1 | """ |
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2 | Migration script to modify the 'file_path' field type in 'sample_dataset' table |
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3 | to 'TEXT' so that it can support large file paths exceeding 255 characters |
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4 | """ |
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5 | |
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6 | from sqlalchemy import * |
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7 | from sqlalchemy.orm import * |
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8 | from migrate import * |
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9 | from migrate.changeset import * |
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10 | from sqlalchemy.exc import * |
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11 | |
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12 | from galaxy.model.custom_types import * |
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13 | from galaxy.util.json import from_json_string, to_json_string |
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14 | |
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15 | import datetime |
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16 | now = datetime.datetime.utcnow |
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17 | |
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18 | import logging |
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19 | log = logging.getLogger( __name__ ) |
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20 | |
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21 | metadata = MetaData( migrate_engine ) |
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22 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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23 | |
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24 | |
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25 | def upgrade(): |
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26 | print __doc__ |
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27 | metadata.reflect() |
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28 | try: |
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29 | SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) |
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30 | except NoSuchTableError, e: |
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31 | SampleDataset_table = None |
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32 | log.debug( "Failed loading table 'sample_dataset'" ) |
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33 | |
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34 | if SampleDataset_table: |
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35 | cmd = "SELECT id, file_path FROM sample_dataset" |
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36 | result = db_session.execute( cmd ) |
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37 | filepath_dict = {} |
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38 | for r in result: |
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39 | id = int(r[0]) |
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40 | filepath_dict[id] = r[1] |
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41 | # remove the 'file_path' column |
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42 | try: |
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43 | SampleDataset_table.c.file_path.drop() |
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44 | except Exception, e: |
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45 | log.debug( "Deleting column 'file_path' from the 'sample_dataset' table failed: %s" % ( str( e ) ) ) |
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46 | # create the column again |
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47 | try: |
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48 | col = Column( "file_path", TEXT ) |
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49 | col.create( SampleDataset_table ) |
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50 | assert col is SampleDataset_table.c.file_path |
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51 | except Exception, e: |
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52 | log.debug( "Creating column 'file_path' in the 'sample_dataset' table failed: %s" % ( str( e ) ) ) |
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53 | |
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54 | for id, file_path in filepath_dict.items(): |
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55 | cmd = "update sample_dataset set file_path='%s' where id=%i" % (file_path, id) |
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56 | db_session.execute( cmd ) |
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57 | |
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58 | def downgrade(): |
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59 | pass |
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