Merge pull request galaxyproject#19997 from jmchilton/selenium_workflows_run_collections

Author: ahmedhamidawan

client/src/components/Collections/common/CollectionCreator.vue

@@ -139,7 +139,10 @@ watch(
             </div>
         </span>
         <BTabs v-else v-model="currentTab" fill justified>
-            <BTab class="collection-creator" :title="localize('Create Collection')">
+            <BTab
+                class="collection-creator"
+                :title="localize('Create Collection')"
+                :title-link-attributes="{ 'data-description': 'collection create tab build' }">
                 <div v-if="props.noItems">
                     <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
                 </div>
@@ -175,7 +178,7 @@ watch(
                     </div>
                 </div>
             </BTab>
-            <BTab>
+            <BTab :title-link-attributes="{ 'data-description': 'collection create tab upload' }">
                 <template v-slot:title>
                     <FontAwesomeIcon :icon="faUpload" fixed-width />
                     <span>{{ localize("Upload Files to Add to Collection") }}</span>

client/src/components/Form/Elements/FormData/FormDataContextButtons.vue

@@ -111,6 +111,7 @@ function createCollectionType(colType: string) {
             "
             v-b-tooltip.bottom.hover.noninteractive
             class="d-flex flex-gapx-1 align-items-center"
+            data-description="upload"
             :title="createTitle"
             :pressed="props.workflowTab === 'create'"
             @click="clickedTab('create')">

client/src/components/Upload/DefaultBox.vue

@@ -364,7 +364,7 @@ defineExpose({
     <div class="upload-wrapper">
         <div class="upload-header">
             <div v-if="props.emitUploaded && historyItemsStateInfo">
-                <BAlert show :variant="historyItemsStateInfo.variant">
+                <BAlert show :variant="historyItemsStateInfo.variant" data-description="upload state alert">
                     <LoadingSpan v-if="historyItemsStateInfo.spin" :message="historyItemsStateInfo.message" />
                     <span v-else>{{ historyItemsStateInfo.message }}</span>
                 </BAlert>

client/src/utils/navigation/navigation.yml

@@ -683,7 +683,33 @@ trs_import:
     url_input: "#trs-import-url-input"
     url_import_button: "#trs-url-import-button"
 
+# not meant as a stand-alone component - just using for the anchor
+upload_mixin:
+  selectors: &upload_mixin
+    create_button: '${_} #btn-new'
+    paste_option: '${_} #upload-row-${n} .upload-source .dropdown-menu .dropdown-item .fa-edit'
+    paste_content: '${_} #upload-row-${n} .upload-text-content'
+    row: '${_} #upload-row-${n}'
+    status: '${_} [data-description="upload state alert"]'
+    embedded_start_button: '${_} #btn-start'
+    use_button: '${_} #btn-emit'
+
 workflow_run:
+  input:
+    selectors:
+      _: '[data-label="${label}"]'
+      upload: '${_} [data-description="upload"]'
+      collection_tab_build_link: '${_} [data-description="collection create tab build"]'
+      collection_tab_upload_link: '${_} [data-description="collection create tab upload"]'
+      # data inputs
+      <<: *upload_mixin
+
+    collection_builder:
+      selectors:
+        _: '[data-label="${label}"] .tabs'
+        create: '${_} .create-collection'
+        <<: *upload_mixin
+
   selectors:
     warning: '[data-description="workflow run warning"]'
     run_error: '[data-description="workflow run error"]'
@@ -1154,6 +1180,7 @@ upload:
     paste_option: '#upload-row-${n} .upload-source .dropdown-menu .dropdown-item .fa-edit'
     paste_content: '#upload-row-${n} .upload-text-content'
     row: '#upload-row-${n}'
+    status: '[data-description="upload state alert"]'
     rule_dataset_dialog: '[data-description="rules dataset dialog"]'
     rule_dataset_selector:
       selector: '.selection-dialog-modal'

client/src/utils/url.ts

@@ -11,7 +11,10 @@ export interface UrlDataOptions {
 }
 
 export const USER_FILE_PREFIX = "gxuserfiles://";
+// TODO: File sources can register custom URI schemes post https://github.com/galaxyproject/galaxy/pull/15497,
+// as such this list should probably be calculated on that backend for correctness.
 export const URI_PREFIXES = [
+    "base64://",
     "http://",
     "https://",
     "ftp://",

lib/galaxy/navigation/components.py

@@ -294,6 +294,8 @@ def from_dict(name, raw_value):
         sub_components = {}
 
         for key, value in raw_value.items():
+            if key.endswith("mixin"):
+                continue
             if key == "selectors":
                 base_selector = None
                 if "_" in value:

lib/galaxy_test/selenium/test_workflow_run.py

@@ -3,6 +3,7 @@
 
 import yaml
 from selenium.webdriver.common.by import By
+from typing_extensions import Literal
 
