Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / microbiomedata/submission-schema issues and pull requests

#171 - analysis_type is both required and recommended for class WaterInterface

Issue - State: closed - Opened by aclum about 1 year ago - 10 comments

#152 - Issue 151 geocoding

Pull Request - State: closed - Opened by turbomam over 1 year ago - 2 comments

#149 - test instantiating biosamples from NCBI

Pull Request - State: closed - Opened by turbomam over 1 year ago - 6 comments

#121 - just set nmdc-schema import tag to `main` for now

Issue - State: closed - Opened by turbomam over 1 year ago - 5 comments

#116 - Align `rna_volume` validation constraints with comments

Issue - State: closed - Opened by turbomam over 1 year ago - 11 comments

#112 - rna_container_id in JgiMtInterface is still accepting strings > 20 charcters

Issue - State: closed - Opened by turbomam over 1 year ago - 5 comments
Labels: yq

#93 - Restore lost slot attribues

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#92 - update GH pages index page with direct link to SoilInterface

Issue - State: open - Opened by turbomam almost 2 years ago - 1 comment

#90 - Use `template` query param to select initial template if given

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago - 1 comment

#89 - Is the run time of linkml-run-examples decreased by the post-1.5.0 linkml runtime?

Issue - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#88 - dh <-> linkml json conversion

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#87 - add DH JSON to LinkML and LinkML JSON to DH data converters

Issue - State: closed - Opened by turbomam almost 2 years ago

#86 - Dependencies and TSV cleanup

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#85 - update dependencies and streamline TSV file names

Issue - State: closed - Opened by turbomam almost 2 years ago

#84 - schemasheets 1.2

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#83 - bump to schemasheets 0.1.20 for unsorted keys option

Issue - State: closed - Opened by turbomam almost 2 years ago

#82 - Too much indentation for the EnvBroadScaleSoilEnum PVs etc

Issue - State: closed - Opened by turbomam almost 2 years ago - 10 comments
Labels: backlog

#81 - Go back to un-indented, alphabetized PVs for MIxS environmental slots

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

#80 - Remove dna/rna organisms and collect_site slots

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#79 - Soil mixs env* enums

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#78 - enum issues

Issue - State: open - Opened by turbomam almost 2 years ago - 1 comment
Labels: enums

#77 - If DnaSampleFormatEnum and RnaSampleFormatEnum have the same PVs, could they be be reformulated as a singe enum?

Issue - State: open - Opened by turbomam almost 2 years ago - 8 comments
Labels: backlog, enums

#76 - enum reuse

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#75 - dna_dnase boolean

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#74 - more direct path to playground

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#73 - Illustrations of LinkML and DH JSON differences

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#72 - illustrate the differences between DH JSON and LinkML JSON

Issue - State: closed - Opened by turbomam almost 2 years ago - 2 comments

#71 - This repo and nmdc-schema still have duped domain_of

Issue - State: closed - Opened by turbomam almost 2 years ago - 4 comments

#70 - cp src/docs/*md docs/ before poetry run mkdocs build -d dist

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#69 - updated slot class assignments, esp regarding mixins

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#68 - add playground link to about.md

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#67 - Commented out *deploy* in Makefile

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#66 - MAM try JSON input into DH sandbox

Issue - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#65 - tidy up mixin/class assignments in do_shuttle sheet

Issue - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#64 - add link to _playground in generated docs index page

Issue - State: closed - Opened by turbomam almost 2 years ago

#62 - scavenge commits from earlier today

Issue - State: closed - Opened by turbomam almost 2 years ago
Labels: yq

#61 - regen

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#60 - Misc minor updates

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago - 2 comments

#59 - JgiMg and JgiMt: Add rule that requires a dna_cont_well when the dna_cont_type is "plate"

Issue - State: closed - Opened by turbomam almost 2 years ago - 7 comments
Labels: yq

#58 - linkml2sheets output -> schema_sheets/populated_tsv/slot_usage_minimal.tsv

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#57 - resume checking in the linkml2sheets output

Issue - State: closed - Opened by turbomam almost 2 years ago

#56 - Update README.md

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#55 - Add DataHarmonizer-based interactive testing interface

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#54 - more shuttling less defining

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#53 - Get slots from the nmdc-schema if available.

Issue - State: closed - Opened by turbomam almost 2 years ago

#52 - jgi and emsl sample data

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#51 - JgiMgInterface slots are under-specified in this schema

Issue - State: closed - Opened by turbomam almost 2 years ago

#50 - Keep the amount of time spent on linkml-run-examples reasonable

Issue - State: closed - Opened by turbomam almost 2 years ago - 2 comments

#49 - use booleans instead of yes/no enumerations

Issue - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#48 - re-use shareable enums

Issue - State: closed - Opened by turbomam almost 2 years ago - 3 comments
Labels: enums

#47 - MIxS triad enums have lost their structure

Issue - State: closed - Opened by turbomam almost 2 years ago - 3 comments
Labels: enums

#46 - Sample soil data with and without elev values

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#45 - project.Makefile with fewer yq commands

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#44 - Example data with all water and soil slots

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#42 - lingering steps for water and soil example data

Issue - State: open - Opened by turbomam almost 2 years ago - 9 comments
Labels: enums

#41 - Less committing from macbook

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#40 - Delete unused sheets_and_friends TSVs

Pull Request - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#39 - Decrease reliance on yq

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

#38 - remove un-used schemasheets and sheets_and_friends TSVs

Issue - State: closed - Opened by turbomam almost 2 years ago

#37 - ignore linkml-run-examples output directory?

Issue - State: open - Opened by turbomam almost 2 years ago - 1 comment

#35 - Add dynamic version to generate schema and artifacts

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#34 - Useful but un-synced files -> local

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#33 - Run schema_cleanup and create placeholder files

Issue - State: closed - Opened by turbomam almost 2 years ago

#32 - Check NMDC-wide parity between soil Biosample capture, validation and serialization

Issue - State: closed - Opened by turbomam almost 2 years ago - 10 comments
Labels: enums

#31 - Fix typos and inconsistencies in `DhMultiviewCommonColumnsMixin` usage

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#30 - sheets-and-friends import requires source schema URL to be pre-merged?

Issue - State: closed - Opened by turbomam almost 2 years ago - 4 comments

#29 - Add titles to dh_section slots

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#28 - slots whose global definitions could be removed?

Issue - State: open - Opened by turbomam almost 2 years ago - 5 comments

#27 - Grouping slots should have human-friendly titles

Issue - State: closed - Opened by pkalita-lbl almost 2 years ago

#25 - Add versioning to schema

Issue - State: closed - Opened by pkalita-lbl almost 2 years ago - 1 comment

#24 - Resolve `DhMultiviewCommonColumns` naming issue

Issue - State: closed - Opened by pkalita-lbl almost 2 years ago - 3 comments

#23 - switch packed multivