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back merging changes in main to metabolink branch #1135

Merged
merged 93 commits into from
Sep 22, 2023
Merged

back merging changes in main to metabolink branch #1135

merged 93 commits into from
Sep 22, 2023

Commits on Jul 5, 2023

  1. update nucleicAcidQuantMethod mapping

    brynn.zalmanek@pnnl.gov committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. retire doi, created dois and subproperties

    brynn.zalmanek@pnnl.gov committed Jul 6, 2023
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Commits on Jul 10, 2023

  1. add curie pattern to dois slot, add study-set valid example file

    brynn.zalmanek@pnnl.gov committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. add function to update study_set doi slots in mongo

    brynn.zalmanek@pnnl.gov committed Jul 11, 2023
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  2. update study_set doi function to account for oddly structured dois

    brynn.zalmanek@pnnl.gov committed Jul 11, 2023
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  3. add py script to generate a doi report tsv, include in makefile

    brynn.zalmanek@pnnl.gov committed Jul 11, 2023
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Commits on Jul 19, 2023

  1. example data passes dois validation 

    emsl_project_dois now is_a dois
    @turbomam
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  2. protype examples (with descriptions) for dois subproperties 

    also added see_alsos and comments on the dois root property
    @turbomam
    turbomam committed Jul 19, 2023
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  3. ssh mongo notes

    @turbomam
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  4. make doi/award_dois values multivalued

    brynn.zalmanek@pnnl.gov committed Jul 19, 2023
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  5. add examples for award and dataset dois

    brynn.zalmanek@pnnl.gov committed Jul 19, 2023
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  6. Brynn and Mark's doi modeling and repair 

    back-merges jgi_portal_study_identifiers
    @turbomam
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  7. Brynn and Mark's doi modeling and repair 

    back-merges jgi_portal_study_identifiers
    @turbomam
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  8. add emsl_project_dois example, add abstract:true to dois, update awar… 

    …d_dois example to include what is not and award
    brynn.zalmanek@pnnl.gov committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. Update description and comments for jgi_portal_study_identifiers

    @aclum
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Commits on Aug 17, 2023

  1. ttl dump incomplete

    @turbomam
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  2. add context generation

    @turbomam
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  3. Merge branch 'main' into issue-1070-content-from-mongo

    @turbomam
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Commits on Aug 18, 2023

  1. not adding unconvertables

    @turbomam
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Commits on Aug 20, 2023

  1. recursive CURIe repair

    @turbomam
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  2. funct anno agg

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Commits on Aug 21, 2023

  1. fxn annotation agg

    @turbomam
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  2. backmerged issue-338-doi-updates 

    migration of migration incomplete
    @turbomam
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  3. added Study.dois migration

    @turbomam
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Commits on Aug 24, 2023

  1. anyURI repair

    @turbomam
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Commits on Aug 25, 2023

  1. Remove invalid water content examples

    @aclum
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Commits on Aug 28, 2023

  1. per-class sparql templater

    @turbomam
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Commits on Aug 29, 2023

  1. descend one level down from target class

    @turbomam
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Commits on Aug 30, 2023

  1. sparqlburger

    @turbomam
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  2. pre-release cleanup

    @turbomam
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  3. tests require accepting-legacy-ids components

    @turbomam
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  4. don't regen mixs.yaml every make all

    @turbomam
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  5. updated .gitignore 

    -f adds will be required for release prep
    @turbomam
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  6. add more to RELEASE_NOTES_v7.7.2_to_v7.8.0.md

    @turbomam
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  7. Merge pull request #1074 from microbiomedata/issue-1070-content-from-… 

    …mongo

doi remodeling and migration, mixed with CURIes coercion, RDF generation, and class-specific SPARQL generation
    @turbomam
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  8. artifacts for nmdc-schema v7.8.0

    @turbomam
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  9. Merge pull request #1094 from microbiomedata/7_8_0_artifacts 

    artifacts for nmdc-schema v7.8.0
    @turbomam
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Commits on Sep 1, 2023

  1. add consortium updates to Study class

    @brynnz22
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  2. add Study class todos

    @brynnz22
    brynnz22 committed Sep 1, 2023
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  3. add example data files and make initiative_type required

    @brynnz22
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  4. make initiative_type true

    @brynnz22
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  5. add example Database study set file

    @brynnz22
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  6. remove close_mappings from Study class

    @brynnz22
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  7. combine todos keys

