Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / microbiomedata/nmdc-schema issues and pull requests
#824 - conflict between `license` and commented-out `classifiers` -> License in `pyproject.toml`
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#823 - `samp_taxon_id` and `host_taxid` need to be CURIEs
Issue -
State: closed - Opened by sujaypatil96 over 1 year ago
- 2 comments
#822 - Enforce `latitude` and `longitude` on `lat_lon` slot
Issue -
State: closed - Opened by sujaypatil96 over 1 year ago
#821 - Always use CURIEs for identifier slots in schema
Issue -
State: closed - Opened by sujaypatil96 over 1 year ago
- 7 comments
#820 - Linkml no longer core dependency of nmdc-schema
Issue -
State: closed - Opened by naglepuff over 1 year ago
- 6 comments
#819 - Prefix list curation
Issue -
State: closed - Opened by sujaypatil96 over 1 year ago
- 6 comments
Labels: rdf owl sparql
#818 - add closed/no additional properties to jsonschema artifact
Issue -
State: open - Opened by turbomam over 1 year ago
#817 - Expressing biosample -> two libraries, with existing terms
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#816 - add nmdc_yaml prefix; comment out some others
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#815 - differentiate nmdc yaml and nmdc terms URLs
Issue -
State: open - Opened by turbomam over 1 year ago
- 1 comment
#814 - pyproject.toml update/cleanup
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#813 - pyproject.toml update
Issue -
State: closed - Opened by turbomam over 1 year ago
#812 - Add raw GH ids for schema files
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#811 - replace https://microbiomedata/schema ids with raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema
Issue -
State: open - Opened by turbomam over 1 year ago
#810 - more mixs slots and better testing
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#809 - manual
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#808 - added mixs slots req by submission schema to Biosample
Pull Request -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#807 - several MIxS slots expected in submission schema missing from nmdc-schema
Issue -
State: open - Opened by turbomam over 1 year ago
#806 - make some example data that illustrates multiple sequencing libraries for the GROW study
Issue -
State: open - Opened by turbomam over 1 year ago
- 1 comment
#805 - change pyproject.toml version 0.0.0 to 7.4.11
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#804 - add 7.4.11 version to nmdc.yaml
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#803 - move slot_usage to global, make slots explicit, for several classes
Pull Request -
State: closed - Opened by dwinston over 1 year ago
- 1 comment
#802 - Notebook instantiates a ReadQcAnalysisActivity with multiple base/read counts and validates
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#801 - output_read_bases/output_base_count
Issue -
State: closed - Opened by turbomam over 1 year ago
- 5 comments
#800 - classes on index page should be hierarchically indented
Pull Request -
State: closed - Opened by sujaypatil96 over 1 year ago
#799 - Exhaustive biosample example data for comparison between schema versions
Pull Request -
State: closed - Opened by turbomam over 1 year ago
#798 - put exhaustive biosmaple examples in current main and issue-796-bye-yq branch
Issue -
State: closed - Opened by turbomam over 1 year ago
#797 - Use sheets_and_friends for MIxS slot modification, not yq
Pull Request -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#796 - do modifications with sheets_and_friends not yq
Issue -
State: open - Opened by turbomam over 1 year ago
- 3 comments
Labels: mixs-text-val-range
#795 - elev range should show as float, not QuantityValue
Issue -
State: closed - Opened by dwinston over 1 year ago
- 6 comments
Labels: bug, documentation
#783 - Biosample slot usage for source_mat_id was not migrated to sheets_and_friends
Issue -
State: open - Opened by turbomam over 1 year ago
- 3 comments
Labels: identifiers, nmdc-schema-mixs-submission, slot usage, prefix-issues
#781 - `linkml-run-examples` script is being run 3 times by main.yaml action
Issue -
State: closed - Opened by turbomam over 1 year ago
- 2 comments
Labels: GH actions
#777 - descriptions shouldn't just rephrase element names
Issue -
State: closed - Opened by turbomam over 1 year ago
#766 - We have no modeling to account for technical replicates
Issue -
State: open - Opened by turbomam over 1 year ago
- 4 comments
Labels: nmdc-schema-mixs-submission
#761 - What is the ideal range for was_informed_by?
