Merge pull request #229 from galaxyproject/dev

2.7.4 Patch Release

Author: ksuderman

abm/VERSION

@@ -1 +1 @@
-2.7.3
+2.8.0-dev.1

abm/lib/benchmark.py

@@ -203,10 +203,11 @@ def run(context: Context, workflow_path, history_prefix: str, experiment: str):
                         inputs[input[0]] = {'id': dsid, 'src': 'hda', 'size': dssize}
                     else:
                         raise Exception(f'Invalid input value')
-            print(f"Running workflow {wfid}")
+            print(f"Running workflow {wfid} in history {new_history_name}")
             invocation = gi.workflows.invoke_workflow(wfid, inputs=inputs, history_name=new_history_name)
             id = invocation['id']
-            invocations = gi.invocations.wait_for_invocation(id, 86400, 10, False)
+            #invocations = gi.invocations.wait_for_invocation(id, 86400, 10, False)
+            invocations = gi.invocations.wait_for_invocation(id, 86400, 10, True)
             print("Waiting for jobs")
             if history_prefix is not None:
                 parts = history_prefix.split()

abm/lib/config.py

@@ -59,7 +59,7 @@ def key(context: Context, args: list):
 
 def url(context: Context, args: list):
     if len(args) != 2:
-        print(f"USAGE: abm config key <cloud> <url>")
+        print(f"USAGE: abm config url <cloud> <url>")
         return
     profile_name = args[0]
     url = args[1]

abm/lib/dataset.py

@@ -1,7 +1,7 @@
 import json
 
 from bioblend.galaxy import dataset_collections
-from common import connect, Context, print_json, _get_dataset_data, _make_dataset_element
+from common import connect, Context, print_json, _get_dataset_data, _make_dataset_element, find_history
 from pprint import pprint
 from pathlib import Path
 
@@ -147,6 +147,7 @@ def collection(context: Context, args: list):
 def import_from_config(context: Context, args: list):
     gi = None
     key = None
+    history = None
     kwargs = {}
     while len(args) > 0:
         arg = args.pop(0)
@@ -178,6 +179,9 @@ def import_from_config(context: Context, args: list):
 
     if gi is None:
         gi = connect(context)
+    if history is not None:
+        history = find_history(gi, history)
+        
     response = gi.tools.put_url(url, history, **kwargs)
     print(json.dumps(response, indent=4))
 

abm/lib/experiment.py

@@ -70,6 +70,8 @@ def run_on_cloud(cloud: str, config: dict):
         chart = config['galaxy']['chart']
     if 'job_configs' in config and len(config['job_configs']) > 0:
         for conf in config['job_configs']:
+            rules_file = f"rules/{conf}.yml"
+            print(f"Applying {rules_file} namespace:{namespace} chart:{chart}")
             if not helm.update(context, [f"rules/{conf}.yml", namespace, chart]):
                 log.warning(f"job configuration not found: rules/{conf}.yml")
                 continue

abm/lib/helm.py

@@ -37,6 +37,8 @@ def update(context: Context, args: list):
         return False
 
     print(f"Applying rules {values} to {context.GALAXY_SERVER}")
+    print(f"Helm update namespace: {namespace}")
+    print(f"Helm update chart: {chart}")
     #command = f'{helm} upgrade galaxy {chart} -n {namespace} --reuse-values --set-file jobs.rules."container_mapper_rules\.yml".content={rules}'
     command = f'{helm} upgrade galaxy {chart} -n {namespace} --reuse-values -f {values}'
     env = get_env(context)
@@ -51,6 +53,8 @@ def update(context: Context, args: list):
         return False
 
     print('Waiting for the new deployments to come online')
+    # Give kubernetes a moment to start processing the update.
+    time.sleep(30)
     wait_until_ready(namespace, env)
     return True