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

#1960 - Omit derived files from repo (generate them locally instead)

Issue - State: open - Opened by eecavanna 5 months ago
Labels: enhancement, infrastructure not content, devops, cleanup

#1959 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#1957 - Class Extraction issues

Issue - State: closed - Opened by aclum 5 months ago - 1 comment

#1956 - local-pure-export-example

Pull Request - State: closed - Opened by turbomam 5 months ago

#1955 - `Database` class has two slots named `planned_process_set`

Issue - State: closed - Opened by eecavanna 5 months ago - 1 comment
Labels: bug

#1954 - `Database` class has two slots named `functional_annotation_agg`

Issue - State: closed - Opened by eecavanna 5 months ago
Labels: bug

#1953 - Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#1951 - Dump local

Pull Request - State: closed - Opened by turbomam 5 months ago

#1949 - Create metabolomics_check_workflow_activity.js

Pull Request - State: closed - Opened by aclum 5 months ago

#1948 - mixed QC tools and targets

Pull Request - State: open - Opened by turbomam 5 months ago - 3 comments

#1947 - Master `Information` class issue

Issue - State: open - Opened by turbomam 5 months ago - 16 comments

#1946 - NMDC schema slots to NCBI MIxS term matching

Pull Request - State: closed - Opened by sujaypatil96 5 months ago - 5 comments

#1940 - Create declarative mapping file for NMDC-to-NCBI push

Issue - State: closed - Opened by sujaypatil96 5 months ago - 3 comments

#1938 - Factor `TextValue` out of nmdc-schema and migrate accordingly

Issue - State: open - Opened by turbomam 5 months ago - 3 comments

#1937 - Add slots to Biosample class to disambiguate standard MG metadata vs long-read MG metadata

Issue - State: open - Opened by pkalita-lbl 6 months ago - 4 comments
Labels: blocked

#1936 - PR to sync metab_re-id branch with main

Pull Request - State: closed - Opened by aclum 6 months ago - 1 comment

#1935 - Update pypi-publish.yaml for trusted publishing

Pull Request - State: closed - Opened by pkalita-lbl 6 months ago - 1 comment

#1934 - Upgrade locked version of bioregistry

Pull Request - State: closed - Opened by pkalita-lbl 6 months ago

#1933 - metabolomics,nom,lipidomics re-id code

Pull Request - State: closed - Opened by aclum 6 months ago - 1 comment

#1932 - GitHub Actions workflow is failing due to inability to install `bioregistry`

Issue - State: closed - Opened by eecavanna 6 months ago - 1 comment
Labels: bug, help wanted, dependencies

#1929 - Migrations: Add example doctests for functions that use adapter methods

Issue - State: open - Opened by eecavanna 6 months ago
Labels: enhancement

#1928 - Review and test NOM re-IDing code

Issue - State: closed - Opened by mbthornton-lbl 6 months ago - 2 comments

#1927 - Display single/multi-valued (cardinality) on slot edges

Pull Request - State: closed - Opened by sujaypatil96 6 months ago

#1926 - wrap `s.range` from class diagram jinja in `gen.name()`

Pull Request - State: closed - Opened by sujaypatil96 6 months ago - 1 comment

#1925 - generate prefixmap for nmdc

Issue - State: open - Opened by sierra-moxon 6 months ago - 2 comments

#1924 - Update identifiers.md

Pull Request - State: closed - Opened by aclum 6 months ago - 2 comments

#1923 - 1914 metabolite identification

Pull Request - State: closed - Opened by brynnz22 6 months ago

#1922 - Add sets to `Database` for the `MaterialProcess` subclasses

Issue - State: closed - Opened by anastasiyaprymolenna 6 months ago - 5 comments

#1921 - Bump idna from 3.6 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#1920 - Create `ChromatographicSeparationConfiguration` class and modify existing `ChromatographicSeparation` to accommodate

Issue - State: closed - Opened by kheal 6 months ago - 5 comments
Labels: berkeley-fy24-refactor

#1919 - Hyperlink class blocks in mermaid class diagram

Pull Request - State: closed - Opened by sujaypatil96 6 months ago

#1918 - Refactor `has_calibration` to use a class

Issue - State: closed - Opened by brynnz22 6 months ago - 5 comments
Labels: berkeley-fy24-refactor

#1917 - Refactor `principal_investigator` slot on `Study`

Issue - State: open - Opened by brynnz22 6 months ago - 2 comments

#1916 - support slot for when document was added

Issue - State: closed - Opened by aclum 6 months ago - 12 comments

#1915 - Bump pymongo from 4.6.2 to 4.6.3

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#1914 - Rename `has_metabolite_quantification` and associated class to `has_metabolite_identification`

Issue - State: closed - Opened by kheal 6 months ago - 5 comments
Labels: berkeley-fy24-refactor

