Cut admin and workflow part.

bin/jflow_admin.py

+#!/usr/bin/env python3
+
+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import sys
+import argparse
+
+try:
+    import _preamble
+except ImportError:
+    sys.exc_clear()
+
+from jflow.workflows_manager import WorkflowsManager
+from jflow.workflow import Workflow
+import jflow.utils as utils
+from jflow.exceptions import RuleException, RuleIgnore
+
+
+from jflow.argument_parser import JflowArgumentParser
+
+if __name__ == '__main__':
+
+    # Create a workflow manager to get access to our workflows
+    wfmanager = WorkflowsManager()
+    
+    # Create the top-level parser
+    parser = JflowArgumentParser()
+    subparsers = parser.add_subparsers(title='Available sub commands')
+    
+    # Add rerun workflow availability
+    sub_parser = subparsers.add_parser("rerun", help="Rerun a specific workflow")
+    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be rerun",
+                            required=True, dest="workflow_id")
+    sub_parser.set_defaults(cmd_object="rerun")
+
+    # Add rerun workflow availability
+    sub_parser = subparsers.add_parser("reset", help="Reset a workflow component")
+    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be used",
+                            required=True, dest="workflow_id")
+    sub_parser.add_argument("--component-name", type=str, help="Which component should be reseted",
+                            required=True, dest="component_name")
+    sub_parser.set_defaults(cmd_object="reset")
+
+    # Add delete workflow availability
+    sub_parser = subparsers.add_parser("delete", help="Delete a workflow")
+    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be deleted",
+                            required=True, dest="workflow_id")
+    sub_parser.set_defaults(cmd_object="delete")
+
+    # Add print details workflow availability
+    sub_parser = subparsers.add_parser("print", help="Print workflow details")
+    sub_parser.add_argument("what", help="What to print [outputs, outputs_logs, execution_graph, programs]",
+                            metavar="COMMAND", choices=["outputs", "outputs_logs", "execution_graph", "programs"])
+    sub_parser.add_argument("--workflow-id", type=str, help="Workflow for which display outputs",
+                            required=True, dest="workflow_id")
+    sub_parser.set_defaults(cmd_object="print")
+
+    # Add status workflow availability
+    sub_parser = subparsers.add_parser("status", help="Monitor a specific workflow")
+    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow status should be displayed",
+                            default=None, dest="workflow_id")
+    sub_parser.add_argument("--all", action="store_true", help="Display all workflows status",
+                            default=False, dest="all")
+    sub_parser.add_argument("--errors", action="store_true", help="Display failed commands",
+                            default=False, dest="display_errors")
+    sub_parser.set_defaults(cmd_object="status")
+    
+    
+    args = vars(parser.parse_args())
+
+    if not "cmd_object" in args:
+        print(parser.format_help())
+        parser.exit(0, "")
+    
+    if args["cmd_object"] in wf_classes:
+        try:
+            workflow = wfmanager.get_workflow_by_class(args["cmd_object"])
+            workflow.check_parameters_rules(args)
+        except RuleException as e:
+            sub_parser.error(e)
+        except RuleIgnore:
+            pass
+        wfmanager.run_workflow(args["cmd_object"], args)
+
+    elif args["cmd_object"] == "rerun":
+        wfmanager.rerun_workflow(args["workflow_id"])
+    elif args["cmd_object"] == "reset":
+        try:
+            wfmanager.reset_workflow_component(args["workflow_id"], args["component_name"])
+        except Exception as e:
+            utils.display_error_message(str(e))
+    elif args["cmd_object"] == "delete":
+        try:
+            wfmanager.delete_workflow(args["workflow_id"])
+        except Exception as e:
+            utils.display_error_message(str(e))
+    elif args["cmd_object"] == "print":
+        my_workflow = None
+        try:
+            my_workflow = wfmanager.get_workflow(args["workflow_id"])
+        except Exception as e:
+            utils.display_error_message(str(e))
+        if my_workflow is not None:
+            my_workflow.print_output(args["what"])
+    elif args["cmd_object"] == "status":
+        if args["workflow_id"]:
+            try:
+                workflow = wfmanager.get_workflow(args["workflow_id"])
+            except Exception as e:
+                utils.display_error_message(str(e))
+            print((Workflow.get_status_under_text_format(workflow, True, args["display_errors"])))
+        else:
+            try:
+                workflows = wfmanager.get_workflows(use_cache=True)
+            except Exception as e:
+                utils.display_error_message(str(e))
+            if len(workflows) > 0:
+                workflows_by_id, wfids = {}, []
+                # first sort workflow by ID
+                for workflow in workflows:
+                    wfids.append(workflow.id)
+                    workflows_by_id[workflow.id] = workflow
+                status = "ID\tNAME\tSTATUS\tELAPSED_TIME\tSTART_TIME\tEND_TIME\n"
+                for i, wfid in enumerate(sorted(wfids, reverse=True)):
+                    status += Workflow.get_status_under_text_format(workflows_by_id[wfid])
+                    if i<len(workflows)-1: status += "\n"
+            else: status = "no workflow available"
+            print(status)
+            
\ No newline at end of file

bin/jflow_cli.py

@@ -31,31 +31,7 @@ import jflow.utils as utils
 from jflow.exceptions import RuleException, RuleIgnore
 