Issue -
State: closed - Opened by turbomam over 1 year ago
- 2 comments
Labels: closed_via_berkeley
#759 - We (I) need better semantic versioning practices
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#756 - we should have valid and invalid examples for all classes in src/data
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#755 - DataObject with no id passed run-linkml-examples
Issue -
State: closed - Opened by turbomam over 1 year ago
- 3 comments
#724 - autogenerate typecodes documentation table
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
Labels: documentation, typecodes
#708 - Add missing file_name_pattern to file type enums for metatranscriptomes
Issue -
State: closed - Opened by ssarrafan over 1 year ago
- 4 comments
Labels: gold
#685 - Some schema elements lack a `description` slot
Issue -
State: open - Opened by turbomam over 1 year ago
- 29 comments
Labels: backlog, EMSL, style-guide
#680 - soil texture measurement
Issue -
State: open - Opened by mslarae13 over 1 year ago
Labels: nmdc-schema-mixs-submission
#679 - link to climate information
Issue -
State: open - Opened by mslarae13 over 1 year ago
Labels: nmdc-schema-mixs-submission
#678 - Determine if and how `link_class_info` will be used in the submission schema
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 18 comments
Labels: backlog, nmdc-schema-mixs-submission
#663 - Re-assess imported dependencies, even for dev
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
Labels: jupyter
#661 - Apply suggestions from LinkMl linter (as available in cookeicutter branch)
Issue -
State: open - Opened by turbomam over 1 year ago
Labels: EMSL, style-guide
#660 - desired degree of modularity for schema source YAML files?
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#659 - Add more valid and invalid examples for run-linkml-examples
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
Labels: schema change post cookiecutter, validation
#658 - Previous cookiecutter lost git history. Try again with Chris M.
Issue -
State: closed - Opened by turbomam over 1 year ago
- 2 comments
Labels: schema change post cookiecutter
#648 - Sujay's GOLD Bioscale conversion OK except ids?
Pull Request -
State: closed - Opened by turbomam over 1 year ago
- 2 comments
#645 - nmdc.schema.json should have corresponding version in "version" field
Issue -
State: closed - Opened by dwinston over 1 year ago
- 6 comments
Labels: versioning
#641 - Reflect modeling from Submission Portal/nmdc-server in nmdc-schema
Pull Request -
State: open - Opened by turbomam over 1 year ago
#639 - add embargoed boolean slot to Biosample
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
#638 - assert rules for Biosamples sent to JGI in plates
Issue -
State: open - Opened by turbomam over 1 year ago
- 3 comments
Labels: nmdc-schema-mixs-submission, rules
#636 - updates to build process inc artifacts bundled in PyPI pacakge
Issue -
State: closed - Opened by turbomam over 1 year ago
- 1 comment
Labels: pydantic
#619 - inconsistent and untested referential integrity in test data files
Issue -
State: open - Opened by turbomam over 1 year ago
Labels: referential integrity
#619 - inconsistent and untested referential integrity in test data files
Issue -
State: open - Opened by turbomam over 1 year ago
Labels: referential integrity
#617 - typecode motivated changes to BiosampleProcessing alternative?
Issue -
State: open - Opened by turbomam over 1 year ago
- 2 comments
Labels: identifiers, gold, typecodes
#612 - depth should be required for relevant sample types, like soil
Issue -
State: closed - Opened by mslarae13 over 1 year ago
- 2 comments
Labels: nmdc-schema-mixs-submission
#611 - NMDC Identifiers issues (In Progress)
Issue -
State: open - Opened by mslarae13 over 1 year ago
Labels: identifiers
#610 - add typecode standard patters to schema
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 1 comment
Labels: typecodes
#609 - update schema activity classes
Issue -
State: open - Opened by mslarae13 over 1 year ago
Labels: typecodes
#607 - nmdc minted identifiers 'view level'
Issue -
State: closed - Opened by mslarae13 over 1 year ago
- 2 comments
Labels: identifiers, typecodes
#606 - Updates to typecode table
Issue -
State: closed - Opened by turbomam over 1 year ago
Labels: identifiers, typecodes
#605 - typecode table re-generation should be automated. GH action?
