Code

Custom cohorts in metamist#615

Code

Merged

vivbak merged 177 commits intodevpopulationgenomics/metamist:devfrom custom-cohortspopulationgenomics/metamist:custom-cohortsCopy head branch name to clipboardApr 30, 2024

+2,478-74

Commits

Commits on Nov 15, 2023

• In progress

  vivbak

  committed
  5ceb5f6

  Copy full SHA for 5ceb5f6

• In progress

  vivbak

  committed
  d7ef222

  Copy full SHA for d7ef222

Commits on Nov 16, 2023

• Cohort GraphQL Skeleton -- functional now

  vivbak

  committed
  da2f9db

  Copy full SHA for da2f9db

• Merge branch 'dev' into custom-cohorts

  vivbak

  committed
  c2ff6c9

  Copy full SHA for c2ff6c9

• This should go in another PR

  vivbak

  committed
  6f1d9da

  Copy full SHA for 6f1d9da

Commits on Nov 17, 2023

• Merge branch 'dev' into custom-cohorts

  vivbak

  committed
  a956cee

  Copy full SHA for a956cee

Commits on Nov 23, 2023

• ignore venv

  daniaki

  committed
  25155ab

  Copy full SHA for 25155ab

• Updated docker mariadb setup instructions

  daniaki

  committed
  7a5d978

  Copy full SHA for 7a5d978

• support for name, derived_from & other fields

  daniaki

  committed
  d5103a1

  Copy full SHA for d5103a1

• Fix error if applying ord to int

  daniaki

  committed
  9d655e9

  Copy full SHA for 9d655e9

• Add all fields to model

  daniaki

  committed
  f69cde0

  Copy full SHA for f69cde0

• Set empty dict to fix GraphQL non-null error

  daniaki

  committed
  5d24669

  Copy full SHA for 5d24669

• Fix error applying ord to int

  daniaki

  committed
  32fc088

  Copy full SHA for 32fc088

• Add name to cohort table

  daniaki

  committed
  7dc373d

  Copy full SHA for 7dc373d

• version bump

  daniaki

  committed
  312c6f8

  Copy full SHA for 312c6f8

Commits on Nov 27, 2023

• Formatting; cohort GQL schema

  daniaki

  committed
  9fb6a06

  Copy full SHA for 9fb6a06

• cohort layer update

  daniaki

  committed
  57afc9f

  Copy full SHA for 57afc9f

• cohort db table update

  daniaki

  committed
  203a49b

  Copy full SHA for 203a49b

• CohortBuilder route

  daniaki

  committed
  60798c1

  Copy full SHA for 60798c1

• Single SG ID form

  daniaki

  committed
  5af95cc

  Copy full SHA for 5af95cc

• SG ID from project(s) form

  daniaki

  committed
  c5cdb17

  Copy full SHA for c5cdb17

• Cohort Builder page

  daniaki

  committed
  58c80d4

  Copy full SHA for 58c80d4

• Re-usable SG scrolling table

  daniaki

  committed
  003ffff

  Copy full SHA for 003ffff

• types definition

  daniaki

  committed
  4cdfde0

  Copy full SHA for 4cdfde0

• Add link to nav bar to cohort builder

  daniaki

  committed
  3f27185

  Copy full SHA for 3f27185

• Add substring search

  daniaki

  committed
  f153df2

  Copy full SHA for f153df2

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  4db1ca7

  Copy full SHA for 4db1ca7

Commits on Nov 28, 2023

• Formatting; add assay filter on sample

  daniaki

  committed
  a0385d5

  Copy full SHA for a0385d5

• Allow hashable assay filter when meta present

  daniaki

  committed
  7858fc7

  Copy full SHA for 7858fc7

• Type for project

  daniaki

  committed
  39e0c8b

  Copy full SHA for 39e0c8b

• Add GQL query to project form

  daniaki

  committed
  adce34b

  Copy full SHA for adce34b

• Add GQL query to ID form

  daniaki

  committed
  b4b0a5b

  Copy full SHA for b4b0a5b

• Handle form submission

  daniaki

  committed
  7f0b62e

  Copy full SHA for 7f0b62e

• Atomic transaction

  daniaki

  committed
  9f361ef

  Copy full SHA for 9f361ef

• Put query params in POST body

  daniaki

  committed
  cd94354

  Copy full SHA for cd94354

• add APIError type

  daniaki

  committed
  1747882

  Copy full SHA for 1747882

• Add TODO note; add loader to search button

  daniaki

  committed
  8217790

  Copy full SHA for 8217790

• merge dupe sgs from search results

  daniaki

  committed
  d6017cb

  Copy full SHA for d6017cb

• Use auto-gen API; better error handling

  daniaki

  committed
  4a334d5

  Copy full SHA for 4a334d5

• clean up imports

  daniaki

  committed
  7f24180

  Copy full SHA for 7f24180

• Make inputs reactive

  daniaki

  committed
  ada2c01

  Copy full SHA for ada2c01

• Cohort detail view

  daniaki

  committed
  7d1c8eb

  Copy full SHA for 7d1c8eb

• import updates

  daniaki

  committed
  706cf01

  Copy full SHA for 706cf01

• add detail route

  daniaki

  committed
  05066b0

  Copy full SHA for 05066b0

• use with router hooks

  daniaki

  committed
  d60db2a

  Copy full SHA for d60db2a

• exclude ids input

  daniaki

  committed
  654b9ae

  Copy full SHA for 654b9ae

• navigate to new detail vie

  daniaki

  committed
  c002f88

  Copy full SHA for c002f88

• make project required

  daniaki

  committed
  af8f4d9

  Copy full SHA for af8f4d9

• Add space between muck and msg

  daniaki

  committed
  f1e491c

  Copy full SHA for f1e491c

• Get project info

  daniaki

  committed
  deaa491

  Copy full SHA for deaa491

• Convert ids to int to fix not found error

  daniaki

  committed
  d2662f2

  Copy full SHA for d2662f2

• cohort project resolver

  daniaki

  committed
  1ca9df4

  Copy full SHA for 1ca9df4

• Update table rendering logic

  daniaki

  committed
  c5f0fd8

  Copy full SHA for c5f0fd8

• Update table rendering logic

  daniaki

  committed
  573b57b

  Copy full SHA for 573b57b

• Add search result info in warning box

  daniaki

  committed
  49a1245

  Copy full SHA for 49a1245

Commits on Dec 3, 2023

• Linter fixes

  daniaki

  committed
  2b9ba76

  Copy full SHA for 2b9ba76

Commits on Dec 4, 2023

• formatting

  daniaki

  committed
  0172dff

  Copy full SHA for 0172dff

• Merge branch 'dev' into custom-cohorts

  daniaki

  authored
  62ea338

  Copy full SHA for 62ea338

• lint fix

  daniaki

  committed
  4b0661a

  Copy full SHA for 4b0661a

• unused import

  daniaki

  committed
  cfd21eb

  Copy full SHA for cfd21eb

• Tmp fix for billing query inside NavBar

  daniaki

  committed
  7a3611c

  Copy full SHA for 7a3611c

Commits on Jan 10, 2024

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  bc5e0b9

  Copy full SHA for bc5e0b9

Commits on Jan 31, 2024

• Custom cohorts SG query optimisation (#630)

