From ec13f2d15f02b94e129340c83f092ac2e8df9fb9 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 12 Dec 2013 15:30:29 +0100
Subject: [PATCH] Use entrypoints instead of bin scripts
---
bin/mutalyzer-cache-sync | 49 ----------
bin/mutalyzer-json-service.wsgi | 45 ---------
bin/mutalyzer-mapping-import | 89 -----------------
bin/mutalyzer-mapping-update | 56 -----------
bin/mutalyzer-soap-service.wsgi | 46 ---------
bin/mutalyzer-website.wsgi | 56 -----------
mutalyzer/entrypoints/__init__.py | 3 +
.../entrypoints/batch_processor.py | 43 +++++---
mutalyzer/entrypoints/cache_sync.py | 52 ++++++++++
mutalyzer/entrypoints/mapping_import.py | 97 +++++++++++++++++++
mutalyzer/entrypoints/mapping_update.py | 56 +++++++++++
.../entrypoints/mutalyzer.py | 58 +++++------
mutalyzer/entrypoints/service_json.py | 52 ++++++++++
mutalyzer/entrypoints/service_soap.py | 53 ++++++++++
mutalyzer/entrypoints/website.py | 72 ++++++++++++++
setup.py | 22 +++--
16 files changed, 451 insertions(+), 398 deletions(-)
delete mode 100755 bin/mutalyzer-cache-sync
delete mode 100755 bin/mutalyzer-json-service.wsgi
delete mode 100755 bin/mutalyzer-mapping-import
delete mode 100755 bin/mutalyzer-mapping-update
delete mode 100755 bin/mutalyzer-soap-service.wsgi
delete mode 100755 bin/mutalyzer-website.wsgi
create mode 100644 mutalyzer/entrypoints/__init__.py
rename bin/mutalyzer-batchd => mutalyzer/entrypoints/batch_processor.py (61%)
mode change 100755 => 100644
create mode 100644 mutalyzer/entrypoints/cache_sync.py
create mode 100644 mutalyzer/entrypoints/mapping_import.py
create mode 100644 mutalyzer/entrypoints/mapping_update.py
rename bin/mutalyzer => mutalyzer/entrypoints/mutalyzer.py (76%)
mode change 100755 => 100644
create mode 100644 mutalyzer/entrypoints/service_json.py
create mode 100644 mutalyzer/entrypoints/service_soap.py
create mode 100644 mutalyzer/entrypoints/website.py
diff --git a/bin/mutalyzer-cache-sync b/bin/mutalyzer-cache-sync
deleted file mode 100755
index 5e012949..00000000
--- a/bin/mutalyzer-cache-sync
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-"""
-Synchronize the database cache with other Mutalyzer instances.
-
-Usage:
- {command} remote_wsdl url_template days
-
- remote_wsdl: Location of the remote WSDL description.
- url_template: URL to remote downloads, where {{file}} is to be substituted
- by the filename.
- days: Number of days to go back in the remote cache.
-
-
-This program is intended to be run daily from cron. Example:
-
- 25 5 * * * mutalyzer-cache-sync 'http://dom1/?wsdl' 'http://dom1/{file}' 7
- 55 5 * * * mutalyzer-cache-sync 'http://dom2/?wsdl' 'http://dom2/{file}' 7
-"""
-
-
-import sys
-
-from mutalyzer.output import Output
-from mutalyzer.sync import CacheSync
-from mutalyzer import Db
-from mutalyzer.util import format_usage
-
-
-def cache_sync(remote_wsdl, url_template, days):
- """
- Synchronize the database cache with other Mutalyzer instances.
- """
- output = Output(__file__)
- database = Db.Cache()
-
- sync = CacheSync(output, database)
- sync.sync_with_remote(remote_wsdl, url_template, days)
-
-
-if __name__ == '__main__':
- if len(sys.argv) < 4:
- print format_usage()
- sys.exit(1)
- try:
- days = int(sys.argv[3])
- except ValueError:
- print 'Last argument must be an integer.'
