diff --git a/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py b/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
index 4d12d11f838c49923383f9ddd95566abe8cbe24c..44845cf12abe87dfa2f7e1823c0424cc679cc1c2 100644
--- a/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
+++ b/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
@@ -12,10 +12,13 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import os
from .openbis_command import OpenbisCommand
+from ..checksum import validate_checksum
from ..command_result import CommandResult
from ..utils import cd
+from ...scripts.click_util import click_echo
class DownloadPhysical(OpenbisCommand):
@@ -23,13 +26,14 @@ class DownloadPhysical(OpenbisCommand):
Command to download physical files of a data set.
"""
- def __init__(self, dm, data_set_id, file):
+ def __init__(self, dm, data_set_id, file, skip_integrity_check):
"""
:param dm: data management
:param data_set_id: permId of the data set to be cloned
"""
self.data_set_id = data_set_id
self.files = [file] if file is not None else None
+ self.skip_integrity_check = skip_integrity_check
self.load_global_config(dm)
super(DownloadPhysical, self).__init__(dm)
@@ -43,4 +47,25 @@ class DownloadPhysical(OpenbisCommand):
with cd(self.data_mgmt.invocation_path):
target_folder = data_set.download(files, destination=self.data_mgmt.invocation_path)
+ if self.skip_integrity_check is not True:
+ invalid_files = validate_checksum(self.openbis, files, data_set.permId,
+ target_folder, None)
+ self.redownload_invalid_files_on_demand(invalid_files, target_folder)
return CommandResult(returncode=0, output="Files downloaded to: %s" % target_folder)
+
+ def redownload_invalid_files_on_demand(self, invalid_files, target_folder):
+ if len(invalid_files) == 0:
+ return
+ yes_or_no = None
+ while yes_or_no != "yes" and yes_or_no != "no":
+ click_echo("Integrity check failed for following files:\n" +
+ str(invalid_files) + "\n" +
+ "Either the download failed or the files where changed after committing to openBIS.\n" +
+ "Should the files be downloaded again? (yes/no)")
+ yes_or_no = input('> ')
+ if yes_or_no == "yes":
+ for file in invalid_files:
+ filename_dest = os.path.join(target_folder, file)
+ os.remove(filename_dest)
+ self.files = invalid_files
+ return self.run()
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 96e5e902c970764a97ffd010c3525a5ec9048c44..15d9b5cdf251815f7ea5c1177ae4f765913e3e4d 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
@@ -210,10 +210,9 @@ class AbstractDataMgmt(metaclass=abc.ABCMeta):
return
@abc.abstractmethod
- def download(self, data_set_id, content_copy_index, file, skip_integrity_check):
+ def download(self, data_set_id, file, skip_integrity_check):
"""Download files of a repository without adding a content copy.
:param data_set_id: Id of the data set to download from.
- :param content_copy_index: Index of the content copy to download from.
:param file: Path of a file in the data set to download. All files are downloaded if it is None.
:param skip_integrity_check: Checksums of files are not verified if true.
"""
@@ -350,7 +349,7 @@ class NoGitDataMgmt(AbstractDataMgmt):
def removeref(self, data_set_id=None):
self.error_raise("removeref", "No git command found.")
- def download(self, data_set_id, content_copy_index, file, skip_integrity_check):
+ def download(self, data_set_id, file, skip_integrity_check):
self.error_raise("download", "No git command found.")
def search_object(self, *_):
@@ -560,7 +559,7 @@ class GitDataMgmt(AbstractDataMgmt):
cmd = Removeref(self, data_set_id=data_set_id)
return cmd.run()
- def download(self, data_set_id, content_copy_index, file, skip_integrity_check):
+ def download(self, data_set_id, file, skip_integrity_check):
self.error_raise("download", "This command is only available for Manager Data.")
#
@@ -646,8 +645,8 @@ class PhysicalDataMgmt(AbstractDataMgmt):
def removeref(self, data_set_id=None):
self.error_raise("removeref", "This command is only available for External Manager Data")
- def download(self, data_set_id, _content_copy_index, file, _skip_integrity_check):
- cmd = DownloadPhysical(self, data_set_id, file)
+ def download(self, data_set_id, file, skip_integrity_check):
+ cmd = DownloadPhysical(self, data_set_id, file, skip_integrity_check)
return cmd.run()
def upload(self, sample_id, data_set_type, files):
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 175356088c911ee97f1a3042fc5bb133a5537c58..be6804e1cc66ecd2c56b5690f95a31fceeb4f1a8 100644
--- a/app-openbis-command-line/src/python/obis/scripts/cli.py
+++ b/app-openbis-command-line/src/python/obis/scripts/cli.py
@@ -270,7 +270,8 @@ def repository_clear(ctx, settings):
_search_params = [
- click.option('-type', '--type', 'type_code', default=None, help='Type code to filter by'),
+ click.option('-object_type', '--object_type', 'type_code', default=None,
+ help='Object type code to filter by'),
click.option('-space', '--space', default=None, help='Space code'),
click.option('-project', '--project', default=None, help='Full project identification code'),
click.option('-experiment', '--experiment', default=None, help='Full experiment code'),
@@ -757,31 +758,29 @@ def removeref(ctx, data_set_id, repository):
# download
_download_params = [
- click.option('-c', '--content_copy_index', type=int, default=None,
- help='Index of the content copy to download from.'),
+ click.argument('data_set_id'),
click.option(
'-f', '--file', help='File in the data set to download - downloading all if not given.'),
- click.option('-s', '--skip_integrity_check', default=False,
- is_flag=True, help='Skip file integrity check with checksums.'),
- click.argument('data_set_id'),
+ click.option('-s', '--skip_integrity_check', default=False, is_flag=True,
+ help='Flag to skip file integrity check with checksums'),
]
@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):
+def data_set_download(ctx, file, data_set_id, skip_integrity_check):
return ctx.obj['runner'].run("download",
- lambda dm: dm.download(data_set_id, content_copy_index, file,
- skip_integrity_check))
+ lambda dm: dm.download(data_set_id=data_set_id, file=file,
+ skip_integrity_check=skip_integrity_check))
@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):
+def download(ctx, file, data_set_id, skip_integrity_check):
ctx.obj['runner'] = DataMgmtRunner(ctx.obj, halt_on_error_log=False)
- ctx.invoke(data_set_download, content_copy_index=content_copy_index, file=file,
+ ctx.invoke(data_set_download, file=file,
data_set_id=data_set_id, skip_integrity_check=skip_integrity_check)
diff --git a/docs/app-openbis-command-line/README.md b/docs/app-openbis-command-line/README.md
index 7a3ffc8f360881c562d4ff0a76dbac7024886222..62505db94e28bfce7854a9bac0370995cae98986 100644
--- a/docs/app-openbis-command-line/README.md
+++ b/docs/app-openbis-command-line/README.md
@@ -199,7 +199,8 @@ it comes to integration with other tools.
obis data_set search [OPTIONS]
Options:
- -type, --type TEXT Type code to filter by
+ -object_type, --object_type TEXT
+ Object type code to filter by
-space, --space TEXT Space code
-project, --project TEXT Full project identification code
-experiment, --experiment TEXT Full experiment code