    @brynnz22
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Commits on Sep 5, 2023

  1. Merge pull request #1084 from microbiomedata/issue-1083 

    Remove invalid water content examples
    @turbomam
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  2. update mappings to put study specific mappings with study enum and in… 

    …vestigation with study class
    @brynnz22
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  3. update test_credit_associations.py to include initiative_type

    @brynnz22
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  4. update Database-nmdc-example.yaml to include initiative_type for stud… 

    …y set
    @brynnz22
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  5. add study set example with parent consortium

    @brynnz22
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  6. update database-study_set-emsl-project_doi.yaml with initiative_type

    @brynnz22
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  7. add initiative_type to src/data/valid/Study-minimal.yaml

    @brynnz22
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  8. add new slots to src/data/valid/Study-exhaustive.yaml

    @brynnz22
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  9. make part_of an array in exhaustive example

    @brynnz22
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  10. add initiative_type to src/data/valid/Database-multi-id-study.yaml

    @brynnz22
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  11. add initiative_type to src/data/valid/Study-credit-1.yaml

    @brynnz22
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  12. add initiative_type to src/data/valid/Database-study-set-with-gnps-id… 

    ….yaml
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  13. add initiative_type to src/data/valid/Database-study-set-with-dois.yaml

    @brynnz22
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Commits on Sep 7, 2023

  1. Change Study class name to ResearchInitiative

    @brynnz22
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  2. delete valid Study.yaml files (changed to ResearchInitiative)

    @brynnz22
    brynnz22 committed Sep 7, 2023
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Commits on Sep 11, 2023

  1. change sample_mass slot to input_mass

    @brynnz22
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Commits on Sep 12, 2023

  1. add migration script

    @brynnz22
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  2. add invalid sample_mass yaml data file

    @brynnz22
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  3. fix schema version in extraction migration function:

    @brynnz22
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  4. fix return indent

    @brynnz22
    brynnz22 committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. fix extraction function version number

    @brynnz22
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  2. Add valid Study.yaml files back (changing class name back to Study)

    @brynnz22
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  3. Revert "Change Study class name to ResearchInitiative" 

    This reverts commit 8a8c3fb.

change back to Study name for class
    @brynnz22
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  4. make slot study_category and change enum to research_study

    @brynnz22
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  5. remove initiative_type from test_credit_associations.py

    @brynnz22
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Commits on Sep 14, 2023

  1. make all test works without default_curi_maps

    @turbomam
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  2. remove AFO mapping

    @brynnz22
    brynnz22 committed Sep 14, 2023
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  3. fix normalize curie function to allow for /

    @brynnz22
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  4. consistently get prefix info from jsonld

    @turbomam
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  5. move BiosampleProcessing under PlannedProcess, etc.

    @brynnz22
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  6. remove duplicate broad_mappings

    @brynnz22
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  7. fix typos in BiosampleProcessing description

    @brynnz22
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Commits on Sep 15, 2023

  1. Merge pull request #1109 from microbiomedata/issue1031-input_sample_mass 

    Issue1031 input sample mass
    @turbomam
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  2. Merge pull request #1118 from microbiomedata/issue-24-omics-processin… 

    …g-move

Issue 24 omics processing move
    @turbomam
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  3. always use jsonld context

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  4. Merge branch 'main' into issue-1115-no-default_curi_maps

    @turbomam
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  5. Merge pull request #1098 from microbiomedata/issue1097-study-consortia 

    Issue1097 study consortia
    @turbomam
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  6. Merge pull request #1036 from microbiomedata/issue1034-update-neon-ma… 

    …pping

update nucleicAcidQuantMethod mapping
    @turbomam
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Commits on Sep 18, 2023

  1. better use of json-ls contexts

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  2. always gold never GOLD

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Commits on Sep 19, 2023

  1. editing src/docs/prefixes_curies_ids_mappings_etc.md

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  2. include metaproteomics

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  3. Merge branch 'main' into issue-1115-no-default_curi_maps

    @turbomam
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  4. backmerge main

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  5. some classes expect str range for used

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  6. no ppprint; click-log = core dep

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Commits on Sep 21, 2023

  1. ready for make all then merge

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  2. Merge pull request #1116 from microbiomedata/issue-1115-no-default_cu… 

    …ri_maps

Prefixes standardization (no default curi maps) and making some slot_usage attributes global
    @turbomam
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  3. regenerated everything for v8.0.0

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