Webservice for getting cache listing.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@312 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bin/mutalyzer-cache-sync

+#!/usr/bin/env python
+
+"""
+Synchronize the database cache with other Mutalyzer instances.
+
+This program is intended to be run daily from cron. Example:
+
+  25 5 * * *  mutalyzer-cache-sync
+"""
+
+
+from mutalyzer.config import Config
+from mutalyzer.output import Output
+
+
+def main():
+    """
+    Synchronize the database cache with other Mutalyzer instances.
+    """
+    config = Config()
+    output = Output(__file__, config.Output)
+    output.addMessage(__file__, -1, 'INFO',
+                      'Starting cache sync')
+
+    # Todo: Actually do something.
+
+    output.addMessage(__file__, -1, 'INFO', 'Cache sync end')
+
+
+if __name__ == '__main__':
+    main()

extras/soap-tools/getcache.py

+#!/usr/bin/env python
+
+# Monkey patch suds, because for some weird reason the location
+# http://www.w3.org/2001/xml.xsd is used for the XML namespace, but the W3C
+# seems to respond too slow on that url. We use therefore use
+# http://www.w3.org/2009/01/xml.xsd which fixes this.
+from suds.xsd.sxbasic import Import
+_import_open = Import.open
+def _import_open_patched(self, *args, **kwargs):
+    if self.location == 'http://www.w3.org/2001/xml.xsd':
+        self.location = 'http://www.w3.org/2009/01/xml.xsd'
+    return _import_open(self, *args, **kwargs)
+Import.open = _import_open_patched
+
+import sys
+from suds.client import Client
+
+URL = 'http://localhost/mutalyzer/services/?wsdl'
+
+c = Client(URL, cache=None)
+o = c.service
+
+print 'Getting cache...'
+
+cache = o.getCache()
+
+if cache:
+    for r in cache.CacheEntry:
+        print r.name
+        if 'gi' in r:
+            print r.gi
+        print r.hash
+        if 'chromosomeName' in r:
+            print r.chromosomeName
+        if 'chromosomeStart' in r:
+            print r.chromosomeStart
+        if 'chromosomeStop' in r:
+            print r.chromosomeStop
+        if 'chromosomeOrientation' in r:
+            print r.chromosomeOrientation
+        if 'url' in r:
+            print r.url
+        print

mutalyzer/Db.py

@@ -1033,6 +1033,24 @@ class Cache(Db) :
         return None
     #getGBFromGI
 
+    def getGB(self):
+        """
+        Get all accession numbers from the cache.
+
+        SQL tables from internalDb:
+            - GBInfo ; Information about cached and uploaded GenBank files.
+
+        @return: The accession number
+        @rtype: string
+        """
+        statement = """
+            SELECT *
+              FROM GBInfo;
+        """, None
+
+        return self.query(statement)
+    #getGB
+
     def getLoc(self, accNo) :
         """
         Get the slicing information of an accession number, typically this
@@ -1523,10 +1541,3 @@ class Batch(Db) :
         return inputl, flags
     #getFromQueue
 #Batch
-
-#
-# Unit test.
-#
-if __name__ == "__main__" :
-    pass
-#if

mutalyzer/config.py

@@ -28,6 +28,7 @@ class Config():
     class Batch(): pass
     class File(): pass
     class GenRecord(): pass
+    class Sync(): pass
 
     def __init__(self, filename=None):
         """

mutalyzer/models.py

@@ -214,4 +214,21 @@ class InfoOutput(ClassModel):
     nomenclatureVersionParts = Array(String)
     serverName = String
     contactEmail = String
-#MutalyzerOutput
+#InfoOutput
+
+
+class CacheEntry(ClassModel):
+    """
+    Used in getCache SOAP method.
+    """
+    __namespace__ = SOAP_NAMESPACE
+
+    name = Mandatory.String
+    gi = String
+    hash = Mandatory.String
+    chromosomeName = String
+    chromosomeStart = Integer
+    chromosomeStop = Integer
+    chromosomeOrientation = Integer
+    url = String
+#CacheEntry

mutalyzer/sync.py

+"""
+Module for synchronizing the database with other Mutalyzer instances.
+"""
+
+
+class CacheSync(object):
+    """
+    Todo.
+    """
+    def __init__(self, config, database):
+        """
+        Todo.
+        """
+        self._config = config
+        self._database = database
+
+    def local_cache(self):
+        """
+        Todo.
+        """
+        return self._database.getGB()

mutalyzer/webservice.py

@@ -35,6 +35,7 @@ import mutalyzer
 from mutalyzer.config import Config
 from mutalyzer.output import Output
 from mutalyzer.grammar import Grammar
+from mutalyzer.sync import CacheSync
 from mutalyzer import variantchecker
 from mutalyzer import Db
 from mutalyzer import Mapper
@@ -880,6 +881,39 @@ class MutalyzerService(DefinitionBase):
         output.addMessage(__file__, -1, 'INFO', 'Finished processing info')
         return result
     #info
+
+    @soap(_returns = Array(CacheEntry))
+    def getCache(self):
+        """
+        Todo: documentation.
+        """
+        output = Output(__file__, self._config.Output)
+
+        output.addMessage(__file__, -1, 'INFO',
+                          'Received request getCache')
+
+        database = Db.Cache(self._config.Db)
+        sync = CacheSync(self._config.Sync, database)
+
+        cache = sync.local_cache()
+
+        def soap_cache_entry(entry):
+            e = CacheEntry()
+            e.name = entry[0]
+            e.gi = entry[1]
+            e.hash = entry[2]
+            e.chromosomeName = entry[3]
+            e.chromosomeStart = entry[4]
+            e.chromosomeStop = entry[5]
+            e.chromosomeOrientation = entry[6]
+            e.url = entry[7]
+            return e
+
+        output.addMessage(__file__, -1, 'INFO',
+                          'Finished processing getCache')
+
+        return map(soap_cache_entry, cache)
+    #getCache
 #MutalyzerService
 
 

setup.py

@@ -17,8 +17,11 @@ setup(
     platforms=['any'],
     packages=find_packages(exclude=['doc', 'extras', 'tests']),
     include_package_data=True,
-    scripts=['bin/mutalyzer', 'bin/mutalyzer-batchd',
-             'bin/mutalyzer-ucsc-update', 'bin/mutalyzer-website.wsgi',
+    scripts=['bin/mutalyzer',
+             'bin/mutalyzer-cache-sync',
+             'bin/mutalyzer-batchd',
+             'bin/mutalyzer-ucsc-update',
+             'bin/mutalyzer-website.wsgi',
              'bin/mutalyzer-webservice.wsgi'],
     zip_safe=False
 )