1 | """ |
---|
2 | Migration script to create tables and columns for sharing visualizations. |
---|
3 | """ |
---|
4 | |
---|
5 | from sqlalchemy import * |
---|
6 | from sqlalchemy.orm import * |
---|
7 | from migrate import * |
---|
8 | from migrate.changeset import * |
---|
9 | |
---|
10 | import logging |
---|
11 | log = logging.getLogger( __name__ ) |
---|
12 | |
---|
13 | metadata = MetaData( migrate_engine ) |
---|
14 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
---|
15 | |
---|
16 | # Sharing visualizations. |
---|
17 | |
---|
18 | VisualizationUserShareAssociation_table = Table( "visualization_user_share_association", metadata, |
---|
19 | Column( "id", Integer, primary_key=True ), |
---|
20 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
21 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
---|
22 | ) |
---|
23 | |
---|
24 | # Tagging visualizations. |
---|
25 | |
---|
26 | VisualizationTagAssociation_table = Table( "visualization_tag_association", metadata, |
---|
27 | Column( "id", Integer, primary_key=True ), |
---|
28 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
29 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
30 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
31 | Column( "user_tname", Unicode(255), index=True), |
---|
32 | Column( "value", Unicode(255), index=True), |
---|
33 | Column( "user_value", Unicode(255), index=True) ) |
---|
34 | |
---|
35 | # Annotating visualizations. |
---|
36 | |
---|
37 | VisualizationAnnotationAssociation_table = Table( "visualization_annotation_association", metadata, |
---|
38 | Column( "id", Integer, primary_key=True ), |
---|
39 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
40 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
41 | Column( "annotation", TEXT, index=False ) ) |
---|
42 | |
---|
43 | Visualiation_table = Table( "visualization", metadata, autoload=True ) |
---|
44 | |
---|
45 | def upgrade(): |
---|
46 | print __doc__ |
---|
47 | metadata.reflect() |
---|
48 | |
---|
49 | # Create visualization_user_share_association table. |
---|
50 | try: |
---|
51 | VisualizationUserShareAssociation_table.create() |
---|
52 | except Exception, e: |
---|
53 | print "Creating visualization_user_share_association table failed: %s" % str( e ) |
---|
54 | log.debug( "Creating visualization_user_share_association table failed: %s" % str( e ) ) |
---|
55 | |
---|
56 | # Get default boolean value 'false' so that columns can be initialized. |
---|
57 | if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': |
---|
58 | default_false = "0" |
---|
59 | elif migrate_engine.name == 'postgres': |
---|
60 | default_false = "false" |
---|
61 | |
---|
62 | # Add columns & create indices for supporting sharing to visualization table. |
---|
63 | deleted_column = Column( "deleted", Boolean, default=False, index=True ) |
---|
64 | importable_column = Column( "importable", Boolean, default=False, index=True ) |
---|
65 | slug_column = Column( "slug", TEXT, index=True ) |
---|
66 | published_column = Column( "published", Boolean, index=True ) |
---|
67 | |
---|
68 | try: |
---|
69 | # Add column. |
---|
70 | deleted_column.create( Visualiation_table ) |
---|
71 | assert deleted_column is Visualiation_table.c.deleted |
---|
72 | |
---|
73 | # Fill column with default value. |
---|
74 | cmd = "UPDATE visualization SET deleted = %s" % default_false |
---|
75 | db_session.execute( cmd ) |
---|
76 | except Exception, e: |
---|
77 | print "Adding deleted column to visualization table failed: %s" % str( e ) |
---|
78 | log.debug( "Adding deleted column to visualization table failed: %s" % str( e ) ) |
---|
79 | |
---|
80 | try: |
---|
81 | i = Index( "ix_visualization_deleted", Visualiation_table.c.deleted ) |
---|
82 | i.create() |
---|
83 | except Exception, e: |
---|
84 | print "Adding index 'ix_visualization_deleted' failed: %s" % str( e ) |
---|
85 | log.debug( "Adding index 'ix_visualization_deleted' failed: %s" % str( e ) ) |
---|
86 | |
---|
87 | try: |
---|
88 | # Add column. |
---|
89 | importable_column.create( Visualiation_table ) |
---|
90 | assert importable_column is Visualiation_table.c.importable |
---|
91 | |
---|
92 | # Fill column with default value. |
---|
93 | cmd = "UPDATE visualization SET importable = %s" % default_false |
---|
94 | db_session.execute( cmd ) |
---|
95 | except Exception, e: |
---|
96 | print "Adding importable column to visualization table failed: %s" % str( e ) |
---|
97 | log.debug( "Adding importable column to visualization table failed: %s" % str( e ) ) |
---|
98 | |
---|
99 | i = Index( "ix_visualization_importable", Visualiation_table.c.importable ) |
---|
100 | try: |
---|
101 | i.create() |
---|
102 | except Exception, e: |
---|
103 | print "Adding index 'ix_visualization_importable' failed: %s" % str( e ) |
---|
104 | log.debug( "Adding index 'ix_visualization_importable' failed: %s" % str( e ) ) |
---|
105 | |
---|
106 | try: |
---|
107 | slug_column.create( Visualiation_table ) |
---|
108 | assert slug_column is Visualiation_table.c.slug |
---|
109 | except Exception, e: |
---|
110 | print "Adding slug column to visualization table failed: %s" % str( e ) |
---|
111 | log.debug( "Adding slug column to visualization table failed: %s" % str( e ) ) |
---|
112 | |
