From 2f4780d5c46c5ac2f25f5d80c2b63646da2f203c Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <chandrasekhar.ramakrishnan@id.ethz.ch>
Date: Fri, 3 Feb 2017 17:36:05 +0100
Subject: [PATCH] SSDM-4670: Simplify commands -- no need to add data. Commit
automatically does this.
---
src/python/OBis/obis/dm/data_mgmt.py | 35 +++++++++++++++--------
src/python/OBis/obis/dm/data_mgmt_test.py | 10 ++-----
2 files changed, 26 insertions(+), 19 deletions(-)
diff --git a/src/python/OBis/obis/dm/data_mgmt.py b/src/python/OBis/obis/dm/data_mgmt.py
index e37fc61e027..c34575f039b 100644
--- a/src/python/OBis/obis/dm/data_mgmt.py
+++ b/src/python/OBis/obis/dm/data_mgmt.py
@@ -138,15 +138,14 @@ class AbstractDataMgmt(metaclass=abc.ABCMeta):
return
@abc.abstractmethod
- def add_content(self, path):
- """Add content to the repository."""
- return
-
- @abc.abstractmethod
- def commit(self, msg):
- """Commit the current repo.
+ def commit(self, msg, auto_add=True):
+ """
+ Commit the current repo.
This issues a git commit and connects to openBIS and creates a data set in openBIS.
+ :param msg: Commit message.
+ :param auto_add: Automatically add all files in the folder to the repo. Defaults to True.
+ :return:
"""
return
@@ -160,10 +159,7 @@ class NoGitDataMgmt(AbstractDataMgmt):
def init_analysis(self, path):
self.error_raise("init analysis", "No git command found.")
- def add_content(self, path):
- self.error_raise("add", "No git command found.")
-
- def commit(self, msg):
+ def commit(self, msg, auto_add=True):
self.error_raise("commit", "No git command found.")
@@ -192,10 +188,20 @@ class GitDataMgmt(AbstractDataMgmt):
self.error(result.output)
return result
- def commit(self, msg):
+ def commit(self, msg, auto_add=True):
+ if auto_add:
+ result = self.git_wrapper.get_top_level_path()
+ if result.returncode != 0:
+ self.error(result.output)
+ return result
+ result = self.add_content(result.output)
+ if result.returncode != 0:
+ self.error(result.output)
+ return result
result = self.git_wrapper.git_commit(msg)
if result.returncode != 0:
self.error(result.output)
+ # TODO create a data set in openBIS
return result
@@ -239,6 +245,8 @@ class GitWrapper(object):
if result.returncode != 0:
return result
+ # TODO Create a .obis directory and add it to gitignore
+
cmd = [self.git_path, "-C", path, "commit", "-m", "Initial commit."]
result = run_shell(cmd)
return result
@@ -248,3 +256,6 @@ class GitWrapper(object):
def git_commit(self, msg):
return run_shell([self.git_path, "commit", '-m', msg])
+
+ def get_top_level_path(self):
+ return run_shell([self.git_path, 'rev-parse', '--show-toplevel'])
diff --git a/src/python/OBis/obis/dm/data_mgmt_test.py b/src/python/OBis/obis/dm/data_mgmt_test.py
index 9cf0f8c24f6..8113f3851aa 100644
--- a/src/python/OBis/obis/dm/data_mgmt_test.py
+++ b/src/python/OBis/obis/dm/data_mgmt_test.py
@@ -56,13 +56,6 @@ def test_data_use_case(shared_dm, tmpdir):
copy_test_data(tmpdir)
with data_mgmt.cd(tmp_dir_path):
- result = shared_dm.add_content(".")
- assert result.returncode == 0
-
- result = git_status()
- assert result.returncode == 0
- assert result.output == "A snb-data.zip\nA test.txt"
-
result = shared_dm.commit("Added data.")
assert result.returncode == 0
@@ -75,6 +68,9 @@ def test_data_use_case(shared_dm, tmpdir):
result = data_mgmt.run_shell(['git', 'annex', 'info', 'test.txt'])
present_p = result.output.split(' ')[-1]
assert present_p == 'failed'
+ result = data_mgmt.run_shell(['git', 'log', '--oneline', 'test.txt'])
+ present_p = " ".join(result.output.split(' ')[1:])
+ assert present_p == 'Added data.'
def copy_test_data(tmpdir):
--
GitLab