- sys.exit(1)
- cache_sync(sys.argv[1], sys.argv[2], int(sys.argv[3]))
diff --git a/bin/mutalyzer-json-service.wsgi b/bin/mutalyzer-json-service.wsgi
deleted file mode 100755
index bb7dc7d9..00000000
--- a/bin/mutalyzer-json-service.wsgi
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env python
-"""
-WSGI interface to the Mutalyzer HTTP/RPC+JSON web service.
-
-The WSGI interface is exposed through the module variable 'application'.
-
-Example Apache/mod_wsgi configuration:
-
- WSGIScriptAlias /json /usr/local/bin/mutalyzer-json-service.wsgi
-
-Be sure to have this line first if you also define a / alias, like this:
-
- WSGIScriptAlias /services /usr/local/bin/mutalyzer-json-service.wsgi
- WSGIScriptAlias / /usr/local/bin/mutalyzer-website.wsgi
-
-You can also use the built-in HTTP server by running this file directly.
-
-To start the built-in HTTP server on port 8082:
-
- /usr/local/bin/mutalyzer-json-service.wsgi 8082
-"""
-
-
-import sys
-from wsgiref.simple_server import make_server
-from spyne.server.wsgi import WsgiApplication
-from mutalyzer.services import json
-
-
-DEFAULT_PORT = 8082
-
-
-application = WsgiApplication(json.application)
-
-
-if __name__ == '__main__':
- port = DEFAULT_PORT
- if len(sys.argv) > 1:
- try:
- port = int(sys.argv[1])
- except ValueError:
- print 'Not a valid port number: %s' % sys.argv[1]
- sys.exit(1)
- print 'Listening at http://localhost:%d/' % port
- make_server('localhost', port, application).serve_forever()
diff --git a/bin/mutalyzer-mapping-import b/bin/mutalyzer-mapping-import
deleted file mode 100755
index e680dc10..00000000
--- a/bin/mutalyzer-mapping-import
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-"""
-Update the database with mapping information for the given gene or genomic
-reference.
-
-Usage:
- {command} source database gene|reference
-
- source: Import source, 'gene' for importing a specific gene from the UCSC
- or 'reference' for importing from genomic reference.
- database: Database to update (i.e. 'hg18' or 'hg19').
- gene: Name of gene to import all transcripts mappings for from the UCSC
- database (e.g. 'TTN').
- reference: Genomic reference to import all genes from (e.g. 'NC_012920.1').
- Not that currently no exon locations are supported, this has only
- been tested on mtDNA.
-
-
-This program is intended to be run manually whenever transcript mappings for
-specific genes are required that are not yet in our database (i.e. they are
-not yet available from the NCBI, or they are mtDNA genes). It will not
-overwrite transcript/version entries that are already in our database.
-"""
-
-
-import sys
-
-from mutalyzer.output import Output
-from mutalyzer.mapping import UCSCUpdater, ReferenceUpdater
-from mutalyzer.util import format_usage
-
-
-def import_gene(database, gene):
- """
- Update the database with information from the UCSC.
-
- @arg database: Database to update (i.e. 'hg18' or 'hg19').
- @type database: string
- @arg gene: Gene name to get transcript mapping info for.
- @type gene: string
-
- @todo: Also report how much was added/updated.
- """
- output = Output(__file__)
- output.addMessage(__file__, -1, 'INFO',
- 'Starting UCSC mapping data update (gene: %s)' % gene)
-
- updater = UCSCUpdater(database)
- updater.load(gene)
- updater.merge()
-
- output.addMessage(__file__, -1, 'INFO',
- 'UCSC mapping data update end (gene: %s)' % gene)
-
-
-def import_reference(database, reference):
- """
- Update the database with information from the given reference.
-
- @arg database: Database to update (i.e. 'hg18' or 'hg19').
- @type database: string
- @arg reference: Reference to get gene mappings from.
- @type reference: string
-
- @todo: Also report how much was added/updated.
