Merge pull request #200 from galaxyproject/dev

Release 2.5.0

Author: ksuderman

abm/VERSION

@@ -1 +1 @@
-2.4.0
+2.5.0

abm/__main__.py

@@ -17,7 +17,7 @@
 
 # These imports are required because we need Python to be load them to the
 # symbol table so the parse_menu method can find them in globals()
-from lib import job, dataset, workflow, history, library, folder, benchmark, helm, kubectl, config, experiment, users, cloudlaunch
+from lib import job, dataset, workflow, history, library, folder, benchmark, helm, kubectl, config, experiment, users, cloudlaunch, invocation
 
 log = logging.getLogger('abm')
 handler = logging.StreamHandler()

abm/lib/common.py

@@ -200,12 +200,12 @@ def summarize_metrics(gi, jobs: list):
     "galaxy_slots",
     # "memory.failcnt",
     "memory.limit_in_bytes",
-    # "memory.max_usage_in_bytes",
+    "memory.max_usage_in_bytes",
     # "memory.memsw.limit_in_bytes",
     # "memory.memsw.max_usage_in_bytes",
     # "memory.oom_control.oom_kill_disable",
     # "memory.oom_control.under_oom",
-    # "memory.soft_limit_in_bytes",
+    "memory.soft_limit_in_bytes",
     "memtotal",
     "processor_count",
     "runtime_seconds",

abm/lib/invocation.py

@@ -0,0 +1,38 @@
+from common import Context, connect, summarize_metrics, print_json
+
+def doList(context: Context, args: list):
+    wid = None
+    hid = None
+    while len(args) > 0:
+        arg = args.pop(0)
+        if args in ['-h', '--history']:
+            hid = args.pop(0)
+        elif arg in ['-w', '--workflow']:
+            wid = args.pop(0)
+        else:
+            print(f'Invalid parameter: {arg}')
+            return
+    gi = connect(context)
+    invocations = gi.invocations.get_invocations(workflow_id=wid, history_id=hid)
+    print('ID\tState\tWorkflow\tHistory')
+    for invocation in invocations:
+        id = invocation['id']
+        state = invocation['state']
+        workflow = invocation['workflow_id']
+        history = invocation['history_id']
+        print(f'{id}\t{state}\t{workflow}\t{history}')
+
+
+def summarize(context: Context, args: list):
+    if len(args) == 0:
+        print("ERROR: Provide one or more invocation ID values.")
+        return
+    gi = connect(context)
+    id = args[0]
+    all_jobs = []
+    jobs = gi.jobs.get_jobs(invocation_id=id)
+    for job in jobs:
+        job['invocation_id'] = id
+        job['workflow_id'] = ''
+        all_jobs.append(job)
+    summarize_metrics(gi, all_jobs)

abm/lib/menu.yml

@@ -243,6 +243,17 @@
       help: playground code
       handler: experiment.test
       params: [VARIES]
+- name: [invocation, inv, invocations]
+  help: get information about job and workflow invocations
+  menu:
+    - name: [list, ls]
+      help: list all invocations.
+      handler: invocation.doList
+      params: "[-w|--workflow ID] [-h|--history ID]"
+    - name: [summarize]
+      help: generate a CSV of job metrics for an invocation
+      params: ID
+      handler: invocation.summarize
 - name: [helm]
   help: execute a helm command
   menu:

abm/lib/workflow.py

@@ -182,8 +182,15 @@ def invocation(context:Context, args:list):
     #     return
     gi = connect(context)
     # result = gi.workflows.show_invocation(workflow_id, invocation_id)
-    result = gi.invocations.get_invocations(workflow_id=workflow_id, view='element', step_details=True)
-    print(json.dumps(result, indent=4))
+    invocations = gi.invocations.get_invocations(workflow_id=workflow_id, view='element', step_details=True)
+    # print(json.dumps(result, indent=4))
+    print('ID\tState\tWorkflow\tHistory')
+    for invocation in invocations:
+        id = invocation['id']
+        state = invocation['state']
+        workflow = invocation['workflow_id']
+        history = invocation['history_id']
+        print(f'{id}\t{state}\t{workflow}\t{history}')
 
 
 def find(context: Context, args: list):