  Show description for 32fac2b
  daniaki

  authored
  32fac2b

  Copy full SHA for 32fac2b

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  146e6b2

  Copy full SHA for 146e6b2

• Merge branch dev into custom-cohorts

  vivbak

  committed
  b8e88c3

  Copy full SHA for b8e88c3

• update dbbase import

  vivbak

  committed
  dcd5e68

  Copy full SHA for dcd5e68

Commits on Feb 5, 2024

• Update to_sql signature to match superclass. An attempt at pleasing the linter

  vivbak

  committed
  9ef10ef

  Copy full SHA for 9ef10ef

Commits on Feb 8, 2024

• Fix click overwriting param to None when not specified

  vivbak

  committed
  f82f816

  Copy full SHA for f82f816

Commits on Feb 16, 2024

• Create endpoint to create cohort from criteria - Project/s

  vivbak

  committed
  9e33d7f

  Copy full SHA for 9e33d7f

• Fix query cohort, call connection directly

  vivbak

  committed
  3fdc803

  Copy full SHA for 3fdc803

Commits on Feb 22, 2024

• Add further criteria to create_cohort_from_criteria endpoint

  Show description for 558b073
  vivbak

  committed
  558b073

  Copy full SHA for 558b073

• Fix the linter, import order, spaces, etc

  vivbak

  committed
  3b00f6c

  Copy full SHA for 3b00f6c

Commits on Feb 26, 2024

• Remove AddFromIdListForm.tsx

  vivbak

  committed
  ae3c271

  Copy full SHA for ae3c271

• Delete AddFromIDListForm

  vivbak

  committed
  9a4668f

  Copy full SHA for 9a4668f

• Delete custom cohorts UI elements

  vivbak

  committed
  bcfe23e

  Copy full SHA for bcfe23e

• Remove link to Cohort Builder from NavBar

  vivbak

  committed
  70673a0

  Copy full SHA for 70673a0

• Remove link to custom cohorts page in routes

  vivbak

  committed
  a2d9fca

  Copy full SHA for a2d9fca

• Revert package-lock to main

  vivbak

  committed
  c529a31

  Copy full SHA for c529a31

• Merge branch dev into custom-cohorts

  vivbak

  committed
  82d0b6b

  Copy full SHA for 82d0b6b

• Handle SG ID exclusion in cohort creation

  vivbak

  committed
  1008612

  Copy full SHA for 1008612

• Add cohort_template table

  vivbak

  committed
  69c8e46

  Copy full SHA for 69c8e46

Commits on Feb 27, 2024

• Add create cohort template endpoint

  vivbak

  committed
  345348a

  Copy full SHA for 345348a

Commits on Feb 28, 2024

• Fix linting issues including;

  vivbak

  committed
  04d208c

  Copy full SHA for 04d208c

• Add basic support for cohort creation from template

  vivbak

  committed
  1b9fe45

  Copy full SHA for 1b9fe45

• Support query template in graphql, including adding project column

  vivbak

  committed
  960f026

  Copy full SHA for 960f026

Commits on Mar 4, 2024

• Handle cohort criteria and cohort template cases

  vivbak

  committed
  e9e2bf2

  Copy full SHA for e9e2bf2

• Handle Templates in the layer and table

  vivbak

  committed
  1e31f43

  Copy full SHA for 1e31f43

• Add skeleton for create_custom_cohort script

  vivbak

  committed
  e5ac19c

  Copy full SHA for e5ac19c

Commits on Mar 5, 2024

• Add dry-run, refactor script to reduce args, fix bug that doesnt allow template to be specified

