diff env/lib/python3.7/site-packages/planemo/galaxy/api.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/planemo/galaxy/api.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-"""A high-level interface to local Galaxy instances using bioblend."""
-from six import StringIO
-
-from planemo.bioblend import ensure_module
-from planemo.bioblend import galaxy
-
-DEFAULT_MASTER_API_KEY = "test_key"
-
-
-def gi(port=None, url=None, key=None):
-    """Return a bioblend ``GalaxyInstance`` for Galaxy on this port."""
-    ensure_module()
-    if key is None:
-        key = DEFAULT_MASTER_API_KEY
-    if port is None:
-        url = url
-    else:
-        url = "http://localhost:%d" % int(port)
-
-    return galaxy.GalaxyInstance(
-        url=url,
-        key=key
-    )
-
-
-def user_api_key(admin_gi):
-    """Use an admin authenticated account to generate a user API key."""
-    ensure_module()
-    # TODO: thread-safe
-    users = admin_gi.users
-    all_users = users.get_users()
-
-    user_id = None
-    for user in all_users:
-        if user["email"] == "[e-mail]":
-            user_id = user["id"]
-
-    if user_id is None:
-        # TODO: Allow override with --user_api_key.
-        galaxy_config = admin_gi.config.get_config()
-        use_remote_user = bool(galaxy_config["use_remote_user"])
-        if not use_remote_user:
-            user_response = users.create_local_user(
-                "planemo",
-                "[e-mail]",
-                "planemo",
-            )
-            user_id = user_response["id"]
-        else:
-            user_response = users.create_remote_user(
-                "[e-mail]",
-            )
-            user_id = user_response["id"]
-    return users.create_user_apikey(user_id)
-
-
-def summarize_history(ctx, gi, history_id):
-    """Summarize a history with print() based on similar code in Galaxy for populators.
-    """
-    if not ctx.verbose:
-        return
-
-    if history_id is None:
-        raise ValueError("summarize_history passed empty history_id")
-    try:
-        history_contents = gi.histories.show_history(history_id, contents=True)
-    except Exception:
-        print("Failed to fetch history contents in summarize_history.")
-        return
-
-    for history_content in history_contents:
-        history_content_id = history_content.get('id', None)
-        print("| %d - %s (HID - NAME) " % (int(history_content['hid']), history_content['name']))
-        if history_content['history_content_type'] == 'dataset_collection':
-            history_contents_json = gi.histories.show_dataset_collection(history_id, history_content["id"])
-            print("| Dataset Collection: %s" % history_contents_json)
-            continue
-        try:
-            dataset_info = gi.histories.show_dataset(history_id, history_content_id)
-            print("| Dataset State:")
-            print(_format_for_summary(dataset_info.get("state"), "Dataset state is unknown."))
-            print("| Dataset Blurb:")
-            print(_format_for_summary(dataset_info.get("misc_blurb", ""), "Dataset blurb was empty."))
-            print("| Dataset Info:")
-            print(_format_for_summary(dataset_info.get("misc_info", ""), "Dataset info is empty."))
-            print("| Peek:")
-            print(_format_for_summary(dataset_info.get("peek", ""), "Peek unavilable."))
-        except Exception:
-            print("| *PLANEMO ERROR FETCHING DATASET DETAILS*")
-        try:
-            provenance_info = _dataset_provenance(gi, history_id, history_content_id)
-            print("| Dataset Job Standard Output:")
-            print(_format_for_summary(provenance_info.get("stdout", ""), "Standard output was empty."))
-            print("| Dataset Job Standard Error:")
-            print(_format_for_summary(provenance_info.get("stderr", ""), "Standard error was empty."))
-        except Exception:
-            print("| *PLANEMO ERROR FETCHING JOB DETAILS*")
-        print("|")
-
-
-def _format_for_summary(blob, empty_message, prefix="|  "):
-    contents = "\n".join(["%s%s" % (prefix, line.strip()) for line in StringIO(blob).readlines() if line.rstrip("\n\r")])
-    return contents or "%s*%s*" % (prefix, empty_message)
-
-
-def _dataset_provenance(gi, history_id, id):
-    provenance = gi.histories.show_dataset_provenance(history_id, id)
-    return provenance
-
-
-__all__ = (
-    "DEFAULT_MASTER_API_KEY",
-    "gi",
-    "user_api_key",
-)