "Return to legacy history panel")]'
|
||||
|
||||
collection_menu_button: '.collection-menu'
|
||||
collection_menu_edit_attributes:
|
||||
type: xpath
|
||||
selector: '//button[@title="Edit attributes"]'
|
||||
new_history_button: '.history-new-button'
|
||||
multi_view_button: '.history-view-multi-button'
|
||||
histories_operation_menu: '.histories-operation-menu'
|
||||
@@ -306,6 +314,16 @@ edit_dataset_attributes:
|
||||
type: xpath
|
||||
selector: '//li[normalize-space() = "${dbkey_text}"]'
|
||||
|
||||
edit_collection_attributes:
|
||||
selectors:
|
||||
database_genome_tab:
|
||||
type: xpath
|
||||
selector: '//a[contains(text(), "Database/Build")]'
|
||||
database_value:
|
||||
type: xpath
|
||||
selector: '//span[contains(text(), "${dbkey}")]'
|
||||
save_btn: '.save-collection-edit'
|
||||
|
||||
|
||||
|
||||
tool_panel:
|
||||
|
||||
@@ -3,14 +3,16 @@ from logging import getLogger
|
||||
import routes
|
||||
|
||||
from galaxy import exceptions
|
||||
from galaxy.datatypes.registry import Registry
|
||||
from galaxy.managers.base import decode_id
|
||||
from galaxy.managers.collections import DatasetCollectionManager
|
||||
from galaxy.managers.collections_util import (
|
||||
api_payload_to_create_params,
|
||||
dictify_dataset_collection_instance,
|
||||
dictify_element_reference
|
||||
dictify_element_reference,
|
||||
)
|
||||
from galaxy.managers.context import ProvidesHistoryContext
|
||||
from galaxy.managers.hdcas import HDCAManager
|
||||
from galaxy.managers.histories import HistoryManager
|
||||
from galaxy.web import expose_api
|
||||
from galaxy.webapps.base.controller import UsesLibraryMixinItems
|
||||
@@ -24,6 +26,9 @@ class DatasetCollectionsController(
|
||||
UsesLibraryMixinItems,
|
||||
):
|
||||
history_manager: HistoryManager = depends(HistoryManager)
|
||||
hdca_manager: HDCAManager = depends(HDCAManager)
|
||||
collection_manager: DatasetCollectionManager = depends(DatasetCollectionManager)
|
||||
datatypes_registry: Registry = depends(Registry)
|
||||
|
||||
@expose_api
|
||||
def index(self, trans, **kwd):
|
||||
@@ -64,6 +69,48 @@ class DatasetCollectionsController(
|
||||
return dictify_dataset_collection_instance(dataset_collection_instance,
|
||||
security=trans.security, parent=create_params["parent"])
|
||||
|
||||
@expose_api
|
||||
def update(self, trans: ProvidesHistoryContext, payload: dict, id):
|
||||
"""
|
||||
Iterate over all datasets of a collection and copy datasets with new attributes to a new collection.
|
||||
e.g attributes = {'dbkey': 'dm3'}
|
||||
|
||||
* PUT /api/dataset_collections/{hdca_id}:
|
||||
create a new dataset collection instance.
|
||||
"""
|
||||
|
||||
if len(payload) != 1:
|
||||
raise exceptions.RequestParameterInvalidException("Update one attribute at a time.")
|
||||
if 'dbkey' not in payload:
|
||||
raise exceptions.RequestParameterInvalidException("This attribute cannot be modified.")
