diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index 613fc88e4a3c..7e178c5369ad 100644 --- a/client/src/api/schema/schema.ts +++ b/client/src/api/schema/schema.ts @@ -15660,6 +15660,7 @@ export interface operations { /** @description Limit listing of jobs to those that match the history_id. If none, jobs from any history may be returned. */ /** @description Limit listing of jobs to those that match the specified workflow ID. If none, jobs from any workflow (or from no workflows) may be returned. */ /** @description Limit listing of jobs to those that match the specified workflow invocation ID. If none, jobs from any workflow invocation (or from no workflows) may be returned. */ + /** @description Limit listing of jobs to those that match the specified implicit collection job ID. If none, jobs from any implicit collection execution (or from no implicit collection execution) may be returned. */ /** @description Sort results by specified field. */ /** * @description A mix of free text and GitHub-style tags used to filter the index operation. @@ -15711,6 +15712,7 @@ export interface operations { history_id?: string; workflow_id?: string; invocation_id?: string; + implicit_collection_jobs_id?: string; order_by?: components["schemas"]["JobIndexSortByEnum"]; search?: string; limit?: number; diff --git a/client/src/components/JobMetrics/JobMetrics.vue b/client/src/components/JobMetrics/JobMetrics.vue index 508de897f543..de1cbe9a1d6e 100644 --- a/client/src/components/JobMetrics/JobMetrics.vue +++ b/client/src/components/JobMetrics/JobMetrics.vue @@ -1,5 +1,5 @@ + + diff --git a/client/src/components/Markdown/Elements/handlesMappingJobs.ts b/client/src/components/Markdown/Elements/handlesMappingJobs.ts new file mode 100644 index 000000000000..fa257872dd69 --- /dev/null +++ b/client/src/components/Markdown/Elements/handlesMappingJobs.ts @@ -0,0 +1,51 @@ +import { format, parseISO } from "date-fns"; +import { computed, Ref, ref, watch } from "vue"; + +import { fetcher } from "@/api/schema"; + +const jobsFetcher = fetcher.path("/api/jobs").method("get").create(); + +export interface SelectOption { + value: string; + text: string; +} + +interface Job { + id: string; + create_time: string; +} + +export function useMappingJobs( + singleJobId: Ref, + implicitCollectionJobsId: Ref +) { + const selectJobOptions = ref([]); + const selectedJob = ref(undefined); + const targetJobId = computed(() => { + if (singleJobId.value) { + return singleJobId.value; + } else { + return selectedJob.value; + } + }); + watch( + implicitCollectionJobsId, + async () => { + if (implicitCollectionJobsId.value) { + const response = await jobsFetcher({ implicit_collection_jobs_id: implicitCollectionJobsId.value }); + const jobs: Job[] = response.data as unknown as Job[]; + selectJobOptions.value = jobs.map((value, index) => { + const isoCreateTime = parseISO(`${value.create_time}Z`); + const prettyTime = format(isoCreateTime, "eeee MMM do H:mm:ss yyyy zz"); + return { value: value.id, text: `${index + 1}: ${prettyTime}` }; + }); + if (jobs[0]) { + const job: Job = jobs[0]; + selectedJob.value = job.id; + } + } + }, + { immediate: true } + ); + return { selectJobOptions, selectedJob, targetJobId }; +} diff --git a/client/src/components/Markdown/MarkdownContainer.vue b/client/src/components/Markdown/MarkdownContainer.vue index a76c465c10d0..9eb19973390c 100644 --- a/client/src/components/Markdown/MarkdownContainer.vue +++ b/client/src/components/Markdown/MarkdownContainer.vue @@ -151,11 +151,13 @@ function argToBoolean(args, name, booleanDefault) { diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py index dbf439364d45..cce10d602971 100644 --- a/lib/galaxy/managers/collections_util.py +++ b/lib/galaxy/managers/collections_util.py @@ -144,6 +144,11 @@ def dictify_dataset_collection_instance( else: element_func = dictify_element_reference dict_value["elements"] = [element_func(_, rank_fuzzy_counts=rest_fuzzy_counts) for _ in elements] + icj = dataset_collection_instance.implicit_collection_jobs + if icj: + dict_value["implicit_collection_jobs_id"] = icj.id + else: + dict_value["implicit_collection_jobs_id"] = None security.encode_all_ids(dict_value, recursive=True) # TODO: Use Kyle's recursive formulation of this. return dict_value diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py index c8eef282b25b..5369e3c105b6 100644 --- a/lib/galaxy/managers/jobs.py +++ b/lib/galaxy/managers/jobs.py @@ -41,6 +41,7 @@ from galaxy.managers.hdas import HDAManager from galaxy.managers.lddas import LDDAManager from galaxy.model import ( + ImplicitCollectionJobs, ImplicitCollectionJobsJobAssociation, Job, JobParameter, @@ -105,12 +106,18 @@ def __init__(self, app: StructuredApp): self.dataset_manager = DatasetManager(app) def index_query(self, trans, payload: JobIndexQueryPayload) -> sqlalchemy.engine.Result: + """The caller is responsible for security checks on the resulting job if + history_id, invocation_id, or implicit_collection_jobs_id is set. + Otherwise this will only return the user's jobs or all jobs if the requesting + user is acting as an admin. + """ is_admin = trans.user_is_admin user_details = payload.user_details decoded_user_id = payload.user_id history_id = payload.history_id workflow_id = payload.workflow_id invocation_id = payload.invocation_id + implicit_collection_jobs_id = payload.implicit_collection_jobs_id search = payload.search order_by = payload.order_by @@ -200,7 +207,9 @@ def add_search_criteria(stmt): if user_details: stmt = stmt.outerjoin(Job.user) else: - stmt = stmt.where(Job.user_id == trans.user.id) + if history_id is None and invocation_id is None and implicit_collection_jobs_id is None: + stmt = stmt.where(Job.user_id == trans.user.id) + # caller better check security stmt = build_and_apply_filters(stmt, payload.states, lambda s: model.Job.state == s) stmt = build_and_apply_filters(stmt, payload.tool_ids, lambda t: model.Job.tool_id == t) @@ -214,7 +223,13 @@ def add_search_criteria(stmt): order_by_columns = Job if workflow_id or invocation_id: stmt, order_by_columns = add_workflow_jobs() - + elif implicit_collection_jobs_id: + stmt = stmt.join( + ImplicitCollectionJobsJobAssociation, ImplicitCollectionJobsJobAssociation.job_id == Job.id + ).join( + ImplicitCollectionJobs, + ImplicitCollectionJobs.id == ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id, + ).where(ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id == implicit_collection_jobs_id) if search: stmt = add_search_criteria(stmt) diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py index 4d0f20b5d2ca..a0931a73485a 100644 --- a/lib/galaxy/managers/markdown_parse.py +++ b/lib/galaxy/managers/markdown_parse.py @@ -50,10 +50,10 @@ class DynamicArguments: "workflow_display": ["workflow_id", "workflow_checkpoint"], "workflow_license": ["workflow_id"], "workflow_image": ["workflow_id", "size", "workflow_checkpoint"], - "job_metrics": ["step", "job_id"], - "job_parameters": ["step", "job_id"], - "tool_stderr": ["step", "job_id"], - "tool_stdout": ["step", "job_id"], + "job_metrics": ["step", "job_id", "implicit_collection_jobs_id"], + "job_parameters": ["step", "job_id", "implicit_collection_jobs_id"], + "tool_stderr": ["step", "job_id", "implicit_collection_jobs_id"], + "tool_stdout": ["step", "job_id", "implicit_collection_jobs_id"], "generate_galaxy_version": [], "generate_time": [], "instance_access_link": [], diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py index 9ef57141375e..c6e8e63993e4 100644 --- a/lib/galaxy/managers/markdown_util.py +++ b/lib/galaxy/managers/markdown_util.py @@ -72,10 +72,10 @@ SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX) # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)') UNENCODED_ID_PATTERN = re.compile( - r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([\d]+)" + r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs_id|invocation_id)=([\d]+)" ) ENCODED_ID_PATTERN = re.compile( - r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([a-z0-9]+)" + r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs_id|invocation_id)=([a-z0-9]+)" ) INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(r"```\s*galaxy\s*") GALAXY_FENCED_BLOCK = re.compile(r"^```\s*galaxy\s*(.*?)^```", re.MULTILINE ^ re.DOTALL) @@ -929,9 +929,13 @@ def find_non_empty_group(match): elif step_match: target_match = step_match name = find_non_empty_group(target_match) - ref_object_type = "job" invocation_step = invocation.step_invocation_for_label(name) - ref_object = invocation_step and invocation_step.job + if invocation_step and invocation_step.job: + ref_object_type = "job" + ref_object = invocation_step.job + elif invocation_step and invocation_step.implicit_collection_jobs: + ref_object_type = "implicit_collection_jobs" + ref_object = invocation_step.implicit_collection_jobs else: target_match = None ref_object = None diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py index 6920fe5dbb94..a88c08546e5b 100644 --- a/lib/galaxy/schema/schema.py +++ b/lib/galaxy/schema/schema.py @@ -1043,6 +1043,9 @@ class HDCADetailed(HDCASummary): elements_datatypes: Set[str] = Field( ..., description="A set