Add support for automatic repo creation

planemo/commands/cmd_shed_upload.py

@@ -59,6 +59,13 @@
     type=tar_path,
     default=None,
 )
+@click.option(
+    '--force_repository_creation',
+    help="If a repository cannot be found for the specified user/repo name "
+         "pair, then automatically create the repository in the toolshed.",
+    is_flag=True,
+    default=False
+)
 @click.option(
     '-r', '--recursive',
     is_flag=True,
@@ -103,16 +110,21 @@ def __handle_upload(ctx, path, **kwds):
     message = kwds.get("message", None)
     if message:
         update_kwds["commit_message"] = message
-
     repo_id = __find_repository(ctx, tsi, path, **kwds)
+    if repo_id is None and kwds["force_repository_creation"]:
+        repo_id = __create_repository(ctx, tsi, path, **kwds)
+    # failing to create the repo, give up
     if repo_id is None:
         return -1
+    # TODO: support updating repo information if it changes in the config file
 
     try:
         tsi.repositories.update_repository(repo_id, tar_path, **update_kwds)
     except Exception as e:
         exception_content = e.read()
         try:
+            # Galaxy passes nice JSON messages as their errors, which bioblend
+            # blindly returns. Attempt to parse those.
             upstream_error = json.loads(exception_content)
             error(upstream_error['err_msg'])
         except Exception as e2:
@@ -124,9 +136,7 @@ def __handle_upload(ctx, path, **kwds):
 
 
 def __find_repository(ctx, tsi, path, **kwds):
-    """Extracted into separate function to reduce complexity though it's not a
-    really sensible change since we now have to catch the error code separately
-    whenever we call this function elsewhere.
+    """More advanced error handling for finding a repository by ID
     """
     try:
         repo_id = shed.find_repository_id(ctx, tsi, path, **kwds)
@@ -140,3 +150,20 @@ def __find_repository(ctx, tsi, path, **kwds):
             # wrapped in try/except
             error("Could not find repository in toolshed")
     return None
+
+
+def __create_repository(ctx, tsi, path, **kwds):
+    """Wrapper for creating the endpoint if it doesn't exist
+    """
+    try:
+        repo = shed.create_repository(ctx, tsi, path, **kwds)
+        return repo['id']
+    # Have to catch missing snyopsis/bioblend exceptions
+    except Exception as e:
+        # TODO: galaxyproject/bioblend#126
+        try:
+            upstream_error = json.loads(e.read())
+            error(upstream_error['err_msg'])
+        except Exception:
+            error(str(e))
+        return None

planemo/shed.py

@@ -95,6 +95,47 @@ def matches(r):
     return repo_id
 
 
+def create_repository(ctx, tsi, path, **kwds):
+    repo_config = shed_repo_config(path)
+    name = kwds.get("name", None) or repo_config.get("name", None)
+
+    description = repo_config.get("description", None)
+    long_description = repo_config.get("long_description", None)
+    type = repo_config.get("type", "unrestricted")
+    remote_repository_url = repo_config.get("remote_repository_url", None)
+    homepage_url = repo_config.get("homepage_url", None)
+    categories = repo_config.get("categories", [])
+    # Translate human readable category names into their associated IDs
+    category_list = tsi.repositories.get_categories()
+
+    category_ids = []
+    for cat in categories:
+        matching_cats = [x for x in category_list if x['name'] == cat]
+        if not matching_cats:
+            message = "Failed to find category %s" % cat
+            raise Exception(message)
+        category_ids.append(matching_cats[0]['id'])
+
+    if name is None:
+        name = os.path.basename(os.path.abspath(path))
+
+    # description is required, as is name.
+    if description is None:
+        message = "description required for automatic creation of repositories"
+        raise Exception(message)
+
+    repo = tsi.repositories.create_repository(
+        name=name,
+        synopsis=description,
+        description=long_description,
+        type=type,
+        remote_repository_url=remote_repository_url,
+        homepage_url=homepage_url,
+        category_ids=category_ids
+    )
+    return repo
+
+
 def download_tarball(ctx, tsi, path, **kwds):
     destination = kwds.get('destination', 'shed_download.tar.gz')
     repo_id = find_repository_id(ctx, tsi, path, **kwds)