 
-class JflowArgumentParser (argparse.ArgumentParser):
-    def _read_args_from_files(self, arg_strings):
-        # expand arguments referencing files
-        new_arg_strings = []
-        for arg_string in arg_strings:
-            # if it's not a comment or an empty line
-            if not arg_string.startswith("#") and arg_string:
-                # for regular arguments, just add them back into the list
-                if not arg_string or arg_string[0] not in self.fromfile_prefix_chars:
-                    new_arg_strings.append(arg_string)
-                # replace arguments referencing files with the file content
-                else:
-                    try:
-                        with open(arg_string[1:]) as args_file:
-                            arg_strings = []
-                            # give to the convert_arg_line_to_args a table of lines instead of line per line
-                            for arg in self.convert_arg_line_to_args(args_file.read().splitlines()):
-                                arg_strings.append(arg)
-                            arg_strings = self._read_args_from_files(arg_strings)
-                            new_arg_strings.extend(arg_strings)
-                    except OSError:
-                        err = _sys.exc_info()[1]
-                        self.error(str(err))
-        # return the modified argument list
-        return new_arg_strings
+from jflow.argument_parser import JflowArgumentParser
 
 if __name__ == '__main__':
 
@@ -66,43 +42,7 @@ if __name__ == '__main__':
     parser = JflowArgumentParser()
     subparsers = parser.add_subparsers(title='Available sub commands')
     
-    # Add rerun workflow availability
-    sub_parser = subparsers.add_parser("rerun", help="Rerun a specific workflow")
-    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be rerun",
-                            required=True, dest="workflow_id")
-    sub_parser.set_defaults(cmd_object="rerun")
-
-    # Add rerun workflow availability
-    sub_parser = subparsers.add_parser("reset", help="Reset a workflow component")
-    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be used",
-                            required=True, dest="workflow_id")
-    sub_parser.add_argument("--component-name", type=str, help="Which component should be reseted",
-                            required=True, dest="component_name")
-    sub_parser.set_defaults(cmd_object="reset")
-
-    # Add delete workflow availability
-    sub_parser = subparsers.add_parser("delete", help="Delete a workflow")
-    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be deleted",
-                            required=True, dest="workflow_id")
-    sub_parser.set_defaults(cmd_object="delete")
-
-    # Add print details workflow availability
-    sub_parser = subparsers.add_parser("print", help="Print workflow details")
-    sub_parser.add_argument("what", help="What to print [outputs, outputs_logs, execution_graph, programs]",
-                            metavar="COMMAND", choices=["outputs", "outputs_logs", "execution_graph", "programs"])
-    sub_parser.add_argument("--workflow-id", type=str, help="Workflow for which display outputs",
-                            required=True, dest="workflow_id")
-    sub_parser.set_defaults(cmd_object="print")
-
-    # Add status workflow availability
-    sub_parser = subparsers.add_parser("status", help="Monitor a specific workflow")
-    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow status should be displayed",
-                            default=None, dest="workflow_id")
-    sub_parser.add_argument("--all", action="store_true", help="Display all workflows status",
-                            default=False, dest="all")
-    sub_parser.add_argument("--errors", action="store_true", help="Display failed commands",
-                            default=False, dest="display_errors")
-    sub_parser.set_defaults(cmd_object="status")
+  
     
     # Add available pipelines
     wf_instances, wf_methodes = wfmanager.get_available_workflows()

src/jflow/argument_parser.py

+#
+# Copyright (C) 2015 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+import argparse
+
+class JflowArgumentParser (argparse.ArgumentParser):
+    def _read_args_from_files(self, arg_strings):
+        # expand arguments referencing files
+        new_arg_strings = []
+        for arg_string in arg_strings:
+            # if it's not a comment or an empty line
+            if not arg_string.startswith("#") and arg_string:
+                # for regular arguments, just add them back into the list
+                if not arg_string or arg_string[0] not in self.fromfile_prefix_chars:
+                    new_arg_strings.append(arg_string)
+                # replace arguments referencing files with the file content
+                else:
+                    try:
+                        with open(arg_string[1:]) as args_file:
+                            arg_strings = []
+                            # give to the convert_arg_line_to_args a table of lines instead of line per line
+                            for arg in self.convert_arg_line_to_args(args_file.read().splitlines()):
+                                arg_strings.append(arg)
+                            arg_strings = self._read_args_from_files(arg_strings)
+                            new_arg_strings.extend(arg_strings)
+                    except OSError:
+                        err = _sys.exc_info()[1]
+                        self.error(str(err))
+        # return the modified argument list
+        return new_arg_strings
\ No newline at end of file