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https://github.com/galaxyproject/galaxy.git
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Vue rewrite of admin data manager (local data): view job page
* Rewrite (old mako, new json interface, new vue component) - View job page (view_job.mako, job_info, DataManagerJob) * Added Selenium test for DataManagerJob component (view job page)
This commit is contained in:
Sebastian Kapust
@@ -0,0 +1,160 @@
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<template>
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<div>
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<b-breadcrumb :items="breadcrumbItems" />
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<Alert :message="message" :variant="status" />
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<Alert v-for="(error, index) in errorMessages" :key="index" :message="error" variant="error" />
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<Alert v-if="viewOnly" message="Not implemented" variant="dark" />
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<b-container v-else>
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<b-row>
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<b-col>
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<b-card header-bg-variant="primary" header-text-variant="white" border-variant="primary" class="mb-3" id="data-manager-card">
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<template slot="header">
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<b-container>
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<b-row align-v="center">
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<b-col cols="auto">
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<b-button v-b-tooltip.hover title="Rerun" :href="runUrl">
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<span class="fa fa-refresh" />
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</b-button>
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</b-col>
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<b-col>
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<b>{{ dataManager["name"] }}</b>
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<i>{{ dataManager['description'] }}</i>
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</b-col>
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</b-row>
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</b-container>
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</template>
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<b-card v-for="(item, i) in tableItems" :key="i" class="mb-4" id="data-card">
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<template slot="header">
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<b-table :fields="fields" :items="[item]" caption-top small stacked>
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<template slot="table-caption">
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<b-container>
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<b-row align-v="center">
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<b-col cols="auto">
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<b-button v-b-tooltip.hover title="View complete info" :href="tableItems[i]['infoUrl']" target="galaxy_main">
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<span class="fa fa-info-circle" />
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</b-button>
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</b-col>
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<b-col>
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<b>{{ item["name"] }}</b>
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</b-col>
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</b-row>
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</b-container>
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</template>
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</b-table>
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</template>
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<b-table v-for="(output, j) in dataManagerOutput[i]" :key="j" :fields="outputFields(output[1])" :items="output[1]" small stacked hover striped>
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<template slot="table-caption">
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Data Table:
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<b>{{ output[0] }}</b>
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</template>
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</b-table>
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</b-card>
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</b-card>
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</b-col>
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</b-row>
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</b-container>
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</div>
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</template>
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<script>
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import axios from "axios";
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import Alert from "components/Alert.vue";
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export default {
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components: {
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Alert
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},
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props: {
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id: {
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type: String,
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required: true
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}
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},
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data() {
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return {
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exitCode: Number,
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runUrl: "#",
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dataManager: [],
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hdaInfo: [],
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dataManagerOutput: [],
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errorMessages: [],
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fields: [
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{ key: "created" },
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{ key: "fileSize", label: "Filesize" },
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{
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key: "fileName",
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label: "Full path",
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tdClass: "table-cell-break-word"
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}
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],
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viewOnly: false,
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message: "",
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status: ""
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};
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},
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computed: {
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breadcrumbItems() {
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return [
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{
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text: "Data Managers",
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to: "/"
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},
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{
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text: this.dataManager["name"] + " ( " + this.dataManager["description"] + " )",
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href: this.dataManager["toolUrl"],
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target: "_blank"
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},
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{
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text: "Jobs",
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to: {
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name: "DataManagerJobs",
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params: { id: this.dataManager["id"] }
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}
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},
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{
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text: "Job " + this.jobId,
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active: true
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}
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];
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},
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tableItems() {
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let tableItems = this.hdaInfo;
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return tableItems;
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}
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},
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methods: {
