obis: implemented init_analysis

src/python/OBis/obis/dm/data_mgmt.py

@@ -179,6 +179,9 @@ class GitDataMgmt(AbstractDataMgmt):
         with cd(path):
             return self.config_resolver.config_dict().get('data_set_id')
 
+    def get_config(self, path, key):
+        with cd(path):
+            return self.config_resolver.config_dict().get(key)
 
     def init_data(self, path, desc=None, create=True, apply_config=False):
         if not os.path.exists(path) and create:
@@ -202,31 +205,24 @@ class GitDataMgmt(AbstractDataMgmt):
         # get data_set_id of parent from current folder or explicit parent argument
         parent_folder = parent if parent is not None and len(parent) > 0 else "."
         parent_data_set_id = self.get_data_set_id(parent_folder)
-        # check that data_set_id is set - parent repository has been added to openBIS
-        if parent_data_set_id is None:
+        # check that parent repository has been added to openBIS
+        if self.get_config(parent_folder, 'repository_id') is None:
             return CommandResult(returncode=-1, output="Parent data set must be committed to openBIS before creating an analysis data set.")
+        # check that analysis repository does not already exist
+        if os.path.exists(path):
+            return CommandResult(returncode=-1, output="Data set already exists: " + path)
         # init analysis repository
         result = self.init_data(path, desc, create, apply_config)
         if result.failure():
             return result
         # add analysis repository folder to .gitignore of parent
         if os.path.exists('.obis'):
-            with open(".gitignore", "a") as gitignore:
-                gitignore.write(path)
-                gitignore.write("\n")
+            self.git_wrapper.git_ignore(path)
         elif parent is None:
             return CommandResult(returncode=-1, output="Not within a repository and no parent set.")
-
+        # set data_set_id to analysis repository so it will be used as parent when committing
         with cd(path):
             cli.config_internal(self, False, "data_set_id", parent_data_set_id)
-
-
-        # TODO init repo and link new data set as child.
-        # add to gitignore of parent data set
-        # add parameter to reference parent in case it's not in the same folder
-
-        # TODO use git check-ignore to not add folder twice
-        # TODO cleanup when something goes wrong
         return result
 
 

src/python/OBis/obis/dm/git.py

@@ -79,6 +79,13 @@ class GitWrapper(object):
     def git_reset_to(self, commit_hash):
         return run_shell([self.git_path, 'reset', commit_hash])
 
+    def git_ignore(self, path):
+        result = run_shell([self.git_path, 'check-ignore', path])
+        if result.returncode == 1:
+            with open(".gitignore", "a") as gitignore:
+                gitignore.write(path)
+                gitignore.write("\n")
+
 
 class GitRepoFileInfo(object):
     """Class that gathers checksums and file lengths for all files in the repo."""

src/python/OBis/obis/scripts/cli.py

@@ -151,11 +151,11 @@ def init_data_impl(ctx, object_id, collection_id, folder, desc):
     init_handle_cleanup(result, object_id, collection_id)
 
 
-def init_analysis_impl(ctx, object_id, collection_id, folder, parent, desc):
+def init_analysis_impl(ctx, parent, object_id, collection_id, folder, description):
     click_echo("init_analysis {}".format(folder))
     data_mgmt = shared_data_mgmt(ctx.obj)
-    desc = desc if desc != "" else None
-    result = data_mgmt.init_analysis(folder, parent, desc, create=True)
+    description = description if description != "" else None
+    result = data_mgmt.init_analysis(folder, parent, description, create=True)
     init_handle_cleanup(result, object_id, collection_id)
 
 
@@ -193,14 +193,14 @@ def init_data(ctx, object_id, collection_id, folder, description):
 
 @cli.command()
 @click.pass_context
+@click.option('-p', '--parent', type=click.Path(exists=False, file_okay=False))
 @click.option('-oi', '--object_id', help='Set the id of the owning sample.')
 @click.option('-ci', '--collection_id', help='Set the id of the owning experiment.')
 @click.argument('folder', type=click.Path(exists=False, file_okay=False))
 @click.argument('description', default="")
-@click.option('-p', '--parent', type=click.Path(exists=False, file_okay=False))
-def init_analysis(ctx, object_id, collection_id, folder, description, parent):
+def init_analysis(ctx, parent, object_id, collection_id, folder, description):
     """Initialize the folder as an analysis folder."""
-    return init_analysis_impl(ctx, object_id, collection_id, folder, description, parent)
+    return init_analysis_impl(ctx, parent, object_id, collection_id, folder, description)
 
 
 @cli.command()