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Implement migrator that creates/populates workflow_chain_set (file: migrator_from_X_to_PR9.py) #127

Merged
merged 37 commits into from
May 17, 2024
Merged

Implement migrator that creates/populates workflow_chain_set (file: migrator_from_X_to_PR9.py) #127

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52d6fe4
Add first go
brynnz22 Apr 9, 2024
0bc66ed
fix dictionary initialization
brynnz22 Apr 10, 2024
6446245
changes
brynnz22 Apr 10, 2024
eef5d3e
add initial dictionary
brynnz22 Apr 10, 2024
d66232b
update function name
brynnz22 Apr 10, 2024
74047a6
fix migration part_of mapping
brynnz22 Apr 10, 2024
02f5d3e
add doc string
brynnz22 Apr 10, 2024
ea1981d
complete metagenome workflow part_of replacement
brynnz22 Apr 11, 2024
342eb2b
add metabolomics and nom part_of mappings
brynnz22 Apr 11, 2024
4d62d5e
update TODOS
brynnz22 Apr 11, 2024
43bb98e
add metagenome_sequencing_activity_set
brynnz22 Apr 11, 2024
ee9c7a3
almost complete...
brynnz22 Apr 11, 2024
e94820c
add note for next time
brynnz22 Apr 11, 2024
e1c6dd4
add workflow chain name capabilities
brynnz22 Apr 16, 2024
98f2824
write doctests that work
brynnz22 Apr 16, 2024
c9a3629
adding project.makefile for now to make testing easier
brynnz22 Apr 16, 2024
3acca1a
add doctest that doesn't work
brynnz22 Apr 16, 2024
ba98b61
make workflowchain name reference omics id
brynnz22 Apr 17, 2024
a39d96a
remove todo
brynnz22 Apr 17, 2024
09bcee6
Use `black` to format the migrator code
eecavanna Apr 18, 2024
6c01e33
Simplify `__init__` function and add explanatory comment
eecavanna Apr 18, 2024
4041be0
Fix failing doctest
eecavanna Apr 18, 2024
043a078
Specify adapter in doctests so cautionary message does not appear
eecavanna Apr 18, 2024
879abdf
try to create doctest for removing was_informed_by function
brynnz22 Apr 18, 2024
2ebb898
update doctest
brynnz22 Apr 18, 2024
6d41957
Simplify doctest by seeding "database" directly
eecavanna Apr 19, 2024
fe0972b
Merge branch 'main' into workflowchain_migrator
brynnz22 Apr 19, 2024
508d48b
add logger message for how many ids need to be minted as of 5/10 ther…
brynnz22 May 10, 2024
67878f0
add asset directory
brynnz22 May 10, 2024
1fd7a19
commit changes to move towards preminted ids
brynnz22 May 14, 2024
8013b13
Prevent `TypeError` when YAML asset file is empty
eecavanna May 15, 2024
a16afa4
add workflow chain ids yaml file filled
brynnz22 May 16, 2024
798464f
Merge branch 'workflowchain_migrator' of https://github.com/microbiom…
brynnz22 May 16, 2024
a4fbcf5
add rest of id functionality
brynnz22 May 16, 2024
8d2ca91
update documentation
brynnz22 May 16, 2024
e8f00ee
make project.makefile back to main's
brynnz22 May 16, 2024
9744140
Standardize variable names and comments
eecavanna May 16, 2024
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