- """
- output = Output(__file__)
- output.addMessage(__file__, -1, 'INFO',
- 'Starting reference mapping data update (reference: %s)' % reference)
-
- updater = ReferenceUpdater(database)
- updater.load(reference, output)
- updater.merge()
-
- output.addMessage(__file__, -1, 'INFO',
- 'Reference mapping data update end (reference: %s)' % reference)
-
-
-if __name__ == '__main__':
- if len(sys.argv) != 4:
- print format_usage()
- sys.exit(1)
- if sys.argv[1] == 'gene':
- import_gene(*sys.argv[2:])
- elif sys.argv[1] == 'reference':
- import_reference(*sys.argv[2:])
- else:
- print format_usage()
- sys.exit(1)
diff --git a/bin/mutalyzer-mapping-update b/bin/mutalyzer-mapping-update
deleted file mode 100755
index 8fe6bb35..00000000
--- a/bin/mutalyzer-mapping-update
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-"""
-Update the database with mapping information from the NCBI.
-
-Usage:
- {command} database mapping_file assembly
-
- database: Database to update (i.e. 'hg18' or 'hg19').
- mapping_file: Path to the NCBI mapping information.
- assembly: Use only entries from this assembly (this is the 'group_name'
- column in the NCBI mapping file).
-
-
-This program is intended to be run daily from cron. Example:
-
- 25 6 * * * mutalyzer-mapping-update hg19 /tmp/seq_gene.md reference
-"""
-
-
-import sys
-
-from mutalyzer.output import Output
-from mutalyzer.mapping import NCBIUpdater
-from mutalyzer.util import format_usage
-
-
-def main(database, mapping_file, assembly):
- """
- Update the database with information from the NCBI.
-
- @arg database: Database to update (i.e. 'hg18' or 'hg19').
- @type database: string
- @arg mapping_file: Path to NCBI mapping information.
- @type mapping_file: string
- @arg assembly: Use only entries from this assembly (this is the
- 'group_name' column in the NCBI mapping file).
- @type assembly: string
-
- @todo: Also report how much was added/updated.
- """
- output = Output(__file__)
- output.addMessage(__file__, -1, 'INFO',
- 'Starting NCBI mapping data update')
-
- updater = NCBIUpdater(database)
- updater.load(mapping_file, assembly)
- updater.merge()
-
- output.addMessage(__file__, -1, 'INFO', 'NCBI mapping data update end')
-
-
-if __name__ == '__main__':
- if len(sys.argv) != 4:
- print format_usage()
- sys.exit(1)
- main(*sys.argv[1:])
diff --git a/bin/mutalyzer-soap-service.wsgi b/bin/mutalyzer-soap-service.wsgi
deleted file mode 100755
index 31f7b797..00000000
--- a/bin/mutalyzer-soap-service.wsgi
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env python
-"""
-WSGI interface to the Mutalyzer SOAP web service.
-
-The WSGI interface is exposed through the module variable 'application'.
-
-Example Apache/mod_wsgi configuration:
-
- WSGIScriptAlias /services /usr/local/bin/mutalyzer-soap-service.wsgi
-
-Be sure to have this line first if you also define a / alias, like this:
-
- WSGIScriptAlias /services /usr/local/bin/mutalyzer-soap-service.wsgi
- WSGIScriptAlias / /usr/local/bin/mutalyzer-website.wsgi
-
-You can also use the built-in HTTP server by running this file directly.
-
-To start the built-in HTTP server on port 8081:
-
- /usr/local/bin/mutalyzer-soap-service.wsgi 8081
-"""
-
-
-import sys
-from wsgiref.simple_server import make_server
-from spyne.server.wsgi import WsgiApplication
-from mutalyzer.services import soap
-
-
-DEFAULT_PORT = 8081
-
-
-application = WsgiApplication(soap.application)
-
-
-if __name__ == '__main__':
- port = DEFAULT_PORT
- if len(sys.argv) > 1:
- try:
- port = int(sys.argv[1])
- except ValueError:
- print 'Not a valid port number: %s' % sys.argv[1]
- sys.exit(1)
- print 'Listening at http://localhost:%d/' % port
- print 'WDSL file is at http://localhost:%d/?wsdl' % port
- make_server('localhost', port, application).serve_forever()
diff --git a/bin/mutalyzer-website.wsgi b/bin/mutalyzer-website.wsgi
deleted file mode 100755
index 237e7279..00000000
--- a/bin/mutalyzer-website.wsgi
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-"""
-WSGI interface to the Mutalyzer website.
