From a61b28b7776016e9f1535c9878ac038306701d05 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 25 Jul 2011 15:25:42 +0000
Subject: [PATCH] Some fixes for cache sync.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@315 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/Db.py | 4 ++--
mutalyzer/config.py | 3 +++
mutalyzer/models.py | 1 +
mutalyzer/sync.py | 32 +++++++++++++++++++++++++-------
mutalyzer/webservice.py | 3 ++-
5 files changed, 33 insertions(+), 10 deletions(-)
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index ea559584..bb57f851 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -1050,8 +1050,8 @@ class Cache(Db) :
@rtype: string
"""
statement = """
- SELECT
- (AccNo, GI, hash, ChrAccVer, ChrStart, ChrStop, orientation, url, created)
+ SELECT AccNo, GI, hash, ChrAccVer, ChrStart,
+ ChrStop, orientation, url, created
FROM GBInfo
WHERE created >= %s;
""", created_since
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index 363d0a88..0314500a 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -134,6 +134,9 @@ class Config():
self.GenRecord.spliceAlarm = int(config["spliceAlarm"])
self.GenRecord.spliceWarn = int(config["spliceWarn"])
+ # Set the variables needed by the sync module.
+ self.Sync.cache = config["cache"]
+
# If we are in a testing environment, use a temporary file for
# logging and a temporary directory for the cache.
# We don't remove these after the tests, since they might be
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index d8b00138..c9e32322 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -233,4 +233,5 @@ class CacheEntry(ClassModel):
chromosomeOrientation = Integer
url = String
created = Mandatory.DateTime
+ cached = Mandatory.Boolean
#CacheEntry
diff --git a/mutalyzer/sync.py b/mutalyzer/sync.py
index 1f4a8231..d5c7a6b7 100644
--- a/mutalyzer/sync.py
+++ b/mutalyzer/sync.py
@@ -4,8 +4,10 @@ Module for synchronizing the database with other Mutalyzer instances.
from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
-from suds.client import Client
+
+import os
from datetime import datetime, timedelta
+from suds.client import Client
DEFAULT_CREATED_SINCE_DAYS = 7
@@ -29,7 +31,19 @@ class CacheSync(object):
if not created_since:
created_since = datetime.today() - \
timedelta(days=DEFAULT_CREATED_SINCE_DAYS)
- return self._database.getGB(created_since)
+ cache = self._database.getGB(created_since)
+
+ entries = []
+
+ # For each entry, check if it is cached on our filesystem.
+ # Todo: refactor
+ for entry in cache:
+ file_path = os.path.join(self._config.cache, '%s.bz2' % entry[0])
+ e = list(entry)
+ e.append(os.path.isfile(file_path))
+ entries.append(e)
+
+ return entries
def remote_cache(self, remote_wsdl, created_since=None):
"""
@@ -47,7 +61,8 @@ class CacheSync(object):
"""
entry_dict = {'name': entry.name,
'hash': entry.hash,
- 'created': entry.created}
+ 'created': entry.created,
+ 'cached': bool(entry.cached)}
for attribute in ('gi', 'chromosomeName', 'chromosomeStart'
'chromosomeStop', 'chromosomeOrientation',
'url'):
@@ -57,7 +72,7 @@ class CacheSync(object):
return map(cache_entry_from_soap, cache.CacheEntry)
- def sync_with_remote(self, remote_wsdl, created_since=None):
+ def sync_with_remote(self, remote_wsdl, remote_cache, created_since=None):
"""
Todo.
"""
@@ -74,7 +89,10 @@ class CacheSync(object):
# entry['chromosomeStop'],
# entry['chromosomeOrientation'],
# entry['url'])
- print 'inserting %s' % entry['name']
- print entry
+ #print 'inserting %s' % entry['name']
+ #print entry
if not entry['chromosomeName'] and not entry['url']:
- print '(downloading file from remote cache...)'
+ if entry['cached']:
+ print 'downloading file from remote cache: %s' % (remote_cache % entry['name'])
+ #else:
+ #print 'cannot download this file from remote cache'
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index f6401e1d..cd480fda 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -907,7 +907,8 @@ class MutalyzerService(DefinitionBase):
e.chromosomeStop,
e.chromosomeOrientation,
e.url,
- e.created) = entry
+ e.created,
+ e.cached) = entry
return e
output.addMessage(__file__, -1, 'INFO',
--
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