 from galaxy_test.base import rules_test_data
 from galaxy_test.base.workflow_fixtures import (
@@ -17,6 +18,7 @@
     WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
     WORKFLOW_WITH_DATA_TAG_FILTER,
     WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
+    WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION,
     WORKFLOW_WITH_OLD_TOOL_VERSION,
     WORKFLOW_WITH_RULES_1,
 )
@@ -389,16 +391,78 @@ def test_workflow_run_tag_filter(self):
         self.dataset_populator.tag_dataset(history_id, dataset["id"], tags=["genomescope_model"])
         # Add another possible input that should not be selected
         self.dataset_populator.new_dataset(history_id, wait=True)
-        wf = json.loads(WORKFLOW_WITH_DATA_TAG_FILTER)
-        wf["name"] = str(uuid4())
-        workflow_id = self.workflow_populator.create_workflow(wf)
-        self.workflow_run_with_name(wf["name"])
+        workflow_id, workflow_name = self._create_workflow_with_unique_name(WORKFLOW_WITH_DATA_TAG_FILTER, "ga")
+        self.workflow_run_with_name(workflow_name)
         self.workflow_run_submit()
         self.sleep_for(self.wait_types.HISTORY_POLL)
         invocations = self.workflow_populator.workflow_invocations(workflow_id=workflow_id)
         invocation = self.workflow_populator.get_invocation(invocations[-1]["id"])
         assert invocation["inputs"]["0"]["id"] == dataset["id"]
 
+    @selenium_test
+    @managed_history
+    def test_upload_dataset_from_workflow_simple(self):
+        history_id = self.current_history_id()
+        self._create_and_run_workflow_with_unique_name(WORKFLOW_SIMPLE_CAT_TWICE)
+        workflow_run = self.components.workflow_run
+        input = workflow_run.input._(label="input1")
+        input.upload.wait_for_and_click()
+        self._upload_hello_world_for_input(input)
+        self.workflow_run_submit()
+        self.history_panel_wait_for_hid_ok(2)
+        content = self.dataset_populator.get_history_dataset_content(history_id, hid=2)
+        assert content.strip() == "hello world\nhello world"
+
+    @selenium_test
+    @managed_history
+    def test_upload_list_from_workflow_simple(self):
+        self._create_and_run_workflow_with_unique_name(WORKFLOW_WITH_MAPPED_OUTPUT_COLLECTION)
+        workflow_run = self.components.workflow_run
+        input = workflow_run.input._(label="input1")
+        input.upload.wait_for_and_click()
+        input.collection_tab_upload_link.wait_for_and_click()
+        builder = workflow_run.input.collection_builder._(label="input1")
+        self._upload_hello_world_for_input(builder, count=2)
+        input.collection_tab_build_link.wait_for_and_click()
+        builder.create.wait_for_and_click()
+        self.workflow_run_submit()
+        self.history_panel_wait_for_hid_ok(6)
+
+    def _upload_hello_world_for_input(self, workflow_input, count=1, from_hid=1):
+        # assumes fresh history...
+        workflow_input.create_button.wait_for_and_click()
+        url = self.dataset_populator.base64_url_for_string("hello world")
+        content = ""
+        for _ in range(count):
+            content += url + "\n"
+        workflow_input.paste_content(n=0).wait_for_and_send_keys(content)
+        workflow_input.embedded_start_button.wait_for_and_click()
+        workflow_input.status.wait_for_present()
+        for i in range(from_hid, from_hid + count):
+            self.history_panel_wait_for_hid_ok(i)
+        workflow_input.use_button.wait_for_and_click()
+
+    def _create_and_run_workflow_with_unique_name(
+        self, workflow_contents: str, format: Literal["ga", "gxformat2"] = "gxformat2"
+    ):
+        workflow_id, workflow_name = self._create_workflow_with_unique_name(workflow_contents, format)
+        self.workflow_run_with_name(workflow_name)
+        return workflow_id, workflow_name
+
+    def _create_workflow_with_unique_name(
+        self, workflow_contents: str, format: Literal["ga", "gxformat2"] = "gxformat2"
+    ):
+        workflow_name = str(uuid4())
+        if format == "gxformat2":
+            wf = yaml.safe_load(workflow_contents)
+            wf["name"] = workflow_name
+            workflow_id = self.workflow_populator.upload_yaml_workflow(wf)
+        else:
+            wf = json.loads(workflow_contents)
+            wf["name"] = workflow_name
+            workflow_id = self.workflow_populator.create_workflow(wf)
+        return (workflow_id, workflow_name)
+
     def _assert_has_3_lines_after_run(self, hid):
         self.workflow_run_wait_for_ok(hid=hid)
         history_id = self.current_history_id()