-
-The WSGI interface is exposed through the module variable 'application'.
-Static files are not handled by this interface and should be served through
-the '/static' url prefix separately.
-
-Example Apache/mod_wsgi configuration:
-
- Alias /static /var/www/mutalyzer/static
- WSGIScriptAlias / /usr/local/bin/mutalyzer-website.wsgi
-
-You can also use the built-in HTTP server by running this file directly.
-Note, however, that static files are only found by this server in a 'static'
-subdirectory of the current working directory. If you're running Mutalyzer
-from its source code directory, you can satisfy this by creating a quick
-symbolic link:
-
- ln -s mutalyzer/templates/static
-
-Another common practice is to use Nginx to directly serve the static files
-and act as a reverse proxy server to the Mutalyzer HTTP server.
-
-Example Nginx configuration:
-
- server {
- listen 80;
- location /static/ {
- root /var/www/mutalyzer/static;
- if (-f $request_filename) {
- rewrite ^/static/(.*)$ /static/$1 break;
- }
- }
- location / {
- proxy_read_timeout 300; # 5 minutes
- proxy_pass http://127.0.0.1:8080;
- }
- }
-
-Now start the built-in HTTP server on port 8080:
-
- mutalyzer-website.wsgi 8080
-
-@todo: Integrate webservice.py (http://webpy.org/cookbook/webservice/).
-"""
-
-
-from mutalyzer import website
-
-
-application = website.app.wsgifunc()
-
-
-if __name__ == '__main__':
- website.app.run()
diff --git a/mutalyzer/entrypoints/__init__.py b/mutalyzer/entrypoints/__init__.py
new file mode 100644
index 00000000..9644b1aa
--- /dev/null
+++ b/mutalyzer/entrypoints/__init__.py
@@ -0,0 +1,3 @@
+"""
+Entry points to Mutalyzer.
+"""
diff --git a/bin/mutalyzer-batchd b/mutalyzer/entrypoints/batch_processor.py
old mode 100755
new mode 100644
similarity index 61%
rename from bin/mutalyzer-batchd
rename to mutalyzer/entrypoints/batch_processor.py
index 84f7869f..18cffd72
--- a/bin/mutalyzer-batchd
+++ b/mutalyzer/entrypoints/batch_processor.py
@@ -1,39 +1,37 @@
-#!/usr/bin/env python
"""
-Daemon for processing scheduled batch jobs.
+Mutalyzer batch processor.
-The process can be shutdown gracefully by sending a SIGINT (Ctrl+C) or SIGTERM
-signal.
-
-@todo: Get rid of ugly exception logging.
-@todo: Reload configuration without restarting (for example, on SIGHUP).
+.. todo: Get rid of ugly exception logging.
+.. todo: Reload configuration without restarting (for example, on SIGHUP).
"""
+import argparse
import signal
import sys
import time
import traceback
-from mutalyzer import config
-from mutalyzer.Db import Batch, Counter
-from mutalyzer.Scheduler import Scheduler
+from .. import config
+from .. import Db
+from .. import Scheduler
-def daemonize():
+def process():
"""
Run forever in a loop processing scheduled batch jobs.
"""
- database = Batch()
- counter = Counter()
- scheduler = Scheduler(database)
+ database = Db.Batch()
+ counter = Db.Counter()
+ scheduler = Scheduler.Scheduler(database)
def handle_exit(signum, stack_frame):
if scheduler.stopped():
sys.stderr.write('mutalyzer-batchd: Terminated\n')
sys.exit(1)
if signum == signal.SIGINT:
- sys.stderr.write('mutalyzer-batchd: Hitting Ctrl+C again will terminate any running job!\n')
+ sys.stderr.write('mutalyzer-batchd: Hitting Ctrl+C again will '
+ 'terminate any running job!\n')
scheduler.stop()
signal.signal(signal.SIGTERM, handle_exit)
@@ -59,5 +57,18 @@ def daemonize():
sys.exit(0)
+def main():
+ """
+ Command line interface to the batch processor.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer batch processor.',
+ epilog='The process can be shutdown gracefully by sending a SIGINT '
+ '(Ctrl+C) or SIGTERM signal.')
