From d1989b1a44ec74d81ded7b0bed488f890043b05f Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Fri, 24 Feb 2023 13:03:56 +0100
Subject: [PATCH] SSDM-13330: Added upload of files to a new dataset flow for
PHYSICAL data.
---
.../src/python/obis/dm/commands/upload.py | 46 +++++++++++++++++++
.../src/python/obis/dm/data_mgmt.py | 21 +++++++++
.../src/python/obis/scripts/cli.py | 33 +++++++++++--
3 files changed, 97 insertions(+), 3 deletions(-)
create mode 100644 app-openbis-command-line/src/python/obis/dm/commands/upload.py
diff --git a/app-openbis-command-line/src/python/obis/dm/commands/upload.py b/app-openbis-command-line/src/python/obis/dm/commands/upload.py
new file mode 100644
index 00000000000..d9ee708b584
--- /dev/null
+++ b/app-openbis-command-line/src/python/obis/dm/commands/upload.py
@@ -0,0 +1,46 @@
+# Copyright ETH 2023 Zürich, Scientific IT Services
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from .openbis_command import OpenbisCommand
+from ..command_result import CommandResult
+from ..utils import cd
+from ...scripts.click_util import click_echo
+
+
+class Upload(OpenbisCommand):
+ """
+ Command to upload physical files to form a data set.
+ """
+
+ def __init__(self, dm, sample_id, data_set_type, files):
+ """
+ :param dm: data management
+ :param sample_id: permId or sample path of the parent sample
+ :param data_set_type: type of newly created data set.
+ :param files: list of files/directories to upload
+ """
+ self.data_set_type = data_set_type
+ self.files = files
+ self.sample_id = sample_id
+ self.load_global_config(dm)
+ super(Upload, self).__init__(dm)
+
+ def run(self):
+ with cd(self.data_mgmt.invocation_path):
+ click_echo(f"Uploading files {self.files} under {self.sample_id}")
+ ds = self.openbis.new_dataset(type=self.data_set_type, sample=self.sample_id,
+ files=self.files)
+ result = ds.save()
+ return CommandResult(returncode=0, output=f"Upload finished. New dataset: {result}")
diff --git a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py b/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
index 93ed3746e1c..326d8bda283 100644
--- a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
+++ b/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
@@ -35,6 +35,7 @@ from .commands.move import Move
from .commands.openbis_sync import OpenbisSync
from .commands.removeref import Removeref
from .commands.search import Search
+from .commands.upload import Upload
from .git import GitWrapper
from .utils import Type
from .utils import cd
@@ -217,6 +218,15 @@ class AbstractDataMgmt(metaclass=abc.ABCMeta):
"""
return
+ @abc.abstractmethod
+ def upload(self, sample_id, data_set_type, files):
+ """Upload files/directories into a new data set.
+ :param sample_id: permId or sample path of the parent sample
+ :param data_set_type: type of created data set
+ :param files: list of files/directories to upload
+ """
+ return
+
@abc.abstractmethod
def search_object(self, type_code, space, project, experiment, property_code, property_value,
save):
@@ -231,6 +241,7 @@ class AbstractDataMgmt(metaclass=abc.ABCMeta):
"""
return
+ @abc.abstractmethod
def search_data_set(self, type_code, space, project, experiment, property_code, property_value,
save):
"""Search for datasets in openBIS using filtering criteria.
@@ -290,6 +301,9 @@ class NoGitDataMgmt(AbstractDataMgmt):
def search_data_set(self, *_):
self.error_raise("search", "No git command found.")
+ def upload(self, *_):
+ self.error_raise("upload", "No git command found.")
+
def restore_signal_handler(data_mgmt):
data_mgmt.restore()
@@ -575,6 +589,9 @@ class GitDataMgmt(AbstractDataMgmt):
def search_data_set(self, *_):
self.error_raise("search", "This functionality is not implemented for data of LINK type.")
+ def upload(self, *_):
+ self.error_raise("upload", "This functionality is not implemented for data of LINK type.")
+
class PhysicalDataMgmt(AbstractDataMgmt):
"""DataMgmt operations for DSS-stored data."""
@@ -624,6 +641,10 @@ class PhysicalDataMgmt(AbstractDataMgmt):
cmd = DownloadPhysical(self, data_set_id, file)
return cmd.run()
+ def upload(self, sample_id, data_set_type, files):
+ cmd = Upload(self, sample_id, data_set_type, files)
+ return cmd.run()
+
def search_object(self, type_code, space, project, experiment, property_code, property_value,
save):
cmd = Search(self, type_code, space, project, experiment, property_code, property_value,
diff --git a/app-openbis-command-line/src/python/obis/scripts/cli.py b/app-openbis-command-line/src/python/obis/scripts/cli.py
index b081071c8e1..db38e2935f4 100644
--- a/app-openbis-command-line/src/python/obis/scripts/cli.py
+++ b/app-openbis-command-line/src/python/obis/scripts/cli.py
@@ -748,7 +748,7 @@ def removeref(ctx, data_set_id, repository):
repository=repository)
-# data set commands: download / clone
+# data set commands: download, upload, clone
# download
@@ -763,7 +763,7 @@ _download_params = [
]
-@data_set.command("download", short_help="Download files of a linked data set.")
+@data_set.command("download", short_help="Download files of a data set.")
@add_params(_download_params)
@click.pass_context
def data_set_download(ctx, content_copy_index, file, data_set_id, skip_integrity_check):
@@ -772,7 +772,7 @@ def data_set_download(ctx, content_copy_index, file, data_set_id, skip_integrity
skip_integrity_check))
-@cli.command(short_help="Download files of a linked data set.")
+@cli.command("download", short_help="Download files of a data set.")
@add_params(_download_params)
@click.pass_context
def download(ctx, content_copy_index, file, data_set_id, skip_integrity_check):
@@ -781,6 +781,33 @@ def download(ctx, content_copy_index, file, data_set_id, skip_integrity_check):
data_set_id=data_set_id, skip_integrity_check=skip_integrity_check)
+# upload
+
+
+_upload_params = [
+ click.option(
+ '-f', '--file', "files", help='file or directory to upload.', required=True, multiple=True),
+ click.argument('sample_id'),
+ click.argument('data_set_type'),
+]
+
+
+@data_set.command("upload", short_help="Upload files to form a data set.")
+@add_params(_upload_params)
+@click.pass_context
+def data_set_upload(ctx, sample_id, data_set_type, files):
+ return ctx.obj['runner'].run("upload",
+ lambda dm: dm.upload(sample_id, data_set_type, files))
+
+
+@cli.command("upload", short_help="Upload files to form a data set.")
+@add_params(_upload_params)
+@click.pass_context
+def download(ctx, sample_id, data_set_type, files):
+ ctx.obj['runner'] = DataMgmtRunner(ctx.obj, halt_on_error_log=False)
+ ctx.invoke(data_set_upload, files=files, sample_id=sample_id, data_set_type=data_set_type)
+
+
# clone
--
GitLab