shed_tools exit code 1 on error

and add --log_level argument

src/ephemeris/_idc_data_managers_to_tools.py

@@ -93,11 +93,7 @@ def main():
     disable_external_library_logging()
     parser = _parser()
     args = parser.parse_args()
-    log = setup_global_logger(name=__name__, log_file=args.log_file)
-    if args.verbose:
-        log.setLevel(logging.DEBUG)
-    else:
-        log.setLevel(logging.INFO)
+    log = setup_global_logger(name=__name__, log_file=args.log_file, log_level=args.log_level)
     write_shed_install_conf(args.data_managers_conf, args.shed_install_output_conf)
 
 

src/ephemeris/_idc_split_data_manager_genomes.py

@@ -314,11 +314,7 @@ def main():
     disable_external_library_logging()
     parser = _parser()
     args = parser.parse_args()
-    log = setup_global_logger(name=__name__, log_file=args.log_file)
-    if args.verbose:
-        log.setLevel(logging.DEBUG)
-    else:
-        log.setLevel(logging.INFO)
+    log = setup_global_logger(name=__name__, log_file=args.log_file, log_level=args.log_level)
 
     if args.complete_check_cvmfs:
         is_build_complete = CVMFSPublishIsComplete(get_cvmfs_publish_records(args))

src/ephemeris/common_parser.py

@@ -27,22 +27,30 @@ def add_verbosity_argument(parser_or_group):
     parser_or_group.add_argument("-v", "--verbose", help="Increase output verbosity.", action="store_true")
 
 
-def add_log_file_argument(parser_or_group):
+def add_log_file_arguments(parser_or_group):
     parser_or_group.add_argument(
         "--log-file",
         "--log_file",
         dest="log_file",
-        help="Where the log file should be stored. " "Default is a file in your system's temp folder",
+        help="Where the log file should be stored. " "Default is a output to screen",
         default=None,
     )
+    parser_or_group.add_argument(
+        "--log-level",
+        "--log_level",
+        dest="log_level",
+        choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'],
+        help="Level of debugging",
+        default='INFO',
+    )
 
 
 def get_common_args(login_required=True, log_file=False):
     parser = argparse.ArgumentParser(add_help=False)
     general_group = parser.add_argument_group("General options")
     add_verbosity_argument(general_group)
     if log_file:
-        add_log_file_argument(general_group)
+        add_log_file_arguments(general_group)
 
     con_group = parser.add_argument_group("Galaxy connection")
     default_galaxy = os.environ.get("EPHEMERIS_GALAXY") or "http://localhost:8080"

src/ephemeris/ephemeris_log.py

@@ -2,35 +2,6 @@
 import tempfile
 
 
-class ProgressConsoleHandler(logging.StreamHandler):
-    """
-    A handler class which allows the cursor to stay on
-    one line for selected messages
-    """
-
-    on_same_line = False
-
-    def emit(self, record):
-        try:
-            msg = self.format(record)
-            stream = self.stream
-            same_line = hasattr(record, "same_line")
-            if self.on_same_line and not same_line:
-                stream.write("\r\n")
-            stream.write(msg)
-            if same_line:
-                stream.write(".")
-                self.on_same_line = True
-            else:
-                stream.write("\r\n")
-                self.on_same_line = False
-            self.flush()
-        except (KeyboardInterrupt, SystemExit):
-            raise
-        except Exception:
-            self.handleError(record)
-
-
 def disable_external_library_logging():
     # Omit (most of the) logging by external libraries
     logging.getLogger("bioblend").setLevel(logging.ERROR)
@@ -41,23 +12,17 @@ def disable_external_library_logging():
         pass
 
 
-def setup_global_logger(name, log_file=None):
+def setup_global_logger(name, log_file=None, log_level='DEBUG'):
     formatter = logging.Formatter("%(asctime)s %(levelname)-5s - %(message)s")
-    progress = ProgressConsoleHandler()
-    console = logging.StreamHandler()
-    console.setFormatter(formatter)
-
+
     logger = logging.getLogger(name)
-    logger.setLevel(logging.DEBUG)
-    logger.addHandler(progress)
+    logger.setLevel(getattr(logging, log_level))
 