+
+ parser.parse_args()
+ process()
+
+
if __name__ == '__main__':
- daemonize()
+ main()
diff --git a/mutalyzer/entrypoints/cache_sync.py b/mutalyzer/entrypoints/cache_sync.py
new file mode 100644
index 00000000..f238ce62
--- /dev/null
+++ b/mutalyzer/entrypoints/cache_sync.py
@@ -0,0 +1,52 @@
+"""
+Synchronize the database cache with other Mutalyzer instances.
+
+This program is intended to be run daily from cron. Example:
+
+ 25 5 * * * mutalyzer-cache-sync 'http://dom1/?wsdl' 'http://dom1/{file}' -H 7
+ 55 5 * * * mutalyzer-cache-sync 'http://dom2/?wsdl' 'http://dom2/{file}' -H 7
+"""
+
+
+import argparse
+
+from .. import Db
+from .. import output
+from .. import sync
+
+
+def sync_cache(remote_wsdl, url_template, history=7):
+ """
+ Synchronize the database cache with other Mutalyzer instances.
+ """
+ output = output.Output(__file__)
+ database = Db.Cache()
+
+ cache_sync = sync.CacheSync(output, database)
+ cache_sync.sync_with_remote(remote_wsdl, url_template, history)
+
+
+def main():
+ """
+ Command-line interface to the cache synchronizer.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer cache synchronizer.')
+ parser.add_argument(
+ 'wsdl', metavar='WSDL',
+ help='location of the remote WSDL description')
+ parser.add_argument(
+ 'url_template', metavar='URL_TEMPLATE',
+ help='URL for remote downloads, in which the filename is to be '
+ 'substituted for {{file}}')
+ parser.add_argument(
+ '-H', '--history', metavar='DAYS', dest='history', type=int,
+ default=7, help='number of days to go back in the remote cache '
+ '(default: 7)')
+
+ args = parser.parse_args()
+ sync_cache(args.wsdl, args.url_template, history=args.history)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/mutalyzer/entrypoints/mapping_import.py b/mutalyzer/entrypoints/mapping_import.py
new file mode 100644
index 00000000..4982ad1a
--- /dev/null
+++ b/mutalyzer/entrypoints/mapping_import.py
@@ -0,0 +1,97 @@
+"""
+Update the database with mapping information for the given gene or genomic
+reference.
+"""
+
+
+import argparse
+
+from .. import output
+from .. import mapping
+
+
+def import_gene(database, gene):
+ """
+ Update the database with information from the UCSC.
+
+ .. todo: Also report how much was added/updated.
+ """
+ o = output.Output(__file__)
+ o.addMessage(__file__, -1, 'INFO',
+ 'Starting UCSC mapping data update (gene: %s)' % gene)
+
+ updater = mapping.UCSCUpdater(database)
+ updater.load(gene)
+ updater.merge()
+
+ o.addMessage(__file__, -1, 'INFO',
+ 'UCSC mapping data update end (gene: %s)' % gene)
+
+
+def import_reference(database, reference):
+ """
+ Update the database with information from the given reference.
+
+ .. todo: Also report how much was added/updated.
+
+ .. note: Currently no exon locations are supported, this has only been
+ tested on mtDNA.
+ """
+ o = output.Output(__file__)
+ o.addMessage(__file__, -1, 'INFO',
+ 'Starting reference mapping data update (reference: %s)' % reference)
+
+ updater = mapping.ReferenceUpdater(database)
+ updater.load(reference, o)
+ updater.merge()
+
+ o.addMessage(__file__, -1, 'INFO',
+ 'Reference mapping data update end (reference: %s)' % reference)
+
+
+def main():
+ """
+ Command-line interface to the mapping importer.
+ """
+ database_parser = argparse.ArgumentParser(add_help=False)
+ database_parser.add_argument(
+ '-d', '--database', metavar='DATABASE', dest='database',
+ default='hg19', help='database to import to (default: hg19)')
+
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer mapping importer.',
+ epilog='This program is intended to be run manually whenever '
+ 'transcript mappings for specific genes are required that are not '
+ 'yet in our database (i.e., they are not yet available from the '
+ 'NCBI, or they are mtDNA genes). It will not overwrite '
+ 'transcript/version entries that are already in our database.',
+ parents=[database_parser])
+
+ subparsers = parser.add_subparsers(
+ title='subcommands', dest='subcommand', help='subcommand help')
+
+ p = subparsers.add_parser(
+ 'gene', help='import gene', parents=[database_parser],
+ description='Import gene mapping from the UCSC.')