---|
113 | try: |
---|
114 | if migrate_engine.name == 'mysql': |
---|
115 | # Have to create index manually. |
---|
116 | cmd = "CREATE INDEX ix_visualization_slug ON visualization ( slug ( 100 ) )" |
---|
117 | db_session.execute( cmd ) |
---|
118 | else: |
---|
119 | i = Index( "ix_visualization_slug", Visualiation_table.c.slug ) |
---|
120 | i.create() |
---|
121 | except Exception, e: |
---|
122 | print "Adding index 'ix_visualization_slug' failed: %s" % str( e ) |
---|
123 | log.debug( "Adding index 'ix_visualization_slug' failed: %s" % str( e ) ) |
---|
124 | |
---|
125 | try: |
---|
126 | # Add column. |
---|
127 | published_column.create( Visualiation_table ) |
---|
128 | assert published_column is Visualiation_table.c.published |
---|
129 | |
---|
130 | # Fill column with default value. |
---|
131 | cmd = "UPDATE visualization SET published = %s" % default_false |
---|
132 | db_session.execute( cmd ) |
---|
133 | except Exception, e: |
---|
134 | print "Adding published column to visualization table failed: %s" % str( e ) |
---|
135 | log.debug( "Adding published column to visualization table failed: %s" % str( e ) ) |
---|
136 | |
---|
137 | i = Index( "ix_visualization_published", Visualiation_table.c.published ) |
---|
138 | try: |
---|
139 | i.create() |
---|
140 | except Exception, e: |
---|
141 | print "Adding index 'ix_visualization_published' failed: %s" % str( e ) |
---|
142 | log.debug( "Adding index 'ix_visualization_published' failed: %s" % str( e ) ) |
---|
143 | |
---|
144 | # Create visualization_tag_association table. |
---|
145 | try: |
---|
146 | VisualizationTagAssociation_table.create() |
---|
147 | except Exception, e: |
---|
148 | print str(e) |
---|
149 | log.debug( "Creating visualization_tag_association table failed: %s" % str( e ) ) |
---|
150 | |
---|
151 | # Create visualization_annotation_association table. |
---|
152 | try: |
---|
153 | VisualizationAnnotationAssociation_table.create() |
---|
154 | except Exception, e: |
---|
155 | print str(e) |
---|
156 | log.debug( "Creating visualization_annotation_association table failed: %s" % str( e ) ) |
---|
157 | |
---|
158 | # Need to create index for visualization annotation manually to deal with errors. |
---|
159 | try: |
---|
160 | if migrate_engine.name == 'mysql': |
---|
161 | # Have to create index manually. |
---|
162 | cmd = "CREATE INDEX ix_visualization_annotation_association_annotation ON visualization_annotation_association ( annotation ( 100 ) )" |
---|
163 | db_session.execute( cmd ) |
---|
164 | else: |
---|
165 | i = Index( "ix_visualization_annotation_association_annotation", VisualizationAnnotationAssociation_table.c.annotation ) |
---|
166 | i.create() |
---|
167 | except Exception, e: |
---|
168 | print "Adding index 'ix_visualization_annotation_association_annotation' failed: %s" % str( e ) |
---|
169 | log.debug( "Adding index 'ix_visualization_annotation_association_annotation' failed: %s" % str( e ) ) |
---|
170 | |
---|
171 | def downgrade(): |
---|
172 | metadata.reflect() |
---|
173 | |
---|
174 | # Drop visualization_user_share_association table. |
---|
175 | try: |
---|
176 | VisualizationUserShareAssociation_table.drop() |
---|
177 | except Exception, e: |
---|
178 | print str(e) |
---|
179 | log.debug( "Dropping visualization_user_share_association table failed: %s" % str( e ) ) |
---|
180 | |
---|
181 | # Drop columns for supporting sharing from visualization table. |
---|
182 | try: |
---|
183 | Visualiation_table.c.deleted.drop() |
---|
184 | except Exception, e: |
---|
185 | print "Dropping deleted column from visualization table failed: %s" % str( e ) |
---|
186 | log.debug( "Dropping deleted column from visualization table failed: %s" % str( e ) ) |
---|
187 | |
---|
188 | try: |
---|
189 | Visualiation_table.c.importable.drop() |
---|
190 | except Exception, e: |
---|
191 | print "Dropping importable column from visualization table failed: %s" % str( e ) |
---|
192 | log.debug( "Dropping importable column from visualization table failed: %s" % str( e ) ) |
---|
193 | |
---|
194 | try: |
---|
195 | Visualiation_table.c.slug.drop() |
---|
196 | except Exception, e: |
---|
197 | print "Dropping slug column from visualization table failed: %s" % str( e ) |
---|
198 | log.debug( "Dropping slug column from visualization table failed: %s" % str( e ) ) |
---|
199 | |
---|
200 | try: |
---|
201 | Visualiation_table.c.published.drop() |
---|
202 | except Exception, e: |
---|
203 | print "Dropping published column from visualization table failed: %s" % str( e ) |
---|
204 | log.debug( "Dropping published column from visualization table failed: %s" % str( e ) ) |
---|
205 | |
---|
206 | # Drop visualization_tag_association table. |
---|
207 | try: |
---|
208 | VisualizationTagAssociation_table.drop() |
---|
209 | except Exception, e: |
---|
210 | print str(e) |
---|
211 | log.debug( "Dropping visualization_tag_association table failed: %s" % str( e ) ) |
---|
212 | |
---|
213 | # Drop visualization_annotation_association table. |
---|
214 | try: |
---|
215 | VisualizationAnnotationAssociation_table.drop() |
---|
216 | except Exception, e: |
---|
217 | print str(e) |
---|
218 | log.debug( "Dropping visualization_annotation_association table failed: %s" % str( e ) ) |
---|