Added list command (#233)

* Added list command that colors output by status and updates the submission database if requested

* Added missing 'tabulate' package to requirements, reformatted with blank and made minor changes to make linters happy

* lint test fixes (#234)

* Changed some variable names for clarity

Co-authored-by: bshifaw <[email protected]>

Author: kvg

requirements.txt

@@ -3,3 +3,4 @@ termcolor>=1.1.0
 click>=8.0.0
 requests>=2.27.1
 pygments>=2.12.0
+tabulate>=0.8.9

src/cromshell/__main__.py

@@ -9,6 +9,7 @@
 from .abort import command as abort
 from .alias import command as alias
 from .counts import command as counts
+from .list import command as list
 from .logs import command as logs
 from .metadata import command as metadata
 from .slim_metadata import command as slim_metadata
@@ -145,6 +146,7 @@ def version():
 main_entry.add_command(metadata.main)
 main_entry.add_command(update_server.main)
 main_entry.add_command(timing.main)
+main_entry.add_command(list.main)
 
 
 if __name__ == "__main__":

src/cromshell/list/__init__.py

@@ -0,0 +1,108 @@
+import csv
+import json
+import logging
+
+import click
+import requests
+from tabulate import tabulate
+
+import cromshell.utilities.submissions_file_utils
+from cromshell.utilities import command_setup_utils, cromshellconfig, http_utils
+
+LOGGER = logging.getLogger(__name__)
+
+
+@click.command(name="list")
+@click.option(
+    "-c",
+    "--color",
+    is_flag=True,
+    default=False,
+    help="Color the output by completion status.",
+)
+@click.option(
+    "-u",
+    "--update",
+    is_flag=True,
+    default=False,
+    help="Check completion status of all unfinished jobs.",
+)
+@click.pass_obj
+def main(config, color, update):
+    """List the status of workflows."""
+
+    LOGGER.info("list")
+
+    # Update the submission database if so requested
+    if update:
+        update_submission_db(config)
+
+    # Iterate over the submissions text database and print to screen in a pretty way
+    with open(cromshellconfig.submission_file_path, "r") as sub_f:
+        reader = csv.reader(sub_f, delimiter="\t", lineterminator="\n")
+        all_table_rows = []
+        for single_table_row in reader:
+            all_table_rows.append(
+                format_status(single_table_row) if color else single_table_row
+            )
+
+        print(tabulate(all_table_rows, headers="firstrow", numalign="left"))
+
+    return 0
+
+
+def update_submission_db(config):
+    # Iterate over the submissions text database and update their status
+    workflow_ids = []
+    with open(cromshellconfig.submission_file_path, "r") as sub_f:
+        reader = csv.reader(sub_f, delimiter="\t", lineterminator="\n")
+        for table_row in reader:
+            if table_row[2] != "RUN_ID" and table_row[4] in [
+                "Submitted",
+                "Running",
+                "DOOMED",
+            ]:
+                workflow_ids.append(table_row[2])
+
+    for workflow_id in workflow_ids:
+        command_setup_utils.resolve_workflow_id_and_server(
+            workflow_id=workflow_id, cromshell_config=config
+        )
+
+        # Request workflow status
+        request_out = requests.get(
+            f"{config.cromwell_api_workflow_id}/status",
+            timeout=config.requests_connect_timeout,
+            verify=config.requests_verify_certs,
+            headers=http_utils.generate_headers(config),
+        )
+
+        workflow_status_description = json.loads(request_out.content)
+
+        # Hold our status string here
+        workflow_status = workflow_status_description["status"]
+
+        # Update config.submission_file:
+        cromshell.utilities.submissions_file_utils.update_row_values_in_submission_db(
+            workflow_database_path=config.submission_file_path,
+            workflow_id=workflow_id,
+            column_to_update="STATUS",
+            update_value=workflow_status,
+        )
+
+
+def format_status(table_row):
+    colorful_status = {
+        "Failed": "\033[1;37;41mFailed\033[0m",
+        "DOOMED": "\033[1;31;47mDOOMED\033[0m",
+        "Succeeded": "\033[1;37;42mSucceeded\033[0m",
+        "Running": "\033[0;30;46mRunning\033[0m",
+        "Aborted": "\033[0;30;43mAborted\033[0m",
+    }
+
+    status_column = -1 if table_row[-1] in colorful_status else -2
+
+    if table_row[status_column] in colorful_status:
+        table_row[status_column] = colorful_status[table_row[status_column]]
+
+    return table_row