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Germplasm Accession Importer #6

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merged 51 commits into from
Feb 9, 2024
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1ad31fb
Started annotation for Germ Accession import
carolyncaron Aug 18, 2023
70976fb
Completed form function
carolyncaron Aug 21, 2023
843bb97
Created configuration for cvterms used by the germplasm accession imp…
carolyncaron Aug 21, 2023
ed299a2
Fixed syntax error in config
carolyncaron Aug 21, 2023
2712d46
Started implementing the run method
carolyncaron Sep 8, 2023
87a9ed0
Setup kernel testing of the form for the Germplasm Accession Importer
carolyncaron Sep 11, 2023
4fccd9e
Finished designing the run function
carolyncaron Sep 18, 2023
5704bf2
Implemented the getOrganismID function
carolyncaron Sep 19, 2023
c5534c7
Mocked the logger for testing, and created first assert for the getOr…
carolyncaron Sep 20, 2023
4a50d29
Started implementing getStockID function
carolyncaron Sep 26, 2023
f570b21
Added a global error tracking variable to the Accession importer class
carolyncaron Sep 27, 2023
b86f3b3
Updated method for specifying upload file format description
carolyncaron Sep 28, 2023
2a5e8a4
Fixed formatting for required columns in input file
carolyncaron Oct 6, 2023
64640f4
Added getStockId() tests and prepared for db dependency injection
carolyncaron Oct 11, 2023
33fe600
Fixed tests to work with dependency injection newly added to ChadoImp…
carolyncaron Oct 16, 2023
92ab7c6
Added tests to getOrganismID and getStockID
carolyncaron Oct 16, 2023
5b06962
Implemented the config factory and started setting and pulling config…
carolyncaron Oct 16, 2023
3012a53
Started implementing getDbxrefID
carolyncaron Oct 17, 2023
70cb9dc
Finished the getDbxrefID function, and caught up with tests
carolyncaron Oct 18, 2023
2262801
Implemented get and setCVterm methods and most of loadStockProperties
carolyncaron Oct 19, 2023
40efcd7
Finished tests for loadStockProperties
carolyncaron Oct 20, 2023
7086b03
Merge branch '4.x' into g2.2-germAccessionImporter
carolyncaron Oct 25, 2023
22ea136
Started the loadSynonyms function
carolyncaron Nov 6, 2023
8a29b39
Finish chado.stock lookup and insert for loadSynonyms
carolyncaron Nov 7, 2023
32b5f02
Added table definition for stock_synonym to install
carolyncaron Nov 8, 2023
f5b464c
Added definition for the stock_synonym custom table
carolyncaron Nov 14, 2023
b0a6803
Merge branch '4.x' into g2.2-germAccessionImporter
laceysanderson Nov 15, 2023
12703af
Completed loadSynonyms function and its tests
carolyncaron Nov 20, 2023
4dfd70d
Included tests for comma and semicolon-separated synonyms
carolyncaron Nov 22, 2023
38d2e53
Started test and example file for run method
carolyncaron Nov 23, 2023
b18e121
Improvements made to the run method and test
carolyncaron Nov 24, 2023
983271c
Simplified setting up of CVterms in run, and added first tests
carolyncaron Nov 27, 2023
a2f2895
Added additional test files and tests, including a test trait to add …
carolyncaron Nov 29, 2023
3867731
Finished tests for run()
carolyncaron Nov 30, 2023
8ba2144
Now throws an exception if the stock_synonym table or input file does…
carolyncaron Dec 4, 2023
15d5b8f
Changed hook_enable to hook_install and made sure to grab the schema
carolyncaron Dec 4, 2023
3388c75
Cleaned up .install file
carolyncaron Dec 4, 2023
f81e23c
Some general cleanup
carolyncaron Dec 4, 2023
8bb301b
Fixed InstallTest so that module is installed after setUp
carolyncaron Dec 5, 2023
e9ef2de
Merge branch '4.x' into g2.2-germAccessionImporter
carolyncaron Dec 11, 2023
5e1ef62
Addressed Lacey's wording suggestings to the form
carolyncaron Dec 15, 2023
19e91ce
Changed the query in getStockID and updated error handling for duplic…
carolyncaron Dec 15, 2023
707ceed
Added additional tests for things that would trigger an exception, an…
carolyncaron Dec 18, 2023
03b4fae
Added a query + assert to ensure no stock records inserted when an er…
carolyncaron Feb 1, 2024
5028b0f
Expanded the error message for pre-existing duplicate stocks to provi…
carolyncaron Feb 1, 2024
708d2e5
Expanded the error which reports multiple synonym ids
carolyncaron Feb 1, 2024
e07af90
Updated importer run command to use the api method for tripal importe…
carolyncaron Feb 2, 2024
3a1392c
Fixed ordering for assertEquals in the Run tests
carolyncaron Feb 2, 2024
371d157
Added a check in loadSynonym for if there is a pre-existing stock_rel…
carolyncaron Feb 2, 2024
6c363da
Added a unique key to stock_synonym table definition
carolyncaron Feb 2, 2024
09f6fe7
Switch from assertTrue to assertEquals so you see the two things bein…
laceysanderson Feb 9, 2024
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
supervisord*
.phpunit.result.cache
.DS_Store
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
terms:
accession: 0
genus: 0
species: 0
name: 0
institute_code: 0
institute_name: 0
pedigree: 0
country_of_origin_code: 0
synonym: 0
biological_status_of_accession_code: 0
breeding_method_DbId: 0
subtaxa: 0
stock_relationship_type_synonym: 0
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
trpcultivate_germplasm.settings:
type: config_object
label: 'Germplasm Package Configuration'
mapping:
terms:
type: mapping
label: 'Package default terms'
mapping:
accession:
type: integer
label: 'The cvterm ID of the accession for a germplasm'
genus:
type: integer
label: 'The cvterm ID of the genus of a germplasm'
species:
type: integer
label: 'The cvterm ID of the species of a germplasm'
name:
type: integer
label: 'The cvterm ID of the name of a germplasm'
institute_code:
type: integer
label: 'The cvterm ID of the institute code where the germplasm was bred'
institute_name:
type: integer
label: 'The cvterm ID of the institute name where the germplasm was bred'
pedigree:
type: integer
label: 'The cvterm ID of the pedigree information for a germplasm'
country_of_origin_code:
type: integer
label: 'The cvterm ID of the country of origin of a germplasm'
synonym:
type: integer
label: 'The cvterm ID of a synonym of a germplasm name'
biological_status_of_accession_code:
type: integer
label: 'The cvterm ID of the biological status of a germplasm accession'
breeding_method_DbId:
type: integer
label: 'The cvterm ID of the germplasm breeding method'
subtaxa:
type: integer
label: 'The cvterm ID of the subtaxa of a germplasm'
stock_relationship_type_synonym:
type: integer
label: 'The cvterm ID of the stock_relationship synonym'
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