|
||||
|
||||
self.collection_manager.copy(trans, trans.history, "hdca", id, copy_elements=True, dataset_instance_attributes=payload)
|
||||
trans.sa_session.flush()
|
||||
|
||||
@expose_api
|
||||
def attributes(self, trans: ProvidesHistoryContext, id, instance_type='history'):
|
||||
"""
|
||||
GET /api/dataset_collections/{hdca_id}/attributes
|
||||
|
||||
Returns dbkey/extension for collection elements
|
||||
"""
|
||||
dataset_collection_instance = self.__service.get_dataset_collection_instance(
|
||||
trans,
|
||||
id=id,
|
||||
instance_type=instance_type,
|
||||
check_ownership=True
|
||||
)
|
||||
return dataset_collection_instance.to_dict(view="dbkeysandextensions")
|
||||
|
||||
@expose_api
|
||||
def suitable_converters(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds):
|
||||
"""
|
||||
GET /api/dataset_collections/{hdca_id}/suitable_converters
|
||||
|
||||
Returns suitable converters for all datatypes in collection
|
||||
"""
|
||||
return self.collection_manager.get_converters_for_collection(trans, id, self.datatypes_registry, instance_type)
|
||||
|
||||
@expose_api
|
||||
def show(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds):
|
||||
"""
|
||||
|
||||
@@ -4,6 +4,8 @@ from json import dumps, loads
|
||||
from typing import Any, cast, Dict, Optional
|
||||
|
||||
from galaxy import exceptions, util, web
|
||||
from galaxy.datatypes.data import get_params_and_input_name
|
||||
from galaxy.managers.collections import DatasetCollectionManager
|
||||
from galaxy.managers.collections_util import dictify_dataset_collection_instance
|
||||
from galaxy.managers.hdas import HDAManager
|
||||
from galaxy.managers.histories import HistoryManager
|
||||
@@ -36,6 +38,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
"""
|
||||
history_manager: HistoryManager = depends(HistoryManager)
|
||||
hda_manager: HDAManager = depends(HDAManager)
|
||||
hdca_manager: DatasetCollectionManager = depends(DatasetCollectionManager)
|
||||
|
||||
@expose_api_anonymous_and_sessionless
|
||||
def index(self, trans: GalaxyWebTransaction, **kwds):
|
||||
@@ -426,6 +429,51 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
rval.append(citation.to_dict('bibtex'))
|
||||
return rval
|
||||
|
||||
@expose_api
|
||||
def conversion(self, trans: GalaxyWebTransaction, tool_id, payload, **kwd):
|
||||
converter = self._get_tool(tool_id, user=trans.user)
|
||||
target_type = payload.get("target_type")
|
||||
source_type = payload.get("source_type")
|
||||
input_src = payload.get("src")
|
||||
input_id = payload.get("id")
|
||||
# List of string of dependencies
|
||||
try:
|
||||
deps = trans.app.datatypes_registry.converter_deps[source_type][target_type]
|
||||
except KeyError:
|
||||
deps = {}
|
||||
# Generate parameter dictionary
|
||||
params, input_name = get_params_and_input_name(converter, deps)
|
||||
params = {}
|
||||
# determine input parameter name and add to params
|
||||
|
||||
params[input_name] = {
|
||||
"values": [
|
||||
{
|
||||
"id": input_id,
|
||||
"src": input_src,
|
||||
}
|
||||
],
|
||||
"batch": input_src == "hdca",
|
||||
}
|
||||
history_id = payload.get('history_id')
|
||||
if history_id:
|
||||
decoded_id = self.decode_id(history_id)
|
||||
target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
|
||||
else:
|
||||
if input_src == "hdca":
|
||||
target_history = self.hdca_manager.get_dataset_collection_instance(trans, instance_type='history', id=input_id).history
|
||||
elif input_src == "hda":
|
||||
decoded_id = trans.app.security.decode_id(input_id)
|
||||
target_history = self.hda_manager.get_accessible(decoded_id, trans.user).history
|
||||
self.history_manager.error_unless_owner(target_history, trans.user, current_history=trans.history)
|
||||
else:
|
||||
raise exceptions.RequestParameterInvalidException("Must run conversion on either hdca or hda.")