     if not log_file:
-        # delete = false is chosen here because it is always nice to have a log file
-        # ready if you need to debug. Not having the "if only I had set a log file"
-        # moment after the fact.
-        temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False)
-        log_file = temp.name
-    file_handler = logging.FileHandler(log_file)
-    logger.addHandler(file_handler)
-    logger.info(f"Storing log file in: {log_file}")
+        handler = logging.StreamHandler()
+    else:
+        handler = logging.FileHandler(log_file)
+
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
     return logger

src/ephemeris/run_data_managers.py

@@ -371,11 +371,7 @@ def main(argv=None):
     disable_external_library_logging()
     parser = _parser()
     args = parser.parse_args(argv)
-    log = setup_global_logger(name=__name__, log_file=args.log_file)
-    if args.verbose:
-        log.setLevel(logging.DEBUG)
-    else:
-        log.setLevel(logging.INFO)
+    log = setup_global_logger(name=__name__, log_file=args.log_file, log_level=args.log_level)
     gi = get_galaxy_connection(args, file=args.config, log=log, login_required=True)
     config = load_yaml_file(args.config)
     data_managers = DataManagers(gi, config)

src/ephemeris/shed_tools.py

@@ -39,6 +39,7 @@
 import logging
 import os
 import re
+import sys
 import time
 from collections import namedtuple
 from concurrent.futures import (
@@ -261,7 +262,8 @@ def install_repositories(
                     [(t["name"], t.get("changeset_revision", "")) for t in errored_repositories],
                 )
             )
-            log.info("All repositories have been installed.")
+            if len(errored_repositories) == 0:
+                log.info("All repositories have been installed.")
             log.info(f"Total run time: {dt.datetime.now() - installation_start}")
         return InstallResults(
             installed_repositories=installed_repositories,
@@ -378,6 +380,8 @@ def test_tools(
                     log.info(f"Failed tool tests ({n_failed}): {[t[0] for t in test_exceptions]}")
                     log.info(f"Total tool test time: {dt.datetime.now() - tool_test_start}")
 
+        return n_failed == 0
+
     def _get_interactor(self, test_user, test_user_api_key):
         if test_user_api_key is None:
             whoami = self.gi.make_get_request(self.gi.url + "/whoami").json()
@@ -600,7 +604,7 @@ def log_repository_install_error(repository, start, msg, log):
     """
     end = dt.datetime.now()
     log.error(
-        "\t* Error installing a repository (after %s seconds)! Name: %s," "owner: %s, " "revision: %s, error: %s",
+        "\tError installing a repository (after %s seconds)! Name: %s," "owner: %s, " "revision: %s, error: %s",
         str(end - start),
         repository.get("name", ""),
         repository.get("owner", ""),
@@ -678,7 +682,7 @@ def args_to_repos(args) -> List[InstallRepoDict]:
 def main(argv=None):
     disable_external_library_logging()
     args = parser().parse_args(argv)
-    log = setup_global_logger(name=__name__, log_file=args.log_file)
+    log = setup_global_logger(name=__name__, log_file=args.log_file, log_level=args.log_level)
     gi = get_galaxy_connection(args, file=args.tool_list_file, log=log, login_required=True)
     install_repository_manager = InstallRepositoryManager(gi)
 
@@ -702,14 +706,15 @@ def main(argv=None):
     # Start installing/updating and store the results in install_results.
     # Or do testing if the action is `test`
     install_results = None
+    test_result = True
     if args.action == "update":
         install_results = install_repository_manager.update_repositories(repositories=repos, log=log, **kwargs)
     elif args.action == "install":
         install_results = install_repository_manager.install_repositories(
             repos, log=log, force_latest_revision=args.force_latest_revision, **kwargs
         )
     elif args.action == "test":
-        install_repository_manager.test_tools(
+        test_result = install_repository_manager.test_tools(
             test_json=args.test_json,
             repositories=repos,
             log=log,
@@ -729,7 +734,7 @@ def main(argv=None):
         if args.test_existing:
             to_be_tested_repositories.extend(install_results.skipped_repositories)
         if to_be_tested_repositories:
-            install_repository_manager.test_tools(
+            test_result = install_repository_manager.test_tools(
                 test_json=args.test_json,
                 repositories=to_be_tested_repositories,
                 log=log,
@@ -739,6 +744,10 @@ def main(argv=None):
                 client_test_config_path=args.client_test_config,
             )
 
+    if install_results:
+        if len(install_results.errored_repositories) > 0:
+            sys.exit(1)
+    sys.exit(test_result)
 
 if __name__ == "__main__":
     main()