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
#1958 - Expand permissible values on `FileTypeEnum` for Metaproteomics related files
Issue -
State: closed - Opened by kheal 5 months ago
- 1 comment
#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
#1952 - Merge `nmdc-schema/main` branch (base) into `berkeley-schema-fy24/main` branch (fork)
Issue -
State: open - Opened by eecavanna 5 months ago
- 1 comment
#1951 - Dump local
Pull Request -
State: closed - Opened by turbomam 5 months ago
#1950 - Range for slots in slots table on class documentation pages account ofor `any_of`/`exactly_one_of`
Pull Request -
State: closed - Opened by sujaypatil96 5 months ago
- 1 comment
#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
#1945 - Ensure that `src/scripts/ncbi_postgres_nmdc_exact_term_matching.py` reads credentials from `local/.env`
Pull Request -
State: closed - Opened by sujaypatil96 5 months ago
#1944 - Ensure consistency of cardinality displayed on edges of Mermaid class diagram
Pull Request -
State: closed - Opened by sujaypatil96 5 months ago
#1943 - Expand `FileTypeEnum` to include "LC-MS Lipidomics Results" with a description of "LC-MS-based lipid assignment results table"
Issue -
State: closed - Opened by kheal 5 months ago
Labels: berkeley-fy24-refactor
#1942 - Update description for `git_url` for `MetabolomicsAnalsysis` to specify that it has to point to an exact workflow (to differentiate lipids, gc_ms metabs (only one right now) and lc_ms metabs
Issue -
State: closed - Opened by brynnz22 5 months ago
Labels: berkeley-fy24-refactor
#1941 - `napa_compliance` branch: Update script to generate request bodies for `/queries:run` endpoint
Pull Request -
State: closed - Opened by eecavanna 5 months ago
- 1 comment
#1940 - Create declarative mapping file for NMDC-to-NCBI push
Issue -
State: closed - Opened by sujaypatil96 5 months ago
- 3 comments
#1939 - `napa_compliance` branch: Update deletion code to generate request bodies for `queries:run` Runtime API endpoint
Issue -
State: closed - Opened by eecavanna 5 months ago
- 1 comment
#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
#1931 - Move executable Python script from `assets/` to `src/scripts/`
Pull Request -
State: closed - Opened by sujaypatil96 6 months ago
#1930 - Use PyPI trusted publisher settings in release publishing workflow
Issue -
State: closed - Opened by pkalita-lbl 6 months ago
#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
#1913 - Create `MassSpectrometryConfiguration` class and modify existing `MassSpectrometry` class to accommodate
Issue -
State: closed - Opened by brynnz22 6 months ago
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
#1910 - Edit slot usages to accommodate multiple detection configurations for single `MassSpectrometry` instance
Issue -
State: closed - Opened by brynnz22 6 months ago
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
#1908 - Add `StorageProcess` class (a subclass of `MaterialProcessing` with slots like `substances_used` (already exists) and `contained_in` slot (already exists), `duration` (already exists), and `temperature` (already exists). With `input` and 'output`
Issue -
State: closed - Opened by brynnz22 6 months ago
- 4 comments
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
#1903 - Biosample.slot_usage.gold_biosample_identifiers.range: external_identifier -> uriorcurie
Issue -
State: closed - Opened by turbomam 6 months ago
#1902 - Update `connect_napa_mongo.py` to output tsv with deleted record identifiers
Pull Request -
State: closed - Opened by mbthornton-lbl 6 months ago
#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
#1899 - Resolve omics processing has output data object referential integrity exceptions
Pull Request -
State: closed - Opened by mbthornton-lbl 6 months ago
#1898 - `slot_usage` parent issue
Issue -
State: open - Opened by turbomam 6 months ago
- 2 comments
#1897 - Resolve referential integrity exceptions for `nmdc:sty-11-547rwq94` Metagenome Omics Processing records
Issue -
State: closed - Opened by mbthornton-lbl 6 months ago
- 3 comments
#1896 - update code to delete unconnected workflow activity and data objects to same logging format as Michael's deletion function
Issue -
State: closed - Opened by aclum 6 months ago
- 1 comment
#1895 - Update instrument model and vendor enumerations
Pull Request -
State: closed - Opened by brynnz22 6 months ago
#1894 - Resolve omics_processing has_output data_object referential integrity exceptions in study nmdc:sty-11-dcqce727
Issue -
State: closed - Opened by mbthornton-lbl 6 months ago
- 3 comments
#1893 - `linkml-sqldb dump` crashes in `berkeley-schema-fy24` because of multiple possible `Study.part_of` paths
Issue -
State: open - Opened by turbomam 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
#1889 - ensure that the origin of all `assets/` files can be determined by Makefile or Python code in the repo or high-quality comments
Issue -
State: open - Opened by turbomam 6 months ago
#1888 - Referential Integrity errors in 2 imported JGI studies
Issue -
State: open - Opened by mbthornton-lbl 6 months ago
#1887 - ensure that each src/schema YAML file can be re-generated in isoloation
Issue -
State: open - Opened by turbomam 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
#1883 - 1865 Extract Re-IDed Napa DB to YAML, Validate and check referential integrity
Pull Request -
State: closed - Opened by mbthornton-lbl 6 months ago
- 1 comment
#1882 - simplify usage of Solution by DissolvingProcess in berkeley-schema-fy24
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
#1880 - Automate MongoDB Referential Integrity Queries
Issue -
State: open - Opened by mbthornton-lbl 6 months ago
#1879 - remove `ecosystem_diagram.md` from berkeley-schema-fy24
Issue -
State: closed - Opened by turbomam 6 months ago
- 3 comments
Labels: closed_via_berkeley
#1878 - merge diagram creation project.Makefile targets into berkeley-schema-fy24
Issue -
State: closed - Opened by turbomam 6 months ago
#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
#1872 - Guidance required wrt use of `name` and `has_raw_value` on `PersonValue`
Issue -
State: open - Opened by turbomam 6 months ago
#1871 - Review slots that aren't used in any classes
Issue -
State: open - Opened by turbomam 6 months ago
- 5 comments
Labels: cleanup
#1870 - Why don't the `src/script`s in nmdc-scehma appear in the berkeley-schema-fy24 repo?
Issue -
State: closed - Opened by turbomam 6 months ago
- 1 comment
#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
#1865 - Extract Re-IDed Napa DB to YAML, Validate and check referential integrity
Issue -
State: closed - Opened by mbthornton-lbl 6 months ago
- 23 comments
#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