|
||||
|
||||
# Make the target datatype available to the converter
|
||||
params['__target_datatype__'] = target_type
|
||||
vars = converter.handle_input(trans, params, history=target_history)
|
||||
return self._handle_inputs_output_to_api_response(trans, converter, target_history, vars)
|
||||
|
||||
@expose_api_anonymous_and_sessionless
|
||||
def xrefs(self, trans: GalaxyWebTransaction, id, **kwds):
|
||||
tool = self._get_tool(id, user=trans.user)
|
||||
@@ -568,6 +616,24 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
|
||||
vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)
|
||||
|
||||
new_pja_flush = False
|
||||
for job in vars.get('jobs', []):
|
||||
if inputs.get('send_email_notification', False):
|
||||
# Unless an anonymous user is invoking this via the API it
|
||||
# should never be an option, but check and enforce that here
|
||||
if trans.user is None:
|
||||
raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
|
||||
else:
|
||||
job_email_action = PostJobAction('EmailAction')
|
||||
job.add_post_job_action(job_email_action)
|
||||
new_pja_flush = True
|
||||
|
||||
if new_pja_flush:
|
||||
trans.sa_session.flush()
|
||||
|
||||
return self._handle_inputs_output_to_api_response(trans, tool, target_history, vars)
|
||||
|
||||
def _handle_inputs_output_to_api_response(self, trans, tool, target_history, vars):
|
||||
# TODO: check for errors and ensure that output dataset(s) are available.
|
||||
output_datasets = vars.get('out_data', [])
|
||||
rval: Dict[str, Any] = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
|
||||
@@ -587,21 +653,8 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
output_dict['output_name'] = output_name
|
||||
outputs.append(trans.security.encode_dict_ids(output_dict, skip_startswith="metadata_"))
|
||||
|
||||
new_pja_flush = False
|
||||
for job in vars.get('jobs', []):
|
||||
rval['jobs'].append(self.encode_all_ids(trans, job.to_dict(view='collection'), recursive=True))
|
||||
if inputs.get('send_email_notification', False):
|
||||
# Unless an anonymous user is invoking this via the API it
|
||||
# should never be an option, but check and enforce that here
|
||||
if trans.user is None:
|
||||
raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
|
||||
else:
|
||||
job_email_action = PostJobAction('EmailAction')
|
||||
job.add_post_job_action(job_email_action)
|
||||
new_pja_flush = True
|
||||
|
||||
if new_pja_flush:
|
||||
trans.sa_session.flush()
|
||||
|
||||
for output_name, collection_instance in vars.get('output_collections', []):
|
||||
history = target_history or trans.history
|
||||
|
||||
@@ -178,6 +178,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
|
||||
webapp.add_client_route('/histories/show_structure')
|
||||
webapp.add_client_route('/datasets/list')
|
||||
webapp.add_client_route('/datasets/edit')
|
||||
webapp.add_client_route('/collection/edit/{collection_id}')
|
||||
webapp.add_client_route('/datasets/error')
|
||||
webapp.add_client_route('/jobs/{job_id}/view')
|
||||
webapp.add_client_route('/datasets/{dataset_id}/details')
|
||||
@@ -425,6 +426,7 @@ def populate_api_routes(webapp, app):
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/test_data', action='test_data', controller="tools")
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools")
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/citations', action='citations', controller="tools")
|
||||
webapp.mapper.connect('/api/tools/{tool_id:.+?}/convert', action='conversion', controller="tools", conditions=dict(method=["POST"]))
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/xrefs', action='xrefs', controller="tools")
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/download', action='download', controller="tools")
|
||||
webapp.mapper.connect('/api/tools/{id:.+?}/requirements', action='requirements', controller="tools")
|
||||
@@ -550,6 +552,22 @@ def populate_api_routes(webapp, app):
|
||||
action='download_dataset_collection',
|
||||
conditions=dict(method=["GET"]))
|
||||
|
||||
webapp.mapper.connect("/api/dataset_collections/{id}",
