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

#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

#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

#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

#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

#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

#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

#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

#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

#496 - automate process of updating schema's `version` value

Issue - State: open - Opened by turbomam almost 2 years ago
Labels: versioning