PXD-2916: implement uniqueKeys

[fantix]

Auto migration is in uc-cdis/datamodelutils#6.

uc-cdis/gen3datamodel#12 replaced indexes on these columns with unique ones:

• program.name
• project.code

also added unique indexes for:

• (project_id, submitter_id) of other nodes

Improvements

• added unique indexes for uniqueKeys

Deployment changes

• Sheepdog will now create (or replace) the missing indexes during migration
• New unique indexes have been added to all nodes PXD-2916: add unique indexes for uniqueKeys gen3datamodel#12

[fantix]

tests to fix 😞

[PlanXCyborg]

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

[fantix]

PyLint bug fixed in pylint-dev/pylint#2760

[fantix]

Closing in favor of #266

[PlanXCyborg]

Jenkins Build 1 : time taken 45 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-259/1/display/redirect

Test results:
Passed: 109, Failed: 0, Skipped: 0

Test	Time (PR)	Time (master)	Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot	0.302	0.274	0.03
@ExportPerformanceTests @performance: Export all nodes of type: case	0.354	0.222	0.13
@ExportPerformanceTests @performance: Export all nodes of type: experiment	0.304	0.261	0.04
@ExportPerformanceTests @performance: Export all nodes of type: project	0.083	0.042	0.04
@ExportPerformanceTests @performance: Export all nodes of type: read_group	0.509	0.428	0.08
@ExportPerformanceTests @performance: Export all nodes of type: sample	0.444	0.359	0.09
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot	0.174	0.146	0.03
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case	0.238	0.214	0.02
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment	0.404	0.174	0.23
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc	0.072	0.056	0.02
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample	0.102	0.094	0.01
@SubmissionPerformanceTests @performance: Submission demographic 1000	30.078	26.739	3.34
@SubmissionPerformanceTests @performance: Submission publication 1000	20.839	19.284	1.56

[PlanXCyborg]

Jenkins Build 2 : time taken 37 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-259/2/display/redirect

Test results:
Passed: 109, Failed: 0, Skipped: 0

Test	Time (PR)	Time (master)	Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot	0.296	0.274	0.02
@ExportPerformanceTests @performance: Export all nodes of type: experiment	0.397	0.261	0.14
@ExportPerformanceTests @performance: Export all nodes of type: program	0.186	0.068	0.12
@ExportPerformanceTests @performance: Export all nodes of type: project	0.046	0.042	0.00
@ExportPerformanceTests @performance: Export all nodes of type: read_group_qc	0.194	0.084	0.11
@ExportPerformanceTests @performance: Export all nodes of type: sample	0.492	0.359	0.13
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot	0.282	0.146	0.14
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case	0.277	0.214	0.06
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment	0.201	0.174	0.03
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group	0.165	0.064	0.10
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc	0.131	0.056	0.07
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample	0.278	0.094	0.18
@QueryPerformanceTests @performance: Executing bottomUp query # 0	0.884	0.615	0.27
@QueryPerformanceTests @performance: Executing topDown query # 0	0.168	0.072	0.10

[PlanXCyborg]

Jenkins Build 3 : time taken 49 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-259/3/display/redirect

Test results:
Passed: 109, Failed: 0, Skipped: 0

Test	Time (PR)	Time (master)	Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot	0.296	0.274	0.02
@ExportPerformanceTests @performance: Export all nodes of type: experiment	0.397	0.261	0.14
@ExportPerformanceTests @performance: Export all nodes of type: program	0.186	0.068	0.12
@ExportPerformanceTests @performance: Export all nodes of type: project	0.046	0.042	0.00
@ExportPerformanceTests @performance: Export all nodes of type: read_group_qc	0.194	0.084	0.11
@ExportPerformanceTests @performance: Export all nodes of type: sample	0.492	0.359	0.13
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot	0.282	0.146	0.14
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case	0.277	0.214	0.06
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment	0.201	0.174	0.03
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group	0.165	0.064	0.10
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc	0.131	0.056	0.07
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample	0.278	0.094	0.18
@QueryPerformanceTests @performance: Executing bottomUp query # 0	0.884	0.615	0.27
@QueryPerformanceTests @performance: Executing topDown query # 0	0.168	0.072	0.10

[PlanXCyborg]

Jenkins Build 5 : time taken 1 hr 13 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-259/5/display/redirect

Test results:
Passed: 109, Failed: 0, Skipped: 0

Test	Time (PR)	Time (master)	Diff
@ExportPerformanceTests @performance: Export all nodes of type: experiment	0.276	0.261	0.01
@ExportPerformanceTests @performance: Export all nodes of type: project	0.056	0.042	0.01
@ExportPerformanceTests @performance: Export all nodes of type: read_group	0.635	0.428	0.21
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case	0.23	0.214	0.02
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment	0.226	0.174	0.05
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group	0.109	0.064	0.04
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc	0.063	0.056	0.01
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample	0.11	0.094	0.02
@SubmissionPerformanceTests @performance: Submission aligned_reads_index 100	17.817	16.87	0.95
@SubmissionPerformanceTests @performance: Submission case 100	2.395	2.235	0.16
@SubmissionPerformanceTests @performance: Submission demographic 100	2.605	2.254	0.35
@SubmissionPerformanceTests @performance: Submission experimental_metadata 100	18.217	16.176	2.04
@SubmissionPerformanceTests @performance: Submission exposure 10	0.388	0.367	0.02
@SubmissionPerformanceTests @performance: Submission exposure 100	2.279	2.169	0.11
@SubmissionPerformanceTests @performance: Submission family_history 100	2.638	2.018	0.62
@SubmissionPerformanceTests @performance: Submission keyword 100	2.167	1.94	0.23
@SubmissionPerformanceTests @performance: Submission publication 1000	22.626	19.284	3.34
@SubmissionPerformanceTests @performance: Submission read_group_qc 100	3.959	3.603	0.36
@SubmissionPerformanceTests @performance: Submission slide_image 10	1.913	1.796	0.12
@SubmissionPerformanceTests @performance: Submission slide_image 100	17.47	14.74	2.73
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 100	17.301	16.181	1.12
@SubmissionPerformanceTests @performance: Submission submitted_methylation 100	20.026	17.149	2.88
@SubmissionPerformanceTests @performance: Submission submitted_somatic_mutation 100	17.699	15.312	2.39
@SubmissionPerformanceTests @performance: Submission submitted_unaligned_reads 100	17.862	16.488	1.37