|
||||
controller='dataset_collections',
|
||||
action='update',
|
||||
conditions=dict(method=["PUT"]))
|
||||
|
||||
webapp.mapper.connect("/api/dataset_collections/{id}/attributes",
|
||||
controller='dataset_collections',
|
||||
action='attributes',
|
||||
conditions=dict(method=["GET"]))
|
||||
|
||||
webapp.mapper.connect("api_suitable_converters",
|
||||
"/api/dataset_collections/{id}/suitable_converters",
|
||||
controller='dataset_collections',
|
||||
action='suitable_converters',
|
||||
conditions=dict(method=['GET']))
|
||||
|
||||
webapp.mapper.connect("/api/histories/{history_id}/jobs_summary",
|
||||
action="index_jobs_summary",
|
||||
controller='history_contents',
|
||||
|
||||
@@ -356,6 +356,94 @@ class DatasetCollectionApiTestCase(ApiTestCase):
|
||||
assert len(offset_contents) == 1
|
||||
assert offset_contents[0]['element_index'] == 1
|
||||
|
||||
def test_get_suitable_converters_single_datatype(self):
|
||||
response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
|
||||
{
|
||||
"name": "test0",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
|
||||
{"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "test1",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "bed"},
|
||||
{"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "bed"},
|
||||
]
|
||||
}
|
||||
])
|
||||
self._assert_status_code_is(response, 200)
|
||||
hdca_list_id = response.json()["outputs"][0]["id"]
|
||||
converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
|
||||
expected = [
|
||||
'CONVERTER_bed_to_fli_0',
|
||||
'CONVERTER_interval_to_bed_0',
|
||||
'CONVERTER_bed_gff_or_vcf_to_bigwig_0',
|
||||
'CONVERTER_bed_to_gff_0',
|
||||
'CONVERTER_interval_to_bgzip_0',
|
||||
'tabular_to_csv',
|
||||
'CONVERTER_interval_to_bed6_0',
|
||||
'CONVERTER_interval_to_bedstrict_0',
|
||||
'CONVERTER_interval_to_tabix_0',
|
||||
'CONVERTER_interval_to_bed12_0']
|
||||
actual = []
|
||||
for converter in converters.json():
|
||||
actual.append(converter["tool_id"])
|
||||
assert sorted(actual) == sorted(expected)
|
||||
|
||||
def test_get_suitable_converters_different_datatypes_matches(self):
|
||||
response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
|
||||
{
|
||||
"name": "test0",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
|
||||
{"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "test1",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "tabular"},
|
||||
{"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "tabular"},
|
||||
]
|
||||
}
|
||||
])
|
||||
self._assert_status_code_is(response, 200)
|
||||
hdca_list_id = response.json()["outputs"][0]["id"]
|
||||
converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
|
||||
expected = ['tabular_to_csv']
|
||||
actual = []
|
||||
for converter in converters.json():
|
||||
actual.append(converter["tool_id"])
|
||||
assert sorted(actual) == sorted(expected)
|
||||
|
||||
def test_get_suitable_converters_different_datatypes_no_matches(self):
|
||||
response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
|
||||
{
|
||||
"name": "test0",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
|
||||
{"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "test1",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "fasta"},
|
||||
{"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "fasta"},
|
||||
]
|
||||
}
|
||||
])
|
||||
self._assert_status_code_is(response, 200)
|
||||
hdca_list_id = response.json()["outputs"][0]["id"]
|
||||
converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
|
||||
expected = []
|
||||
actual = []
|
||||
for converter in converters.json():
|
||||
actual.append(converter["tool_id"])
|
||||
assert sorted(actual) == sorted(expected)
|
||||
|
||||
def test_collection_tools_tag_propagation(self):
|
||||
elements = [{"src": "files", "tags": ["name:element_tag"]}]
|
||||
targets = [{
|
||||
|
||||
@@ -433,6 +433,82 @@ class ToolsTestCase(ApiTestCase, TestsTools):
|
||||
expected_names = {'velveth_test1/Roadmaps', 'velveth_test1/output.html', 'velveth_test1/Sequences', 'velveth_test1/Log', 'velveth_test1/output/', 'velveth_test1/output/1'}
