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Merge branch 'release_21.09' into dev

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This commit is contained in:
Nicola Soranzo
2022-01-04 13:51:51 +00:00
parent 1a3bc169dc 3f8bb2dd46
commit 7fdcb6ac15
8 changed files with 53 additions and 51 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/components/History/ContentItem/Dataset/DatasetMenu.vue
+5 -3
View File
@@ -251,8 +251,9 @@ export default {
// wierd iframe navigation
visualize() {
const showDetailsUrl = `/datasets/${this.dataset.id}/details`;
const redirectParams = {
path: this.dataset.getUrl("show_params"),
path: showDetailsUrl,
title: "Dataset details",
tryIframe: false,
};
@@ -264,13 +265,14 @@ export default {
},
showDetails() {
const showDetailsUrl = `/datasets/${this.dataset.id}/details`;
const redirectParams = {
path: this.dataset.getUrl("show_params"),
path: showDetailsUrl,
title: "Dataset details",
tryIframe: false,
};
if (!this.iframeAdd(redirectParams)) {
this.backboneRoute(this.dataset.getUrl("show_params"));
this.backboneRoute(showDetailsUrl);
}
},
client/src/components/plugins/legacyNavigation.js
+1 -1
View File
@@ -51,7 +51,7 @@ export const legacyNavigationMixin = {
// galaxy router, wrapper for backbone router
backboneRoute(path, ...args) {
try {
getGalaxyInstance().router.push(prependPath(path), ...args);
getGalaxyInstance().router.push(path, ...args);
} catch (err) {
console.warn("Failed galaxy route change", err, ...arguments);
throw err;
client/src/mvc/dataset/dataset-li-edit.js
+2 -1
View File
@@ -177,7 +177,8 @@ var DatasetListItemEdit = _super.extend(
classes: "icon-btn",
href: "#",
faIcon: "fa-question",
onclick: function () {
onclick: function (ev) {
ev.preventDefault();
if (self.$el.find(".toolhelp").length > 0) {
self.$el.find(".toolhelp").toggle();
} else {
client/src/mvc/dataset/dataset-li.js
+3 -2
View File
@@ -280,15 +280,16 @@ export var DatasetListItemView = _super.extend(
faIcon: "fa-info-circle",
onclick: (ev) => {
const Galaxy = getGalaxyInstance();
const showDetailsUrl = `/datasets/${this.model.get("id")}/details`;
if (Galaxy.frame && Galaxy.frame.active) {
ev.preventDefault();
Galaxy.frame.add({
url: this.model.urls.show_params,
url: showDetailsUrl,
title: `Dataset Details of ${this.model.get("name")}`,
});
} else if (Galaxy.router) {
ev.preventDefault();
Galaxy.router.push(this.model.urls.show_params);
Galaxy.router.push(showDetailsUrl);
Galaxy.trigger("activate-hda", this.model.get("id"));
}
},
lib/galaxy/jobs/handler.py
+2 -2
View File
@@ -239,11 +239,11 @@ class JobHandlerQueue(Monitors):
.outerjoin(model.User) \
.filter(model.Job.state.in_(in_list)
& (model.Job.handler == self.app.config.server_name)
& or_((model.Job.user_id == null()), (model.User.active == true()))).all()
& or_((model.Job.user_id == null()), (model.User.active == true()))).yield_per(model.YIELD_PER_ROWS)
else:
jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
.filter(model.Job.state.in_(in_list)
& (model.Job.handler == self.app.config.server_name)).all()
& (model.Job.handler == self.app.config.server_name)).yield_per(model.YIELD_PER_ROWS)
for job in jobs_at_startup:
if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
lib/galaxy/metadata/set_metadata.py
+37 -40
View File
@@ -66,6 +66,9 @@ logging.basicConfig()
log = logging.getLogger(__name__)
MAX_STDIO_READ_BYTES = 100 * 10 ** 6 # 100 MB
def set_validated_state(dataset_instance):
datatype_validation = validate(dataset_instance)
@@ -171,46 +174,40 @@ def set_metadata_portable():
outputs_directory = tool_job_working_directory
# TODO: constants...
if os.path.exists(os.path.join(outputs_directory, "tool_stdout")):
with open(os.path.join(outputs_directory, "tool_stdout"), "rb") as f:
tool_stdout = f.read()
with open(os.path.join(outputs_directory, "tool_stderr"), "rb") as f:
tool_stderr = f.read()
elif os.path.exists(os.path.join(tool_job_working_directory, "stdout")):
with open(os.path.join(tool_job_working_directory, "stdout"), "rb") as f:
tool_stdout = f.read()
with open(os.path.join(tool_job_working_directory, "stderr"), "rb") as f:
tool_stderr = f.read()
elif os.path.exists(os.path.join(outputs_directory, "stdout")):
