From c343a5622205b0dc4ade76a477cb2d4bce1fa8a2 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Mon, 24 Oct 2022 15:58:23 +0200
Subject: [PATCH] fixed changelog
---
pybis/src/python/CHANGELOG.md | 4 ++++
pybis/src/python/pybis/cli.py | 42 ++++++++++++++++++++++++++++++-----
pybis/src/python/setup.cfg | 6 ++++-
3 files changed, 46 insertions(+), 6 deletions(-)
diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index 336d0ad92bb..0da0f92c27a 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -1,3 +1,7 @@
+## Changes with pybis-1.34.0
+
+- add experimental support for datasets via cli
+
## Changes with pybis-1.33.2
- fix openbis.support.email key error
diff --git a/pybis/src/python/pybis/cli.py b/pybis/src/python/pybis/cli.py
index df8a5547156..c70dc522da2 100644
--- a/pybis/src/python/pybis/cli.py
+++ b/pybis/src/python/pybis/cli.py
@@ -130,17 +130,49 @@ def dataset(ctx):
@click.argument("permid", required=True)
def get_dataset(permid, **kwargs):
"""get a dataset by its permId"""
- print(permid)
- print(kwargs)
openbis = get_openbis(**kwargs)
- print(openbis)
+ ds = openbis.get_dataset(permid)
+ click.echo(ds.__repr__())
+ click.echo("")
+ click.echo("Files in this dataset")
+ click.echo("---------------------")
+ click.echo(ds.get_files())
@dataset.command("download")
+@openbis_conn_options
@click.argument("permid", required=True)
-def download_dataset(permid, **kwargs):
+@click.argument("fileno", nargs=-1)
+@click.option(
+ "--destination",
+ "-d",
+ type=click.Path(exists=True),
+ help="where to download your dataset",
+)
+def download_dataset(permid, destination, fileno, **kwargs):
"""download a dataset by permId"""
- click.echo(permid)
+ openbis = get_openbis(**kwargs)
+ try:
+ ds = openbis.get_dataset(permid)
+ except ValueError as exc:
+ raise click.ClickException(exc)
+
+ create_default_folders = False if destination else True
+ if fileno:
+ all_files = ds.get_files()
+ files = []
+ for loc in fileno:
+ files.append(all_files.loc[int(loc)]["pathInDataSet"])
+ print(files)
+ ds.download(
+ destination=destination,
+ create_default_folders=create_default_folders,
+ files=files,
+ )
+ else:
+ ds.download(
+ destination=destination, create_default_folders=create_default_folders
+ )
@cli.command("local", context_settings=dict(ignore_unknown_options=True))
diff --git a/pybis/src/python/setup.cfg b/pybis/src/python/setup.cfg
index 08a6139ae22..a964880f886 100644
--- a/pybis/src/python/setup.cfg
+++ b/pybis/src/python/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = PyBIS
-version = 1.33.2
+version = 1.34.0rc1
author = Swen Vermeul • ID SIS • ETH Zürich
author_email = swen@ethz.ch
license = Apache Software License Version 2.0
@@ -13,6 +13,10 @@ classifiers =
License :: OSI Approved :: Apache Software License
Operating System :: OS Independent
+[options.entry_points]
+console_scripts =
+ pybis = pybis.cli:cli
+
[options]
packages = find:
install_requires =
--
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