  vivbak

  committed
  583004f

  Copy full SHA for 583004f

• Return rich ids in dry mode

  vivbak

  committed
  a8829b7

  Copy full SHA for a8829b7

• Return rich ids when dry-run is false too

  vivbak

  committed
  a54a256

  Copy full SHA for a54a256

Commits on Mar 6, 2024

• Add support for rich custom cohort IDs i.e. COHXXX

  vivbak

  committed
  d95d4e4

  Copy full SHA for d95d4e4

Commits on Mar 13, 2024

• Add initial basic create_cohort_from_criteria() tests

  jmarshall

  committed
  81f4a5b

  Copy full SHA for 81f4a5b

• Merge dev (in particular, the testcontainers fix) into custom-cohorts

  jmarshall

  committed
  2850110

  Copy full SHA for 2850110

• Surely incorrect fix for Field 'timestamp' doesn't have a default value

  jmarshall

  committed
  0414940

  Copy full SHA for 0414940

Commits on Mar 14, 2024

• Fix failing tests, move cohort creation to after dry run exit

  vivbak

  committed
  646740f

  Copy full SHA for 646740f

Commits on Mar 19, 2024

• Rename derived_from to template_id, in line with user feedback, to add clarity

  vivbak

  committed
  78df334

  Copy full SHA for 78df334

• Refactor generating sg_filter, to make room for supporting more inputs

  vivbak

  committed
  8ca7d35

  Copy full SHA for 8ca7d35

• Fix FK issue in project.xml, delete old, add new

  vivbak

  committed
  e265981

  Copy full SHA for e265981

• Handle Sample Type as Cohort Criteria

  vivbak

  committed
  d2fa327

  Copy full SHA for d2fa327

• D'oh, blackify those parentheses

  jmarshall

  committed
  672d751

  Copy full SHA for 672d751

• Add test case exercising template_id foreign key

  jmarshall

  committed
  ab9cdb4

  Copy full SHA for ab9cdb4

• Remove debugging print

  jmarshall

  committed
  f1e6780

  Copy full SHA for f1e6780

• Add tranche of tests that need some sample data

  jmarshall

  committed
  9829c22

  Copy full SHA for 9829c22

• Add cohort-related tables to SYSTEM VERSIONING and TABLES_ORDERED_BY_FK_DEPS

  Show description for 69014ca
  jmarshall

  committed
  69014ca

  Copy full SHA for 69014ca

Commits on Mar 20, 2024

• Merge dev into custom-cohorts

  jmarshall

  committed
  6435265

  Copy full SHA for 6435265

Commits on Mar 21, 2024

• Set audit_log_id when INSERTing into cohort tables

  Show description for 903314d
  jmarshall

  committed
  903314d

  Copy full SHA for 903314d

• Create cohort rows with timestamp set to (localtime) now

  jmarshall

  committed
  e8f0594

  Copy full SHA for e8f0594

Commits on Mar 24, 2024

• Further tests for individual CohortCriteria fields

  jmarshall

  committed
  ffcb24b

  Copy full SHA for ffcb24b

• Validate projects on input for create_template

  vivbak

  committed
  f989ae7

  Copy full SHA for f989ae7

• Remove what I assume is an artefact from a merge mistake

  vivbak

  committed
  bec2fdd

  Copy full SHA for bec2fdd

Commits on Mar 25, 2024

• Add cohorts to analysis objects

  Show description for e576d1f
  

  vivbak

  and

  jmarshall

  committed
  e576d1f

  Copy full SHA for e576d1f

• Account for cohort_ids in test_get_analysis() test case

  jmarshall

  committed
  9a7a379

  Copy full SHA for 9a7a379

• Verify that create_cohort_template now validates projects

  jmarshall

  committed
  7a36150

  Copy full SHA for 7a36150

• Another test for an individual CohortCriteria field

  jmarshall

  committed
  3aec432

  Copy full SHA for 3aec432

Commits on Mar 26, 2024

• Add test exercising re-evaluation of a cohort template

  jmarshall

  committed
  0b1fa91

  Copy full SHA for 0b1fa91

• Add test using all CohortCriteria fields

  Show description for 726a48e
  jmarshall

  committed
  726a48e

  Copy full SHA for 726a48e

• Update schema docs

  vivbak

  committed
  1caeecf

  Copy full SHA for 1caeecf

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  6ace026

  Copy full SHA for 6ace026

• Combine project.xml entries

  vivbak

  committed
  7335354

  Copy full SHA for 7335354

