2.1.0 Release

.github/workflows/devrelease.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Require a label and version bump to package and release
         uses: mheap/github-action-required-labels@v2
         with:
-          mode: minium
+          mode: minimum
           count: 1
           labels: "dev"
       - uses: actions/checkout@v3

abm/VERSION

@@ -1 +1 @@
-2.1.0-dev7
+2.1.0-dev.9

abm/lib/experiment.py

@@ -105,7 +105,7 @@ def summarize(context: Context, args: list):
     :return: None
     """
     separator = None
-    input_dir = None
+    input_dirs = []
     make_row = make_table_row
     header_row = "Run,Cloud,Job Conf,Workflow,History,Inputs,Tool,Tool Version,State,Slots,Memory,Runtime (Sec),CPU,Memory Limit (Bytes),Memory Max usage (Bytes)"
     for arg in args:
@@ -125,35 +125,38 @@ def summarize(context: Context, args: list):
                 return
             separator = ','
             make_row = make_model_row
-            header_row = "job_id,tool_id,tool_version,state,memory.max_usage_in_bytes,cpuacct.usage,process_count,galaxy_slots,runtime_seconds,ref_data_size,input_data_size"
+            header_row = "job_id,tool_id,tool_version,state,memory.max_usage_in_bytes,cpuacct.usage,process_count,galaxy_slots,runtime_seconds,ref_data_size,input_data_size_1,input_data_size_2"
         else:
-            input_dir = arg
+            input_dirs.append(arg)
 
-    if input_dir is None:
-        input_dir = 'metrics'
+    if len(input_dirs) == 0:
+        input_dirs.append('metrics')
 
     if separator is None:
         separator = ','
 
     print(header_row)
-    for file in os.listdir(input_dir):
-        input_path = os.path.join(input_dir, file)
-        if not os.path.isfile(input_path) or not input_path.endswith('.json'):
-            continue
-        try:
-            with open(input_path, 'r') as f:
-                data = json.load(f)
-            row = make_row(data)
-            print(separator.join([ str(x) for x in row]))
-        except Exception as e:
-            # Silently fail to allow the remainder of the table to be generated.
-            # print(e)
-            pass
+    for input_dir in input_dirs:
+        for file in os.listdir(input_dir):
+            input_path = os.path.join(input_dir, file)
+            if not os.path.isfile(input_path) or not input_path.endswith('.json'):
+                continue
+            try:
+                with open(input_path, 'r') as f:
+                    data = json.load(f)
+                if data['metrics']['tool_id'] == 'upload1':
+                    continue
+                row = make_row(data)
+                print(separator.join([ str(x) for x in row]))
+            except Exception as e:
+                # Silently fail to allow the remainder of the table to be generated.
+                # print(f"Unable to process {input_path}")
+                # print(e)
+                pass
 
 
 accept_metrics = ['galaxy_slots', 'galaxy_memory_mb', 'runtime_seconds', 'cpuacct.usage','memory.limit_in_bytes', 'memory.max_usage_in_bytes']  #,'memory.soft_limit_in_bytes']
 
-
 def make_table_row(data: dict):
     row = [ str(data[key]) for key in ['run', 'cloud', 'job_conf', 'workflow_id', 'history_id', 'inputs']]
     row.append(parse_toolid(data['metrics']['tool_id']))

abm/lib/job.py

@@ -52,7 +52,7 @@ def metrics(context: Context, args: list):
         return
     gi = connect(context)
     metrics = gi.jobs.get_metrics(args[0])
-    print(json.dumps(metrics[0], indent=4))
+    print(json.dumps(metrics, indent=4))
     # metrics = {}
     # for m in gi.jobs.get_metrics(args[0]):
     #     metrics[m['name']] = get_value(m)

abm/lib/menu.yml

@@ -192,7 +192,7 @@
       handler: users.show
       params: "[NAME|EMAIL]"
     - name: [ usage ]
-      help: show details about the given user
+      help: display the disk usage for the user
       handler: users.usage
       params: "[NAME|EMAIL]"
 - name: [experiment, exp, ex]