# Puslar style output directory? Was this ever used - did this ever work?
with open(os.path.join(outputs_directory, "stdout"), "rb") as f:
tool_stdout = f.read()
with open(os.path.join(outputs_directory, "stderr"), "rb") as f:
tool_stderr = f.read()
elif os.path.exists(os.path.join(tool_job_working_directory, 'task_0')):
# We have a task splitting job
tool_stdout = b''
tool_stderr = b''
paths = Path(tool_job_working_directory).glob('task_*')
for path in paths:
with open(path / 'outputs' / 'tool_stdout', 'rb') as f:
task_stdout = f.read()
if task_stdout:
tool_stdout = b"%s[%s stdout]\n%s\n" % (tool_stdout, path.name.encode(), task_stdout)
with open(path / 'outputs' / 'tool_stderr', 'rb') as f:
task_stderr = f.read()
if task_stderr:
tool_stderr = b"%s[%s stdout]\n%s\n" % (tool_stderr, path.name.encode(), task_stderr)
locations = [
(outputs_directory, 'tool_'),
(tool_job_working_directory, ''),
(outputs_directory, ''), # # Pulsar style output directory? Was this ever used - did this ever work?
]
for directory, prefix in locations:
if os.path.exists(os.path.join(directory, f"{prefix}stdout")):
with open(os.path.join(directory, f"{prefix}stdout"), 'rb') as f:
tool_stdout = f.read(MAX_STDIO_READ_BYTES)
with open(os.path.join(directory, f"{prefix}stderr"), 'rb') as f:
tool_stderr = f.read(MAX_STDIO_READ_BYTES)
break
else:
wdc = os.listdir(tool_job_working_directory)
odc = os.listdir(outputs_directory)
error_desc = "Failed to find tool_stdout or tool_stderr for this job, cannot collect metadata"
error_extra = f"Working dir contents [{wdc}], output directory contents [{odc}]"
log.warn(f"{error_desc}. {error_extra}")
raise Exception(error_desc)
if os.path.exists(os.path.join(tool_job_working_directory, 'task_0')):
# We have a task splitting job
tool_stdout = b''
tool_stderr = b''
paths = Path(tool_job_working_directory).glob('task_*')
for path in paths:
with open(path / 'outputs' / 'tool_stdout', 'rb') as f:
task_stdout = f.read(MAX_STDIO_READ_BYTES)
if task_stdout:
tool_stdout = b"%s[%s stdout]\n%s\n" % (tool_stdout, path.name.encode(), task_stdout)
with open(path / 'outputs' / 'tool_stderr', 'rb') as f:
task_stderr = f.read(MAX_STDIO_READ_BYTES)
if task_stderr:
tool_stderr = b"%s[%s stdout]\n%s\n" % (tool_stderr, path.name.encode(), task_stderr)
else:
wdc = os.listdir(tool_job_working_directory)
odc = os.listdir(outputs_directory)
error_desc = "Failed to find tool_stdout or tool_stderr for this job, cannot collect metadata"
error_extra = f"Working dir contents [{wdc}], output directory contents [{odc}]"
log.warn(f"{error_desc}. {error_extra}")
raise Exception(error_desc)
job_id_tag = metadata_params["job_id_tag"]
@@ -226,7 +223,7 @@ def set_metadata_portable():
version_string_path = os.path.join('outputs', COMMAND_VERSION_FILENAME)
version_string = collect_shrinked_content_from_path(version_string_path)
expression_context = ExpressionContext(dict(stdout=tool_stdout, stderr=tool_stderr))
expression_context = ExpressionContext(dict(stdout=tool_stdout[:255], stderr=tool_stderr[:255]))
# Load outputs.
export_store = store.DirectoryModelExportStore('metadata/outputs_populated', serialize_dataset_objects=True, for_edit=True, strip_metadata_files=False, serialize_jobs=True)
lib/galaxy/model/__init__.py
+2 -1
View File
@@ -143,6 +143,7 @@ JOB_METRIC_PRECISION = 26
JOB_METRIC_SCALE = 7
# Tags that get automatically propagated from inputs to outputs when running jobs.
AUTO_PROPAGATED_TAGS = ["name"]
YIELD_PER_ROWS = 100
if TYPE_CHECKING:
@@ -940,7 +941,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
back_populates='job')
output_dataset_collections = relationship('JobToImplicitOutputDatasetCollectionAssociation',
back_populates='job')
post_job_actions = relationship('PostJobActionAssociation', back_populates='job', lazy='joined')
post_job_actions = relationship('PostJobActionAssociation', back_populates='job')
input_library_datasets = relationship('JobToInputLibraryDatasetAssociation',
back_populates='job')
output_library_datasets = relationship('JobToOutputLibraryDatasetAssociation',
lib/galaxy/webapps/galaxy/api/jobs.py
+1 -1
View File
@@ -204,7 +204,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
query = query.limit(limit)
out = []
for job in query.all():
for job in query.yield_per(model.YIELD_PER_ROWS):
job_dict = job.to_dict(view, system_details=is_admin)
j = self.encode_all_ids(trans, job_dict, True)
if view == 'admin_job_list':