Issue -
State: closed - Opened by turbomam over 1 year ago
Labels: GH actions, typecodes
#590 - test if biosmaple_set from gold_nmdc_pipeline.py passes 7.1.6 validation
Issue -
State: closed - Opened by turbomam over 1 year ago
- 3 comments
Labels: gold, validation
#587 - schema slot updates
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 6 comments
Labels: identifiers, nmdc-schema-mixs-submission
#586 - Determine if and how `climate_environment` will be used in the submission schema
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 14 comments
Labels: backlog, nmdc-schema-mixs-submission
#585 - Determine if and how various soil type/classification/taxonomy terms will be used in the submission schema
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 13 comments
Labels: backlog, nmdc-schema-mixs-submission, unfinished
#584 - Submission Portal- soil template -horizon
Issue -
State: open - Opened by mslarae13 over 1 year ago
- 3 comments
Labels: nmdc-schema-mixs-submission
#581 - Submission Portal/ DH: samp_name should be required to be unique
Issue -
State: open - Opened by mslarae13 almost 2 years ago
- 14 comments
Labels: identifiers, nmdc-schema-mixs-submission
#578 - submission portal tech stack architecture diagram
Issue -
State: open - Opened by sujaypatil96 almost 2 years ago
- 1 comment
Labels: documentation, MEDIUM, nmdc-schema-mixs-submission, diagrams
#575 - prefix for curie representation of `FieldResearchSite` id
Issue -
State: closed - Opened by sujaypatil96 almost 2 years ago
- 2 comments
Labels: identifiers, gold
#553 - report mixs package/term association counts from sheets-for-nmdc-submission-schema
Issue -
State: open - Opened by turbomam almost 2 years ago
- 1 comment
Labels: documentation, nmdc-schema-mixs-submission
#552 - Provide class/typecode relations
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 1 comment
Labels: identifiers, typecodes
#544 - support remote destination databases for schema migration
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
Labels: enhancement
#544 - support remote destination databases for schema migration
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
Labels: enhancement
#543 - read qc still commented out
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 1 comment
#541 - merge in migration script etc.
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
#538 - jsonasobj 2.0.1 is a yanked version
Issue -
State: closed - Opened by turbomam almost 2 years ago
#533 - metabref SQL -> LinkML
Pull Request -
State: closed - Opened by turbomam almost 2 years ago
- 1 comment
#532 - Convert Anastasiya's SQL DDL to LinkML
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
Labels: sql
#530 - manage elements with empty definitions
Issue -
State: open - Opened by turbomam almost 2 years ago
- 1 comment
Labels: style-guide
#526 - break #486 migration into smaller PRs
Issue -
State: closed - Opened by turbomam almost 2 years ago
#525 - Do we have a way to update the version value in the schema based on a GH tag or vice versa?
Issue -
State: open - Opened by turbomam almost 2 years ago
- 1 comment
Labels: versioning
#523 - NMDC schema with only 2 modules: nmdc.yaml and mixs.yaml
Pull Request -
State: closed - Opened by turbomam almost 2 years ago
- 1 comment
#521 - Warning: The file chosen for install of jsonasobj 2.0.1 (jsonasobj-2.0.1-py3-none-any.whl) is yanked.
Issue -
State: closed - Opened by turbomam almost 2 years ago
#519 - `study_credit_test.json` file using `PersonValue` incorrectly
Issue -
State: open - Opened by sujaypatil96 almost 2 years ago
- 3 comments
Labels: schema change, rdf owl sparql
#517 - path forward for issue-486-data-to-7-0
Issue -
State: closed - Opened by turbomam almost 2 years ago
Labels: nmdc-schema-mixs-submission, rdf and owl, rdf and sparql
#514 - refine metabolomics/sample processing schemasheet
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
Labels: nmdc-schema-mixs-submission, gold
#513 - Update actions versions
Pull Request -
State: closed - Opened by pkalita-lbl almost 2 years ago
- 1 comment
#509 - combine all nmdc-schema modules EXCEPT mixs into a consolidated YAML file
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 2 comments
Labels: nmdc-schema-mixs-submission
#509 - combine all nmdc-schema modules EXCEPT mixs into a consolidated YAML file
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 2 comments
Labels: nmdc-schema-mixs-submission
#507 - NMDC types as they appear in RDF artifact
Issue -
State: open - Opened by turbomam almost 2 years ago
- 3 comments
Labels: nmdc-schema-mixs-submission, gold, envo, type, rdf owl sparql
#506 - MongoDB repair vs Kitware ingest into Postgres
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 2 comments
Labels: gold, EMSL, rdf owl sparql
#505 - attempting to load RDF dump into GraphDB gives "org.eclipse.rdf4j.sail.SailException: Invalid IRI value"
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 1 comment
#503 - Production NMDC MongoDB's `data_object_set collection` has illegally un-prefixed documents
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 4 comments
Labels: EMSL
#502 - ValueError: : Unknown CURIE prefix: @base from RDF conversion
Issue -
State: closed - Opened by turbomam almost 2 years ago
- 3 comments
Labels: rdf owl sparql
#500 - external_database_identifiers range of external identifier -> RDF conversion WARNING "No datatype specified for : external identifier"
Issue -
State: open - Opened by turbomam almost 2 years ago
- 1 comment
Labels: identifiers, rdf owl sparql
#496 - automate process of updating schema's `version` value
Issue -
State: open - Opened by turbomam almost 2 years ago
Labels: versioning