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outputFields(output) {
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let outputFields = [];
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for (const k of Object.keys(output[0])) {
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outputFields.push({ key: k, label: k });
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}
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return outputFields;
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}
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},
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created() {
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axios
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.get(`${Galaxy.root}data_manager/job_info?id=${this.id}`)
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.then(response => {
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this.jobId = response.data.jobId;
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this.exitCode = response.data.exitCode;
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this.runUrl = response.data.runUrl;
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this.dataManager = response.data.dataManager;
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this.hdaInfo = response.data.hdaInfo;
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this.dataManagerOutput = response.data.dataManagerOutput;
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this.errorMessages = response.data.errorMessages;
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this.viewOnly = response.data.viewOnly;
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this.message = response.data.message;
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this.status = response.data.status;
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})
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.catch(error => {
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console.error(error);
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});
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}
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};
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</script>
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<style>
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.table-cell-break-word {
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word-break: break-word;
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}
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</style>
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@@ -35,7 +35,7 @@
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<b-button v-b-tooltip.hover title="Rerun" :href="jobs[row.index]['runUrl']">
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<span class="fa fa-refresh" />
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</b-button>
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<b-button v-b-tooltip.hover title="View Info" :href="jobs[row.index]['infoUrl']" target="galaxy_main" :id="'job-' + jobs[row.index]['encId']">
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<b-button v-b-tooltip.hover title="View Info" :to="{name: 'DataManagerJob', params: { id: jobs[row.index]['encId'] }}" :id="'job-' + jobs[row.index]['encId']">
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<span class="fa fa-info-circle" />
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</b-button>
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<b-button v-if="!showCommandLine" @click.stop="row.toggleDetails()" :pressed.sync="row.detailsShowing">
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@@ -3,6 +3,7 @@ import Vue from "vue";
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import VueRouter from "vue-router";
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import DataManager from "./DataManager.vue";
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import DataManagerJobs from "./DataManagerJobs.vue";
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import DataManagerJob from "./DataManagerJob.vue";
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Vue.use(VueRouter);
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@@ -19,6 +20,12 @@ export default new VueRouter({
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name: "DataManagerJobs",
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component: DataManagerJobs,
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props: true
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},
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{
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path: "/job/:id",
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name: "DataManagerJob",
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component: DataManagerJob,
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props: true
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}
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]
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});
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@@ -7,6 +7,7 @@ from six import string_types
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import galaxy.queue_worker
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from galaxy import web
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from galaxy.util import nice_size, unicodify
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from galaxy.web.base.controller import BaseUIController
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log = logging.getLogger(__name__)
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@@ -64,7 +65,6 @@ class DataManager(BaseUIController):
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'id': j.id,
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'encId': trans.security.encode_id(j.id),
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'runUrl': web.url_for(controller="tool_runner", action="rerun", job_id=trans.security.encode_id(j.id)),
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'infoUrl': web.url_for(controller="data_manager", action="view_job", id=trans.security.encode_id(j.id)),
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'user': j.history.user.email if j.history and j.history.user else "anonymous",
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'updateTime': j.update_time.isoformat(),
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'state': j.state,
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@@ -83,12 +83,13 @@ class DataManager(BaseUIController):
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'status': status}
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@web.expose
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def view_job(self, trans, **kwd):
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@web.json
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def job_info(self, trans, **kwd):
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not_is_admin = not trans.user_is_admin()
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if not_is_admin and not trans.app.config.enable_data_manager_user_view:
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raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
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message = escape(kwd.get('message', ''))
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status = escape(kwd.get('status', 'info'))
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message = kwd.get('message', '')
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status = kwd.get('status', 'info')
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job_id = kwd.get('id', None)
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try:
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job_id = trans.security.decode_id(job_id)
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@@ -101,19 +102,45 @@ class DataManager(BaseUIController):
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data_manager_id = job.data_manager_association.data_manager_id
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data_manager = trans.app.data_managers.get_manager(data_manager_id)
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hdas = [assoc.dataset for assoc in job.get_output_datasets()]
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hda_info = []
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data_manager_output = []
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error_messages = []
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for hda in hdas:
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hda_info.append({'id': hda.id,
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'encId': trans.security.encode_id(hda.id),
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'name': hda.name,
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'created': unicodify(hda.create_time.strftime(trans.app.config.pretty_datetime_format)),
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'fileSize': nice_size(hda.dataset.file_size),
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'fileName': hda.file_name,
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'infoUrl': web.url_for(controller='dataset',
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action='show_params',
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dataset_id=trans.security.encode_id(hda.id))})
