def _transaction(self, project_uuid: str, pipeline_name: str,
pipeline_path: str):
# It is important to normalize the path because
# find_pipelines_in_dir will return normalized paths as well,
# which are used to detect pipelines that were deleted through
# the file system in SyncProjectPipelinesDBState.
pipeline_path = normalize_project_relative_path(pipeline_path)
# Reject creation if a pipeline with this path exists already.
if (Pipeline.query.filter(
Pipeline.project_uuid == project_uuid).filter(
Pipeline.path == pipeline_path).count() > 0):
raise FileExistsError(
f"Pipeline already exists at path {pipeline_path}.")
pipeline_uuid = str(uuid.uuid4())
pipeline = Pipeline(path=pipeline_path,
uuid=pipeline_uuid,
project_uuid=project_uuid)
db.session.add(pipeline)
# To be used by the collateral and revert functions.
self.collateral_kwargs["project_uuid"] = project_uuid
self.collateral_kwargs["pipeline_uuid"] = pipeline_uuid
self.collateral_kwargs["pipeline_name"] = pipeline_name
self.collateral_kwargs["pipeline_path"] = pipeline_path
return pipeline_uuid
def new_pipeline():
"""
Creates a new mock dataset to test
"""
pipeline = Pipeline(id=1,
pipeline_id=12,
owner_id=1,
name='Freesurfer',
version='1.9',
is_private=False,
date_created=datetime.now(),
date_updated=datetime.now())
return pipeline
def _transaction(self, project_uuid: str, pipeline_path: str):
pipeline_json_path = get_pipeline_path(None,
project_uuid,
pipeline_path=pipeline_path)
# Check the uuid of the pipeline. If the uuid is taken by
# another pipeline in the project then generate a new uuid for
# the pipeline.
with open(pipeline_json_path, "r") as json_file:
pipeline_json = json.load(json_file)
file_pipeline_uuid = pipeline_json.get("uuid")
self.collateral_kwargs["new_uuid"] = None
self.collateral_kwargs["project_uuid"] = None
self.collateral_kwargs["pipeline_uuid"] = None
self.collateral_kwargs["pipeline_path"] = None
self.collateral_kwargs["pipeline_json"] = None
# If the pipeline has its own uuid and the uuid is not in
# the DB already then the pipeline does not need to have a
# new uuid assigned and written to disk.
if (file_pipeline_uuid is not None
and Pipeline.query.filter_by(project_uuid=project_uuid,
uuid=file_pipeline_uuid,
status="READY").count() == 0):
self.collateral_kwargs["new_uuid"] = False
else:
self.collateral_kwargs["new_uuid"] = True
# Generate a new uuid for the pipeline.
file_pipeline_uuid = str(uuid.uuid4())
self.collateral_kwargs["project_uuid"] = project_uuid
self.collateral_kwargs["pipeline_uuid"] = file_pipeline_uuid
self.collateral_kwargs["pipeline_path"] = pipeline_path
self.collateral_kwargs["pipeline_json"] = pipeline_json
# Add the pipeline to the db.
new_pipeline = Pipeline(
uuid=file_pipeline_uuid,
path=pipeline_path,
project_uuid=project_uuid,
)
db.session.add(new_pipeline)
def pipelines_create(project_uuid):
pipeline_path = request.json["pipeline_path"]
if (Pipeline.query.filter(
Pipeline.project_uuid == project_uuid).filter(
Pipeline.path == pipeline_path).count() == 0):
pipeline_uuid = str(uuid.uuid4())
pipeline = Pipeline(path=pipeline_path,
uuid=pipeline_uuid,
project_uuid=project_uuid)
db.session.add(pipeline)
db.session.commit()
pipeline_dir = get_pipeline_directory(pipeline_uuid, project_uuid)
pipeline_json_path = get_pipeline_path(pipeline_uuid, project_uuid)
os.makedirs(pipeline_dir, exist_ok=True)
# generate clean pipeline.json
pipeline_json = {
"name": request.json["name"],
"version": "1.0.0",
"uuid": pipeline_uuid,
"settings": {
"auto_eviction": False,
"data_passing_memory_size": "1GB",
},
"steps": {},
}
with open(pipeline_json_path, "w") as pipeline_json_file:
pipeline_json_file.write(json.dumps(pipeline_json, indent=4))
return jsonify({"success": True})
else:
return (
jsonify({
"message":
"Pipeline already exists at path '%s'." % pipeline_path
}),
409,
)
def insert_sample_pipelines(self):
with open(self.pipelines_file, 'r') as pipelines_file:
reader = csv.reader(pipelines_file)
next(reader)
for row in reader:
pipeline = Pipeline(id=row[0],
pipeline_id=row[1],
owner_id=row[2],
name=row[3],
version=row[4],
is_private=row[5] == 'True',
date_created=datetime.now(),
date_updated=datetime.now())
db.session.add(pipeline)
db.session.commit()
pipelines_file.close()
def _transaction(self, project_uuid: str, pipeline_name: str,
pipeline_path: str):
# Reject creation if a pipeline with this path exists already.
if (Pipeline.query.filter(
Pipeline.project_uuid == project_uuid).filter(
Pipeline.path == pipeline_path).count() > 0):
raise FileExistsError(
f"Pipeline already exists at path {pipeline_path}.")
pipeline_uuid = str(uuid.uuid4())
pipeline = Pipeline(path=pipeline_path,
uuid=pipeline_uuid,
project_uuid=project_uuid)
db.session.add(pipeline)
# To be used by the collateral and revert functions.
self.collateral_kwargs["project_uuid"] = project_uuid
self.collateral_kwargs["pipeline_uuid"] = pipeline_uuid
self.collateral_kwargs["pipeline_name"] = pipeline_name
self.collateral_kwargs["pipeline_path"] = pipeline_path
def sync_project_pipelines_db_state(project_uuid):
"""Synchronizes the state of the pipelines of a project (fs/db).