|
||||
assert set(namelist) == expected_names
|
||||
|
||||
@uses_test_history(require_new=False)
|
||||
def test_convert_dataset_explicit_history(self, history_id):
|
||||
fasta1_contents = open(self.get_filename("1.fasta")).read()
|
||||
hda1 = self.dataset_populator.new_dataset(history_id, content=fasta1_contents)
|
||||
|
||||
payload = {
|
||||
"src": "hda",
|
||||
"id": hda1["id"],
|
||||
"source_type": "fasta",
|
||||
"target_type": "tabular",
|
||||
"history_id": history_id
|
||||
}
|
||||
create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", data=payload)
|
||||
self.dataset_populator.wait_for_job(create_response.json()["jobs"][0]["id"], assert_ok=True)
|
||||
create_response.raise_for_status()
|
||||
assert len(create_response.json()["implicit_collections"]) == 0
|
||||
for output in create_response.json()["outputs"]:
|
||||
assert output["file_ext"] == "tabular"
|
||||
|
||||
@uses_test_history(require_new=False)
|
||||
def test_convert_dataset_implicit_history(self, history_id):
|
||||
fasta1_contents = open(self.get_filename("1.fasta")).read()
|
||||
hda1 = self.dataset_populator.new_dataset(history_id, content=fasta1_contents)
|
||||
|
||||
payload = {
|
||||
"src": "hda",
|
||||
"id": hda1["id"],
|
||||
"source_type": "fasta",
|
||||
"target_type": "tabular"
|
||||
}
|
||||
create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", data=payload)
|
||||
self.dataset_populator.wait_for_job(create_response.json()["jobs"][0]["id"], assert_ok=True)
|
||||
create_response.raise_for_status()
|
||||
assert len(create_response.json()["implicit_collections"]) == 0
|
||||
for output in create_response.json()["outputs"]:
|
||||
assert output["file_ext"] == "tabular"
|
||||
|
||||
@uses_test_history(require_new=False)
|
||||
def test_convert_hdca(self, history_id):
|
||||
data = [
|
||||
{
|
||||
"name": "test0",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "fasta"},
|
||||
{"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "fasta"},
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "test1",
|
||||
"elements": [
|
||||
{"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "fasta"},
|
||||
{"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "fasta"},
|
||||
]
|
||||
}
|
||||
]
|
||||
hdca1 = self.dataset_collection_populator.upload_collection(history_id, "list:paired", elements=data)
|
||||
self._assert_status_code_is(hdca1, 200)
|
||||
|
||||
payload = {
|
||||
"src": "hdca",
|
||||
"id": hdca1.json()["outputs"][0]["id"],
|
||||
"source_type": "fasta",
|
||||
"target_type": "tabular",
|
||||
"history_id": history_id
|
||||
}
|
||||
create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", payload)
|
||||
|
||||
self.dataset_populator.wait_for_job(create_response.json()["jobs"][0]["id"], assert_ok=True)
|
||||
create_response.raise_for_status()
|
||||
|
||||
assert create_response.json()["implicit_collections"] != []
|
||||
hdca_id = create_response.json()["implicit_collections"][0]["hid"]
|
||||
fetchedResponse = self.dataset_populator.get_history_collection_details(history_id, hid=hdca_id)
|
||||
for element in fetchedResponse["elements"][0]["object"]["elements"]:
|
||||
assert element["object"]["file_ext"] == "tabular"
|
||||
|
||||
def test_unzip_collection(self):
|
||||
with self.dataset_populator.test_history() as history_id:
|
||||
hdca_id = self._build_pair(history_id, ["123", "456"])
|
||||
|
||||
@@ -0,0 +1,74 @@
|
||||
from selenium.webdriver.common.keys import Keys
|
||||
|
||||
from .framework import (
|
||||
selenium_test,
|
||||
SeleniumTestCase
|
||||
)
|
||||
|
||||
|
||||
class CollectionEditTestCase(SeleniumTestCase):
|
||||
|
||||
ensure_registered = True
|
||||
|
||||
@selenium_test
|
||||
def test_change_dbkey_simple_list(self):
|
||||
self.use_beta_history()
|
||||
self.create_simple_list_collection()
|
||||
self.open_collection_edit_view()
|
||||
self.navigate_to_database_tab()
|
||||
dbkeyValue = "Additional"
|
||||
self.check_current_dbkey_value(dbkeyValue)