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try:
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data_manager_json = loads(open(hda.get_file_name()).read())
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except Exception as e:
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data_manager_json = {}
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error_messages.append(escape("Unable to obtain data_table info for hda (%s): %s" % (hda.id, e)))
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error_messages.append("Unable to obtain data_table info for hda (%s): %s" % (hda.id, e))
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values = []
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for key, value in data_manager_json.get('data_tables', {}).items():
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values.append((key, value))
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data_manager_output.append(values)
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return trans.fill_template("data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status, error_messages=error_messages)
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return {'jobId': job_id,
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'exitCode': job.exit_code,
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'runUrl': web.url_for(controller="tool_runner",
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action="rerun",
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job_id=trans.security.encode_id(job.id)),
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'commandLine': job.command_line,
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'dataManager': {'id': data_manager_id,
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'name': data_manager.name,
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'description': data_manager.description.lower(),
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'toolUrl': web.url_for(controller='root',
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tool_id=data_manager.tool.id)},
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'hdaInfo': hda_info,
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'dataManagerOutput': data_manager_output,
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'errorMessages': error_messages,
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'viewOnly': not_is_admin,
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'message': message,
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'status': status}
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@web.expose
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def manage_data_table(self, trans, **kwd):
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@@ -1,63 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<% from galaxy.util import nice_size, unicodify %>
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<%def name="title()">Data Manager: ${ data_manager.name | h } - ${ data_manager.description | h }</%def>
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%if message:
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${render_msg( message, status )}
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%endif
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%if error_messages:
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%for error_message in error_messages:
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${ render_msg( error_message, 'error' ) }
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%endfor
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%endif
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%if view_only:
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<p>Not implemented</p>
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%else:
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%for i, hda in enumerate( hdas ):
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<table class="tabletip">
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<thead>
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<tr><th colspan="2" style="font-size: 120%;">
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Data Manager: <a href="${ h.url_for( controller='root', tool_id=data_manager.tool.id ) }" target="_blank">${ data_manager.name | h }</a> - ${ data_manager.description | h } <a class="icon-btn" href="${ h.url_for( controller="tool_runner", action="rerun", job_id=trans.security.encode_id( job.id ) ) }" title="Rerun" data-placement="bottom"><span class="fa fa-refresh"></span></a>
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</th></tr>
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</thead>
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<tbody>
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<tr><td>Name:</td><td>${hda.name | h}</td></tr>
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<tr><td>Created:</td><td>${unicodify(hda.create_time.strftime(trans.app.config.pretty_datetime_format)) | h}</td></tr>
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<tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size) | h}</td></tr>
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<tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr>
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<tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr>
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<tr><td>View complete info:</td><td><a href="${h.url_for( controller='dataset', action='show_params', dataset_id=trans.security.encode_id( hda.id ))}">${ hda.id | h }</a></td></tr>
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</table>
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<br />
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<% json_tables = data_manager_output[i]%>
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%for table_name, json_table in json_tables:
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<table class="tabletip">
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<thead>
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<tr><th colspan="2" style="font-size: 120%;">
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Data Table: <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}">${ table_name | h }</a>
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</th></tr>
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</thead>
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<% len_json_table = len( json_table ) %>
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%for j, table_row in enumerate( json_table ):
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<tbody>
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%if len_json_table > 1:
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<tr><td><strong>Entry #${j | h}</strong></td><td> </td></tr>
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%endif
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%for name, value in table_row.iteritems():
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<tr><td>${name | h}:</td><td>${value | h}</td></tr>
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%endfor
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%endfor
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</tbody>
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</table>
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<br />
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%endfor
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%endfor
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%endif
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@@ -308,6 +308,9 @@ admin:
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dm_jobs_button: '#${data_manager}-jobs'
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dm_jobs_breadcrumb: '#breadcrumb'
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dm_jobs_table: '#jobs-table'
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dm_job: '#job-${job_id}'
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dm_job_data_manager_card: '#data-manager-card'
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dm_job_data_card: '#data-card'
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users_grid: '#users-grid'
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users_grid_create_button: '.manage-table-actions .action-button'
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groups_grid_create_button: '.manage-table-actions .action-button'
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@@ -91,3 +91,8 @@ class AdminAppTestCase(SeleniumTestCase):
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admin_component.dm_jobs_breadcrumb.wait_for_visible()
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admin_component.dm_jobs_table.wait_for_visible()
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self.screenshot("admin_data_manager_jobs")
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admin_component.dm_job(job_id=job_id).wait_for_and_click()
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admin_component.dm_job_data_manager_card.wait_for_visible()
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admin_component.dm_job_data_card.wait_for_visible()
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self.screenshot("admin_data_manager_job")
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Block a user