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Type: Improvement
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Resolution: Won't Do
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Priority: Major
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Affects Version/s: master, 5.0.0
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Component/s: CLI: pegasus-db-admin
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None
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Environment:i updated one of the workflow databases to 5.0.1dev by running command
corbusier:run0001 vahi$ pegasus-db-admin update -s . -t workflow
2021-08-19 15:24:28,626:WARNING:Pegasus.tools.properties(260): cannot access properties file /home/scitech/shared-data/CatsAndDogs2/scitech/pegasus/Cats_and_Dogs/run0001/pegasus.4550006990323691958.properties... continuing...
2021-08-19 15:24:28,626:WARNING:Pegasus.tools.properties(282): no properties file parsed whatsoever!
Your database has been updated.
Your database is compatible with Pegasus version: 5.0.1dev
You have mail in /var/mail/vahi
(virtualenv) corbusier:run0001 vahi$ pegasus-analyzer .
2021-08-19 15:24:35,249:WARNING:Pegasus.tools.properties(260): cannot access properties file /home/scitech/shared-data/CatsAndDogs2/scitech/pegasus/Cats_and_Dogs/run0001/pegasus.4550006990323691958.properties... continuing...
2021-08-19 15:24:35,249:WARNING:Pegasus.tools.properties(282): no properties file parsed whatsoever!
Your database is compatible with Pegasus version: 5.0.1dev
i updated one of the workflow databases to 5.0.1dev by running command corbusier:run0001 vahi$ pegasus-db-admin update -s . -t workflow 2021-08-19 15:24:28,626:WARNING:Pegasus.tools.properties(260): cannot access properties file /home/scitech/shared-data/CatsAndDogs2/scitech/pegasus/Cats_and_Dogs/run0001/pegasus.4550006990323691958.properties... continuing... 2021-08-19 15:24:28,626:WARNING:Pegasus.tools.properties(282): no properties file parsed whatsoever! Your database has been updated. Your database is compatible with Pegasus version: 5.0.1dev You have mail in /var/mail/vahi (virtualenv) corbusier:run0001 vahi$ pegasus-analyzer . 2021-08-19 15:24:35,249:WARNING:Pegasus.tools.properties(260): cannot access properties file /home/scitech/shared-data/CatsAndDogs2/scitech/pegasus/Cats_and_Dogs/run0001/pegasus.4550006990323691958.properties... continuing... 2021-08-19 15:24:35,249:WARNING:Pegasus.tools.properties(282): no properties file parsed whatsoever! Your database is compatible with Pegasus version: 5.0.1dev
however it seems to have corrupted my master workflow database
021-08-19 15:38:40,214:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
Created Pegasus database in: sqlite:////Volumes/lfs1/work/monitord/bugs/PM-1761-panalyzer/run0011/bad-wf-0.stampede.db
2021-08-19 15:38:40,217:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
Your database is compatible with Pegasus version: 5.0.0
2021-08-19 15:38:40,272:INFO:Pegasus.monitoring.event_output(704): output type=DB namespace=stampede. name=sqlite:////Volumes/lfs1/work/monitord/bugs/PM-1761-panalyzer/run0011/bad-wf-0.stampede.db
2021-08-19 15:38:40,272:INFO:Pegasus.monitoring.event_output(630): Connecting workflow event sink to sqlite:////Users/vahi/.pegasus/workflow.db
2021-08-19 15:38:40,272:DEBUG:Pegasus.db.connection(131): Connecting to: sqlite:////Users/vahi/.pegasus/workflow.db with connection params as {}
2021-08-19 15:38:40,273:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
2021-08-19 15:38:40,274:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
2021-08-19 15:38:40,275:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
2021-08-19 15:38:40,277:DEBUG:Pegasus.db.connection(414): Turning on foreign keys
/Volumes/lfs1/devel/Pegasus/git/pegasus/packages/pegasus-python/src/Pegasus/db/admin/admin_loader.py:488: SAWarning: relationship 'Workflow.parent_wf' will copy column workflow.wf_id to column workflow.parent_wf_id, which conflicts with relationship(s): 'Workflow.root_wf' (copies workflow.wf_id to workflow.parent_wf_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="root_wf"' to the 'Workflow.parent_wf' relationship.
db.query(DBVersion.version).order_by(DBVersion.id.desc()).first()
/Volumes/lfs1/devel/Pegasus/git/pegasus/packages/pegasus-python/src/Pegasus/db/admin/admin_loader.py:488: SAWarning: relationship 'Workflow.files' will copy column workflow.wf_id to column workflow_files.wf_id, which conflicts with relationship(s): 'Workflow.workflow_files' (copies workflow.wf_id to workflow_files.wf_id), 'WorkflowFiles.workflow' (copies workflow.wf_id to workflow_files.wf_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="workflow,workflow_files"' to the 'Workflow.files' relationship.
db.query(DBVersion.version).order_by(DBVersion.id.desc()).first()
/Volumes/lfs1/devel/Pegasus/git/pegasus/packages/pegasus-python/src/Pegasus/db/admin/admin_loader.py:488: SAWarning: relationship 'Task.files' will copy column task.task_id to column workflow_files.task_id, which conflicts with relationship(s): 'Task.task_files' (copies task.task_id to workflow_files.task_id), 'WorkflowFiles.task' (copies task.task_id to workflow_files.task_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="task,task_files"' to the 'Task.files' relationship.
db.query(DBVersion.version).order_by(DBVersion.id.desc()).first()
/Volumes/lfs1/devel/Pegasus/git/pegasus/packages/pegasus-python/src/Pegasus/db/admin/admin_loader.py:488: SAWarning: relationship 'Task.files' will copy column rc_lfn.lfn_id to column workflow_files.lfn_id, which conflicts with relationship(s): 'Workflow.files' (copies rc_lfn.lfn_id to workflow_files.lfn_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="files"' to the 'Task.files' relationship.
db.query(DBVersion.version).order_by(DBVersion.id.desc()).first()
/Volumes/lfs1/devel/Pegasus/git/pegasus/packages/pegasus-python/src/Pegasus/db/admin/admin_loader.py:488: SAWarning: relationship 'WorkflowFiles.lfn' will copy column rc_lfn.lfn_id to column workflow_files.lfn_id, which conflicts with relationship(s): 'Task.files' (copies rc_lfn.lfn_id to workflow_files.lfn_id), 'Workflow.files' (copies rc_lfn.lfn_id to workflow_files.lfn_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="files,files"' to the 'WorkflowFiles.lfn' relationship.
db.query(DBVersion.version).order_by(DBVersion.id.desc()).first()
2021-08-19 15:38:40,350:DEBUG:Pegasus.db.admin.admin_loader(548): Your database is already updated.