#1912 - Add permissible values to `FileTypeEnum` and `DataCategoryEnum` to accomodate workflow configuration `DataObject`s

Issue - State: closed - Opened by brynnz22 6 months ago - 3 comments
Labels: berkeley-fy24-refactor

#1911 - Add `workflow_version` slot to `WorkflowExecution` classes

Issue - State: closed - Opened by brynnz22 6 months ago - 1 comment
Labels: berkeley-fy24-refactor

#1909 - Expand `StationaryPhaseEnum` to include values needed for GC-MS and LC-MS metab data

Issue - State: closed - Opened by brynnz22 6 months ago - 1 comment
Labels: berkeley-fy24-refactor

#1907 - Add `sample_portion` to `SubsamplingProcess`

Issue - State: closed - Opened by brynnz22 6 months ago - 1 comment
Labels: berkeley-fy24-refactor

#1906 - Flush out `SubstanceRoleEnum`

Issue - State: closed - Opened by brynnz22 6 months ago - 1 comment
Labels: berkeley-fy24-refactor

#1905 - Metabolomics Schema Updates Meta Issue

Issue - State: closed - Opened by brynnz22 6 months ago - 6 comments

#1904 - QuantityValue.slot_usage.has_numeric_value.range: Float -> Double

Issue - State: open - Opened by turbomam 6 months ago - 3 comments

#1901 - fix inconsistent `slot_usages`

Issue - State: open - Opened by turbomam 6 months ago - 1 comment

#1900 - remove redundant `slot_usage`s

Issue - State: closed - Opened by turbomam 6 months ago - 1 comment

#1898 - `slot_usage` parent issue

Issue - State: open - Opened by turbomam 6 months ago - 2 comments

#1895 - Update instrument model and vendor enumerations

Pull Request - State: closed - Opened by brynnz22 6 months ago

#1892 - `Study.slot_usage.protocol_link` should not assert `multivalued: true`

Issue - State: open - Opened by turbomam 6 months ago - 2 comments

#1891 - update UML class diagram relationship arrow types

Pull Request - State: closed - Opened by sujaypatil96 6 months ago

#1890 - Automate `data_qc` scripts

Issue - State: closed - Opened by mbthornton-lbl 6 months ago - 1 comment

#1886 - 1885 determine schema imports graph

Pull Request - State: closed - Opened by turbomam 6 months ago

#1885 - determine schema imports graph

Issue - State: closed - Opened by turbomam 6 months ago - 1 comment

#1884 - MobilePhaseComponents instead of Solutions

Issue - State: closed - Opened by turbomam 6 months ago

#1881 - DataPortal can be searched for `Pathway`s and `OntologyGroup`s... does that justify leaving them in nmdc-schema?

Issue - State: closed - Opened by turbomam 6 months ago - 9 comments
Labels: cleanup, berkeley-fy24-refactor

#1879 - remove `ecosystem_diagram.md` from berkeley-schema-fy24

Issue - State: closed - Opened by turbomam 6 months ago - 3 comments
Labels: closed_via_berkeley

#1877 - analyse build log from berkeley-schema-fy24

Issue - State: closed - Opened by turbomam 6 months ago - 2 comments

#1876 - Assess the usefulness of nmdc-schema (not MIxS) subsets

Issue - State: open - Opened by turbomam 6 months ago - 3 comments

#1875 - Find elements whose names contain white-space

Issue - State: open - Opened by turbomam 6 months ago - 2 comments

#1874 - Review types that aren't used in any slot

Issue - State: open - Opened by turbomam 6 months ago - 1 comment

#1873 - Review enums that aren't used by any slot

Issue - State: open - Opened by turbomam 6 months ago - 1 comment
Labels: cleanup

#1871 - Review slots that aren't used in any classes

Issue - State: open - Opened by turbomam 6 months ago - 5 comments
Labels: cleanup

#1869 - Remove extra logic to handle legacy identifiers

Issue - State: closed - Opened by aclum 6 months ago - 13 comments

#1868 - update example data to napa -style identifiers

Issue - State: closed - Opened by aclum 6 months ago - 8 comments

#1867 - initial style guide with chemistry emphasis

Pull Request - State: open - Opened by turbomam 6 months ago

#1866 - 1855 add instrument enums

Pull Request - State: closed - Opened by brynnz22 6 months ago

#1864 - Trust `ChemicalEntity` as the home `domain` for `inchi` etc.

Issue - State: closed - Opened by turbomam 6 months ago - 1 comment
Labels: chemistry

#1863 - Add query to delete non-conforming bioscales data objects

Pull Request - State: closed - Opened by mbthornton-lbl 6 months ago

#1862 - Create chemical_entity_set Database slot etc

Pull Request - State: closed - Opened by turbomam 6 months ago

#1861 - create `chemical_entity_set`

Issue - State: closed - Opened by turbomam 6 months ago