+ p.add_argument(
+ 'gene', metavar='GENE_SYMBOL',
+ help='gene to import all transcript mappings for from the UCSC '
+ 'database (example: TTN)')
+
+ p = subparsers.add_parser(
+ 'reference', help='import reference', parents=[database_parser],
+ description='Import genomic reference file')
+ p.add_argument(
+ 'reference', metavar='FILE',
+ help='genomic reference to import all genes from (example: '
+ 'NC_012920.1)')
+
+ args = parser.parse_args()
+ if args.subcommand == 'gene':
+ import_gene(args.database, args.gene)
+ if args.subcommand == 'reference':
+ import_reference(args.database, args.reference)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/mutalyzer/entrypoints/mapping_update.py b/mutalyzer/entrypoints/mapping_update.py
new file mode 100644
index 00000000..d63fbe7b
--- /dev/null
+++ b/mutalyzer/entrypoints/mapping_update.py
@@ -0,0 +1,56 @@
+"""
+Update the database with mapping information from the NCBI.
+
+This program is intended to be run daily from cron. Example:
+
+ 25 6 * * * mutalyzer-mapping-update hg19 /tmp/seq_gene.md reference
+"""
+
+
+import argparse
+
+from .. import output
+from .. import mapping
+
+
+def update_mapping(database, mapping_file, assembly):
+ """
+ Update the database with information from the NCBI.
+
+ .. todo: Also report how much was added/updated.
+ """
+ o = output.Output(__file__)
+ o.addMessage(__file__, -1, 'INFO',
+ 'Starting NCBI mapping data update')
+
+ updater = mapping.NCBIUpdater(database)
+ updater.load(mapping_file, assembly)
+ updater.merge()
+
+ o.addMessage(__file__, -1, 'INFO', 'NCBI mapping data update end')
+
+
+def main():
+ """
+ Command-line interface to the mapping updater.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer mapping updater.')
+
+ parser.add_argument(
+ 'mapping', metavar='FILE',
+ help='Path to the NCBI mapping information (example: seq_gene.md)')
+ parser.add_argument(
+ 'assembly', metavar='ASSEMBLY',
+ help='use only entries from this assembly (this is the group_name '
+ 'column in the NCBI mapping file)')
+ parser.add_argument(
+ '-d', '--database', metavar='DATABASE', dest='database',
+ default='hg19', help='database to update (default: hg19)')
+
+ args = parser.parse_args()
+ update_mapping(args.database, args.mapping, args.assembly)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bin/mutalyzer b/mutalyzer/entrypoints/mutalyzer.py
old mode 100755
new mode 100644
similarity index 76%
rename from bin/mutalyzer
rename to mutalyzer/entrypoints/mutalyzer.py
index 67c4e33f..d123482f
--- a/bin/mutalyzer
+++ b/mutalyzer/entrypoints/mutalyzer.py
@@ -1,38 +1,28 @@
-#!/usr/bin/env python
"""
-Command-line interface to the nomenclature checker.
+Mutalyzer command-line name checker.
-Usage:
- {command} variant
-
- variant: The variant description to check.
-
-
-@todo: Refactor this file.
+.. todo: Refactor this file.
"""
-import sys
-import os
+import argparse
-from mutalyzer import variantchecker
-from mutalyzer.output import Output
-from mutalyzer.util import format_usage
-from mutalyzer import describe
+from .. import describe
+from .. import output
+from .. import variantchecker
-def main(cmd):
- """
- Command line interface to the name checker.
- @todo: documentation
+def check_name(description):
+ """
+ Run the name checker.