containing all the different element datatypes in the collection." ) + implicit_collection_jobs_id: Optional[EncodedDatabaseIdField] = Field( + None, description="Encoded ID for the ICJ object describing the collection of jobs corresponding to this collection" + ) class HistoryBase(Model): @@ -1391,6 +1394,7 @@ class JobIndexQueryPayload(Model): history_id: Optional[DecodedDatabaseIdField] = None workflow_id: Optional[DecodedDatabaseIdField] = None invocation_id: Optional[DecodedDatabaseIdField] = None + implicit_collection_jobs_id: Optional[DecodedDatabaseIdField] = None order_by: JobIndexSortByEnum = JobIndexSortByEnum.update_time search: Optional[str] = None limit: int = 500 diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index bd19370dd6ae..32def1bdfc13 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -150,6 +150,12 @@ description="Limit listing of jobs to those that match the specified workflow invocation ID. If none, jobs from any workflow invocation (or from no workflows) may be returned.", ) +ImplicitCollectionJobsIdQueryParam: Optional[DecodedDatabaseIdField] = Query( + default=None, + title="Implicit Collection Jobs ID", + description="Limit listing of jobs to those that match the specified implicit collection job ID. If none, jobs from any implicit collection execution (or from no implicit collection execution) may be returned.", +) + SortByQueryParam: JobIndexSortByEnum = Query( default=JobIndexSortByEnum.update_time, title="Sort By", @@ -216,6 +222,7 @@ def index( history_id: Optional[DecodedDatabaseIdField] = HistoryIdQueryParam, workflow_id: Optional[DecodedDatabaseIdField] = WorkflowIdQueryParam, invocation_id: Optional[DecodedDatabaseIdField] = InvocationIdQueryParam, + implicit_collection_jobs_id: Optional[DecodedDatabaseIdField] = ImplicitCollectionJobsIdQueryParam, order_by: JobIndexSortByEnum = SortByQueryParam, search: Optional[str] = SearchQueryParam, limit: int = LimitQueryParam, @@ -233,6 +240,7 @@ def index( history_id=history_id, workflow_id=workflow_id, invocation_id=invocation_id, + implicit_collection_jobs_id=implicit_collection_jobs_id, order_by=order_by, search=search, limit=limit, diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py index ec9e42467482..b1453a704343 100644 --- a/lib/galaxy/webapps/galaxy/services/jobs.py +++ b/lib/galaxy/webapps/galaxy/services/jobs.py @@ -10,6 +10,7 @@ exceptions, model, ) +from galaxy.managers.base import security_check from galaxy.managers import hdas from galaxy.managers.context import ProvidesUserContext from galaxy.managers.jobs import ( @@ -74,13 +75,16 @@ def index( payload.user_details = True user_details = payload.user_details decoded_user_id = payload.user_id - if not is_admin: self._check_nonadmin_access(view, user_details, decoded_user_id, trans.user.id) + check_security_of_jobs = payload.invocation_id is not None or payload.implicit_collection_jobs_id is not None or payload.history_id is not None jobs = self.job_manager.index_query(trans, payload) out = [] for job in jobs.yield_per(model.YIELD_PER_ROWS): + # TODO: optimize if this crucial + if check_security_of_jobs and not security_check(trans, job.history, check_accessible=True): + raise exceptions.ItemAccessibilityException("Cannot access the request job objects.") job_dict = job.to_dict(view, system_details=is_admin) j = security.encode_all_ids(job_dict, True) if view == JobIndexViewEnum.admin_job_list: diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py index af77499417d7..e537e0c6c975 100644 --- a/lib/galaxy_test/api/test_jobs.py +++ b/lib/galaxy_test/api/test_jobs.py @@ -739,6 +739,22 @@ def test_search_delete_outputs(self, history_id): search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs) self._search(search_payload, expected_search_count=0) + def test_implicit_collection_jobs(self, history_id): + run_response = self._run_map_over_error(history_id) + implicit_collection_id = run_response["implicit_collections"][0]["id"] + failed_hdca = self.dataset_populator.get_history_collection_details( + history_id=history_id, + content_id=implicit_collection_id, + assert_ok=False, + ) + job_id = run_response["jobs"][0]["id"] + icj_id = failed_hdca["implicit_collection_jobs_id"] + assert icj_id + index = self.__jobs_index(data=dict(implicit_collection_jobs_id=icj_id)) + assert len(index) == 1 + assert index[0]["id"] == job_id + assert index[0]["state"] == "error", index + @pytest.mark.require_new_history def test_search_with_hdca_list_input(self, history_id): list_id_a = self.__history_with_ok_collection(collection_type="list", history_id=history_id)