From 57cda6ff60319f6a32ab988111eccac2f7a89367 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 21 Jul 2011 15:41:26 +0000
Subject: [PATCH] Creation timestamp for cache entries.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@313 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/post-install.sh | 4 +++-
extras/soap-tools/getcache.py | 10 +++++++++-
mutalyzer/Db.py | 13 +++++++++----
mutalyzer/models.py | 4 +++-
mutalyzer/sync.py | 9 +++++++--
mutalyzer/webservice.py | 9 +++++----
6 files changed, 36 insertions(+), 13 deletions(-)
diff --git a/extras/post-install.sh b/extras/post-install.sh
index 123f3850..b24e2c8b 100644
--- a/extras/post-install.sh
+++ b/extras/post-install.sh
@@ -303,9 +303,11 @@ CREATE TABLE GBInfo (
ChrStop int(12) DEFAULT NULL,
orientation int(2) DEFAULT NULL,
url char(255) DEFAULT NULL,
+ created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (AccNo),
UNIQUE KEY hash (hash),
- UNIQUE KEY alias (GI)
+ UNIQUE KEY alias (GI),
+ INDEX (created)
);
CREATE TABLE Link (
mrnaAcc char(20) NOT NULL,
diff --git a/extras/soap-tools/getcache.py b/extras/soap-tools/getcache.py
index 9e44d31f..fc8cd298 100755
--- a/extras/soap-tools/getcache.py
+++ b/extras/soap-tools/getcache.py
@@ -13,6 +13,7 @@ def _import_open_patched(self, *args, **kwargs):
Import.open = _import_open_patched
import sys
+from datetime import datetime, timedelta
from suds.client import Client
URL = 'http://localhost/mutalyzer/services/?wsdl'
@@ -20,9 +21,15 @@ URL = 'http://localhost/mutalyzer/services/?wsdl'
c = Client(URL, cache=None)
o = c.service
+days = 1
+if len(sys.argv) > 1:
+ days = int(sys.argv[1])
+
+created_since = datetime.today() - timedelta(minutes=days)
+
print 'Getting cache...'
-cache = o.getCache()
+cache = o.getCache(created_since)
if cache:
for r in cache.CacheEntry:
@@ -40,4 +47,5 @@ if cache:
print r.chromosomeOrientation
if 'url' in r:
print r.url
+ print r.created
print
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index 8bc326e9..ce7b8e32 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -1033,20 +1033,25 @@ class Cache(Db) :
return None
#getGBFromGI
- def getGB(self):
+ def getGB(self, created_since):
"""
- Get all accession numbers from the cache.
+ Get all accession number entries starting with creation date
+ {created_since}.
SQL tables from internalDb:
- GBInfo ; Information about cached and uploaded GenBank files.
+ @arg created_since: Only entries with later creation dates are returned.
+ @type created_since: datatime.datetime
+
@return: The accession number
@rtype: string
"""
statement = """
SELECT *
- FROM GBInfo;
- """, None
+ FROM GBInfo
+ WHERE created >= %s;
+ """, created_since
return self.query(statement)
#getGB
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index c6fba15c..d8b00138 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -17,7 +17,7 @@ Additional attributes values for the soaplib String model:
"""
-from soaplib.core.model.primitive import String, Integer, Boolean
+from soaplib.core.model.primitive import String, Integer, Boolean, DateTime
from soaplib.core.model.clazz import ClassModel, Array
from mutalyzer import SOAP_NAMESPACE
@@ -31,6 +31,7 @@ class Mandatory(object):
String = String(min_occurs=1, nillable=False)
Integer = Integer(min_occurs=1, nillable=False)
Boolean = Boolean(min_occurs=1, nillable=False)
+ DateTime = DateTime(min_occurs=1, nillable=False)
#Mandatory
@@ -231,4 +232,5 @@ class CacheEntry(ClassModel):
chromosomeStop = Integer
chromosomeOrientation = Integer
url = String
+ created = Mandatory.DateTime
#CacheEntry
diff --git a/mutalyzer/sync.py b/mutalyzer/sync.py
index 2ece6e61..b99cf116 100644
--- a/mutalyzer/sync.py
+++ b/mutalyzer/sync.py
@@ -3,6 +3,9 @@ Module for synchronizing the database with other Mutalyzer instances.
"""
+from datetime import datetime, timedelta
+
+
class CacheSync(object):
"""
Todo.
@@ -14,8 +17,10 @@ class CacheSync(object):
self._config = config
self._database = database
- def local_cache(self):
+ def local_cache(self, created_since=None):
"""
Todo.
"""
- return self._database.getGB()
+ if not created_since:
+ created_since = datetime.today() - timedelta(days=7)
+ return self._database.getGB(created_since)
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index 6798ba02..720ba445 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -23,7 +23,7 @@ import logging; logging.basicConfig()
from soaplib.core import Application
from soaplib.core.service import soap
from soaplib.core.service import DefinitionBase
-from soaplib.core.model.primitive import String, Integer
+from soaplib.core.model.primitive import String, Integer, DateTime
from soaplib.core.model.clazz import Array
from soaplib.core.model.exception import Fault
from soaplib.core.server import wsgi
@@ -882,8 +882,8 @@ class MutalyzerService(DefinitionBase):
return result
#info
- @soap(_returns = Array(CacheEntry))
- def getCache(self):
+ @soap(DateTime, _returns = Array(CacheEntry))
+ def getCache(self, created_since=None):
"""
Todo: documentation.
"""
@@ -895,7 +895,7 @@ class MutalyzerService(DefinitionBase):
database = Db.Cache(self._config.Db)
sync = CacheSync(self._config.Sync, database)
- cache = sync.local_cache()
+ cache = sync.local_cache(created_since)
def soap_cache_entry(entry):
e = CacheEntry()
@@ -907,6 +907,7 @@ class MutalyzerService(DefinitionBase):
e.chromosomeStop = entry[5]
e.chromosomeOrientation = entry[6]
e.url = entry[7]
+ e.created = entry[8]
return e
output.addMessage(__file__, -1, 'INFO',
--
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