"""
- O = Output(__file__)
+ O = output.Output(__file__)
- O.addMessage(__file__, -1, "INFO", "Received variant " + cmd)
+ O.addMessage(__file__, -1, "INFO", "Received variant " + description)
- RD = variantchecker.check_variant(cmd, O)
+ RD = variantchecker.check_variant(description, O)
- O.addMessage(__file__, -1, "INFO", "Finished processing variant " + cmd)
+ O.addMessage(__file__, -1, "INFO", "Finished processing variant " + description)
### OUTPUT BLOCK ###
gn = O.getOutput("genename")
@@ -116,16 +106,20 @@ def main(cmd):
print extractedProt
#print "+++ %s" % O.getOutput("myTranscriptDescription")
- #if
- ### OUTPUT BLOCK ###
- del O
-#main
+def main():
+ """
+ Command-line interface to the name checker.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer command-line name checker.')
+ parser.add_argument(
+ 'description', metavar='DESCRIPTION',
+ help='variant description to run the name checker on')
-if __name__ == '__main__':
+ args = parser.parse_args()
+ check_name(args.description)
- if len(sys.argv) < 2:
- print format_usage()
- sys.exit(1)
- main(sys.argv[1])
+if __name__ == '__main__':
+ main()
diff --git a/mutalyzer/entrypoints/service_json.py b/mutalyzer/entrypoints/service_json.py
new file mode 100644
index 00000000..9dd1952e
--- /dev/null
+++ b/mutalyzer/entrypoints/service_json.py
@@ -0,0 +1,52 @@
+"""
+WSGI interface to the Mutalyzer HTTP/RPC+JSON webservice.
+
+Example Apache/mod_wsgi configuration:
+
+ WSGIScriptAlias /json /usr/local/bin/mutalyzer-service-json
+
+Be sure to have this line first if you also define a / alias, like this:
+
+ WSGIScriptAlias /json /usr/local/bin/mutalyzer-service-json
+ WSGIScriptAlias / /usr/local/bin/mutalyzer-website
+
+You can also use the built-in HTTP server by running this file directly.
+"""
+
+
+import argparse
+import sys
+
+from wsgiref.simple_server import make_server
+from spyne.server.wsgi import WsgiApplication
+
+from ..services import json
+
+
+application = WsgiApplication(json.application)
+
+
+def debugserver(port):
+ """
+ Run the webservice with the Python built-in HTTP server.
+ """
+ sys.stderr.write('Listening on http://localhost:%d/\n' % port)
+ make_server('localhost', port, application).serve_forever()
+
+
+def main():
+ """
+ Command-line interface to the HTTP/RPC+JSON webservice.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer HTTP/RPC+JSON webservice.')
+ parser.add_argument(
+ '-p', '--port', metavar='NUMBER', dest='port', type=int,
+ default=8082, help='port to run the webservice on (default: 8082)')
+
+ args = parser.parse_args()
+ debugserver(args.port)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/mutalyzer/entrypoints/service_soap.py b/mutalyzer/entrypoints/service_soap.py
new file mode 100644
index 00000000..eb91a82e
--- /dev/null
+++ b/mutalyzer/entrypoints/service_soap.py
@@ -0,0 +1,53 @@
+"""
+WSGI interface to the Mutalyzer SOAP webservice.
+
+Example Apache/mod_wsgi configuration:
+
+ WSGIScriptAlias /soap /usr/local/bin/mutalyzer-service-soap
+
+Be sure to have this line first if you also define a / alias, like this:
+
+ WSGIScriptAlias /soap /usr/local/bin/mutalyzer-service-soap
+ WSGIScriptAlias / /usr/local/bin/mutalyzer-website
+
+You can also use the built-in HTTP server by running this file directly.
+"""
+
+
+import argparse
+import sys
+
+from wsgiref.simple_server import make_server
+from spyne.server.wsgi import WsgiApplication
+
+from ..services import soap
+
+
+application = WsgiApplication(soap.application)
+
+
+def debugserver(port):
+ """
+ Run the webservice with the Python built-in HTTP server.
+ """
+ sys.stderr.write('Listening on http://localhost:%d/\n' % port)
+ sys.stderr.write('WDSL file is at http://localhost:%d/?wsdl\n' % port)
+ make_server('localhost', port, application).serve_forever()
+
+
+def main():
+ """
+ Command-line interface to the SOAP webservice.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer SOAP webservice.')