• Add human readable CTPL prefix to templates

  vivbak

  committed
  d705285

  Copy full SHA for d705285

• Fix incorrect call of lunh_compute instead of lunh_is_valid

  vivbak

  committed
  92091b5

  Copy full SHA for 92091b5

• Combine John's project.xml entries into Vivian's

  jmarshall

  committed
  14aebd3

  Copy full SHA for 14aebd3

• Add sample-type to cohort builder, fix typos

  vivbak

  committed
  f570e03

  Copy full SHA for f570e03

• Return all the cohort details in builder

  vivbak

  committed
  d7a61b5

  Copy full SHA for d7a61b5

Commits on Mar 27, 2024

• Add function to query analyses by cohort

  vivbak

  committed
  6b17473

  Copy full SHA for 6b17473

• Catch value error sooner when template ID is invalid

  vivbak

  committed
  52b86bb

  Copy full SHA for 52b86bb

• return None instead of error

  vivbak

  committed
  d6f4ac4

  Copy full SHA for d6f4ac4

Commits on Apr 10, 2024

• Add tests exercising cohort queries

  jmarshall

  committed
  31ebd7c

  Copy full SHA for 31ebd7c

• Add test_query_cohort

  jmarshall

  committed
  8aa7b17

  Copy full SHA for 8aa7b17

Commits on Apr 15, 2024

• Cohort -> cohorts

  vivbak

  committed
  5993bcf

  Copy full SHA for 5993bcf

• Fix indent

  vivbak

  committed
  8801c27

  Copy full SHA for 8801c27

• Remove passing author to cohortlayer explicitly.

  vivbak

  committed
  ac5cb09

  Copy full SHA for ac5cb09

• Add type hints

  vivbak

  committed
  8e94421

  Copy full SHA for 8e94421

• Rename clayer and cohortlayer to cohort_layer

  vivbak

  committed
  bcc4541

  Copy full SHA for bcc4541

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  19ae714

  Copy full SHA for 19ae714

• fix lint, author removed. Add newline

  vivbak

  committed
  2e08db4

  Copy full SHA for 2e08db4

• Fix whitespace for linter

  vivbak

  committed
  669341e

  Copy full SHA for 669341e

Commits on Apr 16, 2024

• Merge branch 'dev' into custom-cohorts

  vivbak

  committed
  ffb1847

  Copy full SHA for ffb1847

• template id should not be nullable

  vivbak

  committed
  892128b

  Copy full SHA for 892128b

Commits on Apr 18, 2024

• Remove template_id, specify as strawberry field instead. Rename CohortTemplateModel to CohortTemplate.

  vivbak

  committed
  68cd5b8

  Copy full SHA for 68cd5b8

• Fix CohortTemplateInternal object is not subscriptable

  vivbak

  committed
  6f42610

  Copy full SHA for 6f42610

• Fix failing tests by modifying type hints, dict[str,str] -> CohortTemplateInternal

  vivbak

  committed
  3ee14ba

  Copy full SHA for 3ee14ba

Commits on Apr 19, 2024

• Add project ID checks

  vivbak

  committed
  e1c6b86

  Copy full SHA for e1c6b86

• Raise ValueError instead of assertion, to ensure it is caught

  vivbak

  committed
  750a18c

  Copy full SHA for 750a18c

• Remove author being explicitly passed, use one from connection

  vivbak

  committed
  65b2212

  Copy full SHA for 65b2212

• Plural cohort, cohort_template fields

  vivbak

  committed
  f594167

  Copy full SHA for f594167

• map to dict later, pass model

  vivbak

  committed
  ae19d20

  Copy full SHA for ae19d20

• execute -> execute_many

  vivbak

  committed
  ef9d85e

  Copy full SHA for ef9d85e

• Fix type of id on Cohort model

  vivbak

  committed
  c8021f7

  Copy full SHA for c8021f7

• New model for creating cohorts, fix project missing bug, rename Cohort to CohortInternal, fix tests accordingly

  vivbak

  committed
  f82103a

  Copy full SHA for f82103a

• Fix lint, although interesting that my linter didnt catch it

  vivbak

  committed
  8dac650

  Copy full SHA for 8dac650

• Fix type hint, cohort_ids should be int not str

  vivbak

  committed
  8be79e7

  Copy full SHA for 8be79e7

• Fix create_analysis, so it can handle no sgs as inputs

  vivbak

  committed
  3d9c0b6

  Copy full SHA for 3d9c0b6

• Create two where_strs, remove unused import

  vivbak

  committed
  7ba3371

  Copy full SHA for 7ba3371

• Remove sgs from cohortinternal model!

