Changeset 136

Timestamp:

02/13/10 19:38:32 (2 years ago)

Author:

mauro

Message:

update indexes

Location:

plone4bio.biosql/trunk

Files:

• MANIFEST.in (modified) (1 diff)
• docs/CHANGES.txt (modified) (2 diffs)
• setup.py (modified) (1 diff)
• src/plone4bio/biosql/README.txt (modified) (1 diff)
• src/plone4bio/biosql/content/seqrecord.py (modified) (2 diffs)
• src/plone4bio/biosql/profiles/default/catalog.xml (modified) (1 diff)
• src/plone4bio/biosql/tests/test_integration.py (added)

plone4bio.biosql/trunk/MANIFEST.in

@@ -1 +1 @@
 recursive-include src *
-global-exclude *.pyc *.pyo
+global-exclude *.pyc *.pyo *.mo

plone4bio.biosql/trunk/docs/CHANGES.txt

@@ -8 +8 @@
 Features
 --------
-
-* rebuild catalog action
-
-* choice seqrecord key field (fix #6)
+* more indexes (see #12) [mauro]
+* rebuild catalog action [mauro]
+* choice seqrecord key field (fix #6) [mauro]
 
 Bug fixes
@@ -25 +24 @@
 
 * mysql / postgresql support
-
 * initial read/write biosql support
 

plone4bio.biosql/trunk/setup.py

@@ -1 +1 @@
 from setuptools import setup, find_packages
+import os
 version = '1.0.1'
 
-tests_require = ['collective.testcaselayer']
+tests_require = ['collective.testcaselayer', 'pysqlite', ]
 
 setup(name='plone4bio.biosql',

plone4bio.biosql/trunk/src/plone4bio/biosql/README.txt

@@ -4 +4 @@
 =================
 
+Create a mockup for a biopython's biosql database:
+
+ import tempfile
+ import os
+ from BioSQL import BioSeqDatabase
+
+ (dbh, dbpath) = tempfile.mkstemp(suffix=".db")
+ server = BioSeqDatabase.open_database(driver = 'sqlite3', db = dbpath)
+ server.load_database_sql('biosqldb-sqlite.sql')
+ server.commit()
+ server.close()
+
+Create a plone4bio's biosqlroot:
+
+    >>> self.login()
+    >>> self.setRoles(('Manager',))
+    >>> self.portal.invokeFactory('BioSQLRoot', u'biosqlroot')
+    'biosqlroot'
+    >>> biosqlroot = getattr(self.portal, u'biosqlroot')
+    >>> biosqlroot.dsn = u'postgres://user:pass@server:port/db'
+
+Search catalog:
+ 
+    >>> brains = self.portal_catalog.searchResults(portal_type='BioSQLSeqRecord', path=biosqlroot.path)
+    >>> len(brains)
+    5
+
+    >>> os.unlink(dbpath)

plone4bio.biosql/trunk/src/plone4bio/biosql/content/seqrecord.py

@@ -71 +71 @@
     #TODO: plone4bio.base
     def SearchableText(self):
-        text = "%s %s %s" % (self.name, self.accession, self.description)
-        if self.annotations.has_key('references'):
-            for ref in self.annotations['references']:
-                text = "%s %s" % (text, ref)
+        text = "%s %s %s %s" % (self.name, self.accessions, self.organism, self.description)
+        for ref in self.references:
+            text = "%s %s" % (text, ref)
         return text
     
@@ -155 +154 @@
     references = property(fget=getReferences)
 
+    def getReferences(self):
+        if self.annotations.has_key('references'):
+            return self.annotations['references']
+        else:
+            return []
+    references = property(fget=getReferences)
+
+    def getOrganism(self):
+        if self.annotations.has_key('organism'):
+            return self.annotations['organism']
+        else:
+            return ""
+    organism = property(fget=getOrganism)
+
+    def getAccessions(self):
+        if self.annotations.has_key('accessions'):
+            return self.annotations['accessions']
+        else:
+            return ""
+    accessions = property(fget=getAccessions)
+
 InitializeClass(BioSQLSeqRecord)
 

plone4bio.biosql/trunk/src/plone4bio/biosql/profiles/default/catalog.xml

@@ -18 +18 @@
   <index name="motives" meta_type="FieldIndex" />
   <index name="comments" meta_type="FieldIndex" />
-  <index name="primm" meta_type="FieldIndex" />
-  <index name="organism" meta_type="FieldIndex" />
+  <index name="organism" meta_type="FieldIndex">
+    <indexed_attr value="organism" />
+  </index>
+  <index name="accessions" meta_type="KeywordIndex">
+    <indexed_attr value="accessions" />
+  </index>
   <index name="keywords" meta_type="FieldIndex" />
   <index name="identifier" meta_type="FieldIndex" />