+ parser.add_argument(
+ '-p', '--port', metavar='NUMBER', dest='port', type=int,
+ default=8081, help='port to run the webservice on (default: 8081)')
+
+ args = parser.parse_args()
+ debugserver(args.port)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/mutalyzer/entrypoints/website.py b/mutalyzer/entrypoints/website.py
new file mode 100644
index 00000000..3a16feff
--- /dev/null
+++ b/mutalyzer/entrypoints/website.py
@@ -0,0 +1,72 @@
+"""
+WSGI interface to the Mutalyzer website.
+
+The WSGI interface is exposed through the module variable 'application'.
+Static files are not handled by this interface and should be served through
+the '/static' url prefix separately.
+
+Example Apache/mod_wsgi configuration:
+
+ Alias /static /var/www/mutalyzer/static
+ WSGIScriptAlias / /usr/local/bin/mutalyzer-website
+
+You can also use the built-in HTTP server by running this file directly.
+Note, however, that static files are only found by this server in a 'static'
+subdirectory of the current working directory. If you're running Mutalyzer
+from its source code directory, you can satisfy this by creating a quick
+symbolic link:
+
+ ln -s mutalyzer/templates/static
+
+Another common practice is to use Nginx to directly serve the static files
+and act as a reverse proxy server to the Mutalyzer HTTP server.
+
+Example Nginx configuration:
+
+ server {
+ listen 80;
+ location /static/ {
+ root /var/www/mutalyzer/static;
+ if (-f $request_filename) {
+ rewrite ^/static/(.*)$ /static/$1 break;
+ }
+ }
+ location / {
+ proxy_read_timeout 300; # 5 minutes
+ proxy_pass http://127.0.0.1:8080;
+ }
+ }
+"""
+
+
+import argparse
+
+from .. import website
+
+
+application = website.app.wsgifunc()
+
+
+def debugserver():
+ """
+ Run the website with the Python built-in HTTP server.
+ """
+ website.app.run()
+
+
+def main():
+ """
+ Command-line interface to the website.
+ """
+ parser = argparse.ArgumentParser(
+ description='Mutalyzer website.')
+ parser.add_argument(
+ 'port', metavar='NUMBER', type=int, nargs='?', default=8080,
+ help='port to run the website on (default: 8080)')
+
+ args = parser.parse_args()
+ debugserver()
+
+
+if __name__ == '__main__':
+ main()
diff --git a/setup.py b/setup.py
index 707c8b0f..d7f16f16 100644
--- a/setup.py
+++ b/setup.py
@@ -40,16 +40,20 @@ setup(
license='Not distributable',
platforms=['any'],
install_requires=install_requires,
- packages=['mutalyzer', 'mutalyzer.parsers', 'mutalyzer.services'],
+ packages=['mutalyzer',
+ 'mutalyzer.entrypoints',
+ 'mutalyzer.parsers',
+ 'mutalyzer.services'],
include_package_data=True,
- scripts=['bin/mutalyzer',
- 'bin/mutalyzer-batchd',
- 'bin/mutalyzer-cache-sync',
- 'bin/mutalyzer-mapping-update',
- 'bin/mutalyzer-mapping-import',
- 'bin/mutalyzer-soap-service.wsgi',
- 'bin/mutalyzer-json-service.wsgi',
- 'bin/mutalyzer-website.wsgi'],
+ entry_points = {'console_scripts': [
+ 'mutalyzer = mutalyzer.entrypoints.mutalyzer:main',
+ 'mutalyzer-batch-processor = mutalyzer.entrypoints.batch_processor:main',
+ 'mutalyzer-cache-sync = mutalyzer.entrypoints.cache_sync:main',
+ 'mutalyzer-mapping-import = mutalyzer.entrypoints.mapping_import:main',
+ 'mutalyzer-mapping-update = mutalyzer.entrypoints.mapping_update:main',
+ 'mutalyzer-service-json = mutalyzer.entrypoints.service_json:main',
+ 'mutalyzer-service-soap = mutalyzer.entrypoints.service_soap:main',
+ 'mutalyzer-website = mutalyzer.entrypoints.website:main']},
zip_safe=False
)
--
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