  vivbak

  committed
  64349cd

  Copy full SHA for 64349cd

• Add strict param to id transform function

  vivbak

  committed
  ac89b83

  Copy full SHA for ac89b83

• redundant, no? remove a type check that already happened above

  vivbak

  committed
  37d300c

  Copy full SHA for 37d300c

• Add typing to function, raise value error if template nor projects provided

  vivbak

  committed
  b2c5efb

  Copy full SHA for b2c5efb

Commits on Apr 21, 2024

• Fetch assay external ids too

  vivbak

  committed
  7db7f7b

  Copy full SHA for 7db7f7b

• Move escape_like_terms to utils, apply to contains filter

  vivbak

  committed
  1b7632b

  Copy full SHA for 1b7632b

Commits on Apr 22, 2024

• Implement Internal and External models for all objects. Move transform rich to raw, to be on the route. Handle raw ids only from layers onward. Update tests accordingly

  vivbak

  committed
  3c2af5f

  Copy full SHA for 3c2af5f

• Use UTC for test_query_with_creation_date comparisons

  Show description for 86e9237
  jmarshall

  committed
  86e9237

  Copy full SHA for 86e9237

Commits on Apr 23, 2024

• Add basic tests for scripts/create_custom_cohort.py

  Show description for b10f10e
  jmarshall

  committed
  b10f10e

  Copy full SHA for b10f10e

Commits on Apr 24, 2024

• Add separate CohortCriteria/Template.to_internal() tests

  Show description for 6f78b9b
  jmarshall

  committed
  6f78b9b

  Copy full SHA for 6f78b9b

Commits on Apr 28, 2024

• Switch get_project_write_connection to get_project_readonly_connection as noone will be able to use it at present

  vivbak

  committed
  9aaaa10

  Copy full SHA for 9aaaa10

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  ed2d840

  Copy full SHA for ed2d840

• Return [] if no template meets criteria, switch return order of project and templates

  vivbak

  committed
  b7b9d1a

  Copy full SHA for b7b9d1a

• Cohort ID should be None in dry-run mode

  vivbak

  committed
  f52af30

  Copy full SHA for f52af30

Commits on Apr 29, 2024

• sample_types -> sample_type

  vivbak

  committed
  c347309

  Copy full SHA for c347309

• Merge dev (in particular, the empty list SQL fix) into custom-cohorts

  jmarshall

  committed
  49b146d

  Copy full SHA for 49b146d

Commits on Apr 30, 2024

• Only run _query_cohort_ids query if :analysis_ids will be non-empty

  jmarshall

  committed
  5f5cf23

  Copy full SHA for 5f5cf23

• Improve mocking in test_cohort_builder.py tests

  Show description for 0d1757f
  jmarshall

  committed
  0d1757f

  Copy full SHA for 0d1757f

• Escape metacharacters in icontains query string (and add tests)

  jmarshall

  committed
  f793927

  Copy full SHA for f793927

• Make --dry-run an argumentless flag option

  jmarshall

  committed
  b8e1252

  Copy full SHA for b8e1252

• Bump version: 6.9.1 → 6.10.0

  vivbak

  committed
  9fcc2a9

  Copy full SHA for 9fcc2a9

• Merge branch 'custom-cohorts' of github.com:populationgenomics/sample-metadata into custom-cohorts

  vivbak

  committed
  dfe3c20

  Copy full SHA for dfe3c20