| | 6 | Create a mockup for a biopython's biosql database: |
| | 7 | |
| | 8 | import tempfile |
| | 9 | import os |
| | 10 | from BioSQL import BioSeqDatabase |
| | 11 | |
| | 12 | (dbh, dbpath) = tempfile.mkstemp(suffix=".db") |
| | 13 | server = BioSeqDatabase.open_database(driver = 'sqlite3', db = dbpath) |
| | 14 | server.load_database_sql('biosqldb-sqlite.sql') |
| | 15 | server.commit() |
| | 16 | server.close() |
| | 17 | |
| | 18 | Create a plone4bio's biosqlroot: |
| | 19 | |
| | 20 | >>> self.login() |
| | 21 | >>> self.setRoles(('Manager',)) |
| | 22 | >>> self.portal.invokeFactory('BioSQLRoot', u'biosqlroot') |
| | 23 | 'biosqlroot' |
| | 24 | >>> biosqlroot = getattr(self.portal, u'biosqlroot') |
| | 25 | >>> biosqlroot.dsn = u'postgres://user:pass@server:port/db' |
| | 26 | |
| | 27 | Search catalog: |
| | 28 | |
| | 29 | >>> brains = self.portal_catalog.searchResults(portal_type='BioSQLSeqRecord', path=biosqlroot.path) |
| | 30 | >>> len(brains) |
| | 31 | 5 |
| | 32 | |
| | 33 | >>> os.unlink(dbpath) |
