From 71c22f2d6daecdf3b22f06d07c112fc7a01ffb87 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 10 Feb 2014 17:59:59 +0100
Subject: [PATCH] Group mutalyzer-admin subcommands in subsubcommands
---
mutalyzer/entrypoints/admin.py | 105 ++++++++++++++++++++++-----------
1 file changed, 70 insertions(+), 35 deletions(-)
diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index ce0445ab..1d8fea65 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/mutalyzer/entrypoints/admin.py
@@ -3,15 +3,6 @@ Command line interface to Mutalyzer administrative tools.
"""
-# Todo: Group subcommands to subsubcommands. For example:
-#
-# mutalyzer-admin announcement unset
-#
-# instead of
-#
-# mutalyzer-admin unset-announcement
-
-
import argparse
import json
import os
@@ -35,9 +26,9 @@ class UserError(Exception):
pass
-def import_assembly(assembly_file):
+def add_assembly(assembly_file):
"""
- Import genome assembly definition from a JSON file.
+ Add genome assembly definition from a JSON file.
"""
try:
definition = json.load(assembly_file)
@@ -75,6 +66,24 @@ def import_assembly(assembly_file):
session.commit()
+def list_assemblies():
+ """
+ List genome assemblies.
+ """
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+
+ for assembly in assemblies:
+ if assembly.alias:
+ name = '%s (%s)' % (assembly.name, assembly.alias)
+ else:
+ name = assembly.name
+ print '%s, %s (%s)' % (name, assembly.taxonomy_common_name,
+ assembly.taxonomy_id)
+
+
def import_mapview(assembly_name_or_alias, mapview_file, group_label):
"""
Import transcript mappings from an NCBI mapview file.
@@ -179,16 +188,30 @@ def main():
subparsers = parser.add_subparsers(
title='subcommands', dest='subcommand', help='subcommand help')
- p = subparsers.add_parser(
- 'import-assembly', help='import assembly definition from JSON file',
- description=import_assembly.__doc__.split('\n\n')[0])
- p.set_defaults(func=import_assembly)
+ # Subparsers for 'assemblies'.
+ s = subparsers.add_parser(
+ 'assemblies', help='manage genome assemblies',
+ description='Manage genome assemblies and their transcript mappings.'
+ ).add_subparsers()
+
+ # Subparser 'assemblies list'.
+ p = s.add_parser(
+ 'list', help='list assemblies',
+ description=list_assemblies.__doc__.split('\n\n')[0])
+ p.set_defaults(func=list_assemblies)
+
+ # Subparser 'assemblies add'.
+ p = s.add_parser(
+ 'add', help='add assembly definition from JSON file',
+ description=add_assembly.__doc__.split('\n\n')[0])
+ p.set_defaults(func=add_assembly)
p.add_argument(
'assembly_file', metavar='FILE', type=argparse.FileType('r'),
help='genome assembly definition JSON file (example: '
'extras/assemblies/GRCh37.json)')
- p = subparsers.add_parser(
+ # Subparser 'assemblies import-mapview'.
+ p = s.add_parser(
'import-mapview', help='import mappings from NCBI mapview file',
parents=[assembly_parser],
description=import_mapview.__doc__.split('\n\n')[0],
@@ -204,7 +227,8 @@ def main():
help='use only entries with this group label (example: '
'GRCh37.p2-Primary Assembly)')
- p = subparsers.add_parser(
+ # Subparser 'assemblies import-gene'.
+ p = s.add_parser(
'import-gene', help='import mappings by gene from UCSC database',
parents=[assembly_parser],
description=import_gene.__doc__.split('\n\n')[0],
@@ -217,7 +241,8 @@ def main():
help='gene to import all transcript mappings for from the UCSC '
'database (example: TTN)')
- p = subparsers.add_parser(
+ # Subparser 'assemblies import-reference'.
+ p = s.add_parser(
'import-reference', help='import mappings from reference',
parents=[assembly_parser],
description=import_reference.__doc__.split('\n\n')[0],
@@ -230,6 +255,32 @@ def main():
help='genomic reference to import all genes from (example: '
'NC_012920.1)')
+ # Subparsers for 'announcement'.
+ s = subparsers.add_parser(
+ 'announcement', help='manage user announcement',
+ description='Manage announcement to show to the user.',
+ epilog='The announcement is shown on every page of the website.'
+ ).add_subparsers()
+
+ # Subparser 'announcement set'.
+ p = s.add_parser(
+ 'set', help='set user announcement',
+ description=set_announcement.__doc__.split('\n\n')[0])
+ p.set_defaults(func=set_announcement)
+ p.add_argument(
+ 'body', metavar='ANNOUNCEMENT',
+ help='announcement text to show to the user')
+ p.add_argument(
+ '--url', metavar='URL', dest='url',
+ help='URL to more information on the announcement')
+
+ # Subparser 'announcement unset'.
+ p = s.add_parser(
+ 'unset', help='unset user announcement',
+ description=unset_announcement.__doc__.split('\n\n')[0])
+ p.set_defaults(func=unset_announcement)
+
+ # Subparser 'sync-cache'.
p = subparsers.add_parser(
'sync-cache', help='synchronize cache with remote Mutalyzer',
description=sync_cache.__doc__.split('\n\n')[0],
@@ -246,23 +297,7 @@ def main():
default=7, help='number of days to go back in the remote cache '
'(default: 7)')
- p = subparsers.add_parser(
- 'set-announcement', help='set user announcement',
- description=set_announcement.__doc__.split('\n\n')[0],
- epilog='The announcement is shown on every page of the website.')
- p.set_defaults(func=set_announcement)
- p.add_argument(
- 'body', metavar='ANNOUNCEMENT',
- help='announcement text to show to the user')
- p.add_argument(
- '--url', metavar='URL', dest='url',
- help='URL to more information on the announcement')
-
- p = subparsers.add_parser(
- 'unset-announcement', help='unset user announcement',
- description=unset_announcement.__doc__.split('\n\n')[0])
- p.set_defaults(func=unset_announcement)
-
+ # Subparser 'setup-database'.
p = subparsers.add_parser(
'setup-database', help='setup database',
description=setup_database.__doc__.split('\n\n')[0],
--
GitLab