1 | """ |
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2 | Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and \ |
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3 | (b) add table for doing individual and community tagging of workflows. |
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4 | |
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5 | SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against \ |
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6 | SQLite; however, script does execute successfully against SQLite. |
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7 | """ |
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8 | |
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9 | from sqlalchemy import * |
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10 | from sqlalchemy.orm import * |
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11 | from migrate import * |
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12 | from migrate.changeset import * |
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13 | |
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14 | import logging |
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15 | log = logging.getLogger( __name__ ) |
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16 | |
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17 | metadata = MetaData( migrate_engine ) |
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18 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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19 | |
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20 | StoredWorkflowTagAssociation_table = Table( "stored_workflow_tag_association", metadata, |
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21 | Column( "id", Integer, primary_key=True ), |
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22 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
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23 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
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24 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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25 | Column( "user_tname", Unicode(255), index=True), |
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26 | Column( "value", Unicode(255), index=True), |
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27 | Column( "user_value", Unicode(255), index=True) ) |
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28 | |
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29 | WorkflowTagAssociation_table = Table( "workflow_tag_association", metadata, |
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30 | Column( "id", Integer, primary_key=True ), |
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31 | Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True ), |
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32 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
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33 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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34 | Column( "user_tname", Unicode(255), index=True), |
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35 | Column( "value", Unicode(255), index=True), |
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36 | Column( "user_value", Unicode(255), index=True) ) |
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37 | |
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38 | def upgrade(): |
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39 | print __doc__ |
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40 | metadata.reflect() |
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41 | |
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42 | # Create user_id column in history_tag_association table. |
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43 | HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) |
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44 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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45 | try: |
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46 | c.create( HistoryTagAssociation_table ) |
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47 | assert c is HistoryTagAssociation_table.c.user_id |
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48 | except Exception, e: |
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49 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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50 | print str(e) |
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51 | log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) |
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52 | |
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53 | # Create user_id index for history_tag_association table. |
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54 | try: |
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55 | i = Index( "ix_history_tag_association_user_id", HistoryTagAssociation_table.c.user_id ) |
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56 | i.create() |
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57 | except: |
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58 | # Mysql doesn't have a named index, but alter should work |
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59 | HistoryTagAssociation_table.c.user_id.alter( unique=False ) |
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60 | |
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61 | # Populate column so that user_id is the id of the user who owns the history (and, up to now, was the only person able to tag the history). |
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62 | if c is HistoryTagAssociation_table.c.user_id: |
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63 | db_session.execute( |
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64 | "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )" |
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65 | ) |
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66 | |
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67 | # Create user_id column in history_dataset_association_tag_association table. |
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68 | HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) |
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69 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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70 | try: |
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71 | c.create( HistoryDatasetAssociationTagAssociation_table ) |
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72 | assert c is HistoryDatasetAssociationTagAssociation_table.c.user_id |
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73 | except Exception, e: |
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74 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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75 | print str(e) |
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76 | log.debug( "Adding user_id column to history_dataset_association_tag_association table failed: %s" % str( e ) ) |
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77 | |
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78 | # Create user_id index for history_dataset_association_tag_association table. |
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79 | try: |
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80 | i = Index( "ix_history_dataset_association_tag_association_user_id", HistoryDatasetAssociationTagAssociation_table.c.user_id ) |
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81 | i.create() |
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82 | except: |
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83 | # Mysql doesn't have a named index, but alter should work |
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84 | HistoryDatasetAssociationTagAssociation_table.c.user_id.alter( unique=False ) |
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85 | |
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86 | # Populate column so that user_id is the id of the user who owns the history_dataset_association (and, up to now, was the only person able to tag the page). |
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87 | if c is HistoryDatasetAssociationTagAssociation_table.c.user_id: |
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88 | db_session.execute( |
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89 | "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)" |
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90 | ) |
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91 | |
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92 | # Create user_id column in page_tag_association table. |
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93 | PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) |
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94 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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95 | try: |
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96 | c.create( PageTagAssociation_table ) |
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97 | assert c is PageTagAssociation_table.c.user_id |
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98 | except Exception, e: |
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99 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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100 | print str(e) |
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101 | log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) |
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102 | |
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103 | # Create user_id index for page_tag_association table. |
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104 | try: |
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105 | i = Index( "ix_page_tag_association_user_id", PageTagAssociation_table.c.user_id ) |
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106 | i.create() |
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107 | except: |
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108 | # Mysql doesn't have a named index, but alter should work |
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109 | PageTagAssociation_table.c.user_id.alter( unique=False ) |
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110 | |
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111 | # Populate column so that user_id is the id of the user who owns the page (and, up to now, was the only person able to tag the page). |
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112 | if c is PageTagAssociation_table.c.user_id: |
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113 | db_session.execute( |
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114 | "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )" |
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115 | ) |
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116 | |
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117 | # Create stored_workflow_tag_association table. |
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118 | try: |
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119 | StoredWorkflowTagAssociation_table.create() |
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120 | except Exception, e: |
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121 | print str(e) |
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122 | log.debug( "Creating stored_workflow_tag_association table failed: %s" % str( e ) ) |
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123 | |
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124 | # Create workflow_tag_association table. |
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125 | try: |
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126 | WorkflowTagAssociation_table.create() |
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127 | except Exception, e: |
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128 | print str(e) |
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129 | log.debug( "Creating workflow_tag_association table failed: %s" % str( e ) ) |
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130 | |
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131 | def downgrade(): |
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132 | metadata.reflect() |
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133 | |
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134 | # Drop user_id column from history_tag_association table. |
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135 | HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) |
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136 | try: |
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137 | HistoryTagAssociation_table.c.user_id.drop() |
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138 | except Exception, e: |
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139 | print str(e) |
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140 | log.debug( "Dropping column user_id from history_tag_association table failed: %s" % str( e ) ) |
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141 | |
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142 | |
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143 | # Drop user_id column from history_dataset_association_tag_association table. |
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144 | HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) |
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145 | try: |
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146 | HistoryDatasetAssociationTagAssociation_table.c.user_id.drop() |
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147 | except Exception, e: |
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148 | print str(e) |
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149 | log.debug( "Dropping column user_id from history_dataset_association_tag_association table failed: %s" % str( e ) ) |
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150 | |
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151 | # Drop user_id column from page_tag_association table. |
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152 | PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) |
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153 | try: |
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154 | PageTagAssociation_table.c.user_id.drop() |
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155 | except Exception, e: |
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156 | print str(e) |
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157 | log.debug( "Dropping column user_id from page_tag_association table failed: %s" % str( e ) ) |
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158 | |
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159 | # Drop stored_workflow_tag_association table. |
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160 | try: |
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161 | StoredWorkflowTagAssociation_table.drop() |
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162 | except Exception, e: |
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163 | print str(e) |
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164 | log.debug( "Dropping stored_workflow_tag_association table failed: %s" % str( e ) ) |
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165 | |
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166 | # Drop workflow_tag_association table. |
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167 | try: |
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168 | WorkflowTagAssociation_table.drop() |
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169 | except Exception, e: |
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170 | print str(e) |
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171 | log.debug( "Dropping workflow_tag_association table failed: %s" % str( e ) ) |
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