|
||||
dbkeyNew = "hg17"
|
||||
self.change_dbkey_value_and_click_submit(dbkeyValue, dbkeyNew)
|
||||
self.history_panel_wait_for_hid_ok(4)
|
||||
self.use_beta_history()
|
||||
self.open_collection_edit_view()
|
||||
self.navigate_to_database_tab()
|
||||
self.check_current_dbkey_value(dbkeyNew)
|
||||
|
||||
def create_simple_list_collection(self):
|
||||
self.perform_upload(self.get_filename("1.fasta"))
|
||||
self._wait_for_and_select([1])
|
||||
|
||||
self._collection_dropdown("build list")
|
||||
|
||||
self.collection_builder_set_name("my cool list")
|
||||
self.screenshot("collection_builder_list")
|
||||
self.collection_builder_create()
|
||||
self._wait_for_hid_visible(2)
|
||||
|
||||
def open_collection_edit_view(self):
|
||||
self.components.history_panel.collection_menu_edit_attributes.wait_for_and_click()
|
||||
|
||||
def navigate_to_database_tab(self):
|
||||
self.components.edit_collection_attributes.database_genome_tab.wait_for_and_click()
|
||||
|
||||
def check_current_dbkey_value(self, dbkeyValue):
|
||||
self.components.edit_collection_attributes.database_value(dbkey=dbkeyValue).wait_for_visible()
|
||||
|
||||
def change_dbkey_value_and_click_submit(self, dbkeyValue, dbkeyNew):
|
||||
self.components.edit_collection_attributes.database_value(dbkey=dbkeyValue).wait_for_and_click()
|
||||
self.driver.find_element_by_css_selector("input.multiselect__input").send_keys(dbkeyNew)
|
||||
self.driver.find_element_by_css_selector("input.multiselect__input").send_keys(Keys.ENTER)
|
||||
self.components.edit_collection_attributes.save_btn.wait_for_and_click()
|
||||
|
||||
def _wait_for_and_select(self, hids):
|
||||
"""
|
||||
Waits for uploads to pass through queued, running, ok. Not all the states are not guaranteed
|
||||
depending on how fast the upload goes compared to the history polling updates, it might just
|
||||
skip to the end for a really fast upload
|
||||
"""
|
||||
|
||||
for hid in hids:
|
||||
timeout = self.wait_length(self.wait_types.JOB_COMPLETION)
|
||||
row_selector = self.content_item_by_attributes(hid=hid, state="ok")
|
||||
row = self.wait_for_present(row_selector, timeout=timeout)
|
||||
row.send_keys(" ")
|
||||
|
||||
def _collection_dropdown(self, option_description):
|
||||
return self.use_bootstrap_dropdown(option=option_description, menu="new content menu")
|
||||
|
||||
def _wait_for_hid_visible(self, hid, state="ok"):
|
||||
timeout = self.wait_length(self.wait_types.JOB_COMPLETION)
|
||||
row_selector = self.content_item_by_attributes(hid=hid, state=state)
|
||||
self.wait_for_visible(row_selector, timeout=timeout)
|
||||
@@ -417,6 +417,21 @@ class MappingTests(BaseModelTestCase):
|
||||
assert c4.dataset_elements == [dce1, dce2]
|
||||
assert c4.element_identifiers_extensions_and_paths == [(('outer_list', 'inner_list', 'forward'), 'bam', 'mock_dataset_14.dat'), (('outer_list', 'inner_list', 'reverse'), 'txt', 'mock_dataset_14.dat')]
|
||||
|
||||
def test_dataset_dbkeys_and_extensions_summary(self):
|
||||
model = self.model
|
||||
u = model.User(email="mary2@example.com", password="password")
|
||||
h1 = model.History(name="History 1", user=u)
|
||||
d1 = model.HistoryDatasetAssociation(extension="bam", dbkey="hg19", history=h1, create_dataset=True, sa_session=model.session)
|
||||
d2 = model.HistoryDatasetAssociation(extension="txt", dbkey="hg19", history=h1, create_dataset=True, sa_session=model.session)
|
||||
c1 = model.DatasetCollection(collection_type='paired')
|
||||
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
|
||||
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
|
||||
hdca = model.HistoryDatasetCollectionAssociation(collection=c1, history=h1)
|
||||
model.session.add_all([d1, d2, c1, dce1, dce2, hdca])
|
||||
model.session.flush()
|
||||
assert hdca.dataset_dbkeys_and_extensions_summary[0] == {"hg19"}
|
||||
assert hdca.dataset_dbkeys_and_extensions_summary[1] == {"bam", "txt"}
|
||||
|
||||
def test_default_disk_usage(self):
|
||||
model = self.model
|
||||
|
||||
|
||||
Reference in New Issue
Block a user