Synchronizes the state of the filesystem with the db
when it comes to the pipelines of a project. Pipelines removed
from the file system are removed, new pipelines (or pipelines
that were there after, for example, a project import) are
registered in the db.
Args:
project_uuid:
Raises:
FileNotFoundError: If the project directory is not found.
"""
project_path = project_uuid_to_path(project_uuid)
project_dir = os.path.join(app.config["USER_DIR"], "projects",
project_path)
if not os.path.isdir(project_dir):
raise FileNotFoundError("Project directory not found")
# find all pipelines in project dir
pipeline_paths = find_pipelines_in_dir(project_dir, project_dir)
# cleanup pipelines that have been manually removed
fs_removed_pipelines = [
pipeline for pipeline in Pipeline.query.filter(
Pipeline.path.notin_(pipeline_paths)).filter(
Pipeline.project_uuid == project_uuid).all()
]
for fs_removed_pipeline in fs_removed_pipelines:
cleanup_pipeline_from_orchest(fs_removed_pipeline)
# identify all pipeline paths that are not yet a pipeline
existing_pipeline_paths = [
pipeline.path for pipeline in Pipeline.query.filter(
Pipeline.path.in_(pipeline_paths)).filter(
Pipeline.project_uuid == project_uuid).all()
]
# TODO: handle existing pipeline assignments
new_pipeline_paths = set(pipeline_paths) - set(existing_pipeline_paths)
for new_pipeline_path in new_pipeline_paths:
# write pipeline uuid to file
pipeline_json_path = get_pipeline_path(
None, project_uuid, pipeline_path=new_pipeline_path)
try:
with open(pipeline_json_path, "r") as json_file:
pipeline_json = json.load(json_file)
file_pipeline_uuid = pipeline_json.get("uuid")
new_pipeline_uuid = file_pipeline_uuid
# see if pipeline_uuid is taken
if (Pipeline.query.filter(
Pipeline.uuid == file_pipeline_uuid).filter(
Pipeline.project_uuid == project_uuid).count() > 0
or len(file_pipeline_uuid) == 0):
new_pipeline_uuid = str(uuid.uuid4())
with open(pipeline_json_path, "w") as json_file:
pipeline_json["uuid"] = new_pipeline_uuid
json_file.write(json.dumps(pipeline_json, indent=4))
# only commit if writing succeeds
new_pipeline = Pipeline(
uuid=new_pipeline_uuid,
path=new_pipeline_path,
project_uuid=project_uuid,
)
db.session.add(new_pipeline)
db.session.commit()
except Exception as e:
logging.info(e)
def pipelines_get(project_uuid):
project_path = project_uuid_to_path(project_uuid)
project_dir = os.path.join(app.config["USER_DIR"], "projects",
project_path)
if not os.path.isdir(project_dir):
return jsonify({"message": "Project directory not found."}), 404
# find all pipelines in project dir
pipeline_paths = find_pipelines_in_dir(project_dir, project_dir)
# identify all pipeline paths that are not yet a pipeline
existing_pipeline_paths = [
pipeline.path for pipeline in Pipeline.query.filter(
Pipeline.path.in_(pipeline_paths)).filter(
Pipeline.project_uuid == project_uuid).all()
]
# TODO: handle existing pipeline assignments
new_pipeline_paths = set(pipeline_paths) - set(existing_pipeline_paths)
for new_pipeline_path in new_pipeline_paths:
# write pipeline uuid to file
pipeline_json_path = get_pipeline_path(
None, project_uuid, pipeline_path=new_pipeline_path)
try:
with open(pipeline_json_path, "r") as json_file:
pipeline_json = json.load(json_file)
file_pipeline_uuid = pipeline_json.get("uuid")
new_pipeline_uuid = file_pipeline_uuid
# see if pipeline_uuid is taken
if (Pipeline.query.filter(
Pipeline.uuid == file_pipeline_uuid).filter(
Pipeline.project_uuid == project_uuid).count() > 0
or len(file_pipeline_uuid) == 0):
new_pipeline_uuid = str(uuid.uuid4())
with open(pipeline_json_path, "w") as json_file:
pipeline_json["uuid"] = new_pipeline_uuid
json_file.write(json.dumps(pipeline_json, indent=2))
# only commit if writing succeeds
new_pipeline = Pipeline(
uuid=new_pipeline_uuid,
path=new_pipeline_path,
project_uuid=project_uuid,
)
db.session.add(new_pipeline)
db.session.commit()
except Exception as e:
logging.info(e)
pipelines = Pipeline.query.filter(
Pipeline.project_uuid == project_uuid).all()
pipelines_augmented = []
for pipeline in pipelines:
pipeline_json_path = get_pipeline_path(pipeline.uuid,
pipeline.project_uuid)
pipeline_augmented = {
"uuid": pipeline.uuid,
"path": pipeline.path,
}
if os.path.isfile(pipeline_json_path):
with open(pipeline_json_path, "r") as json_file:
pipeline_json = json.load(json_file)
pipeline_augmented["name"] = pipeline_json["name"]
else:
pipeline_augmented[
"name"] = "Warning: pipeline file was not found."
pipelines_augmented.append(pipeline_augmented)
json_string = json.dumps({
"success": True,
"result": pipelines_augmented
})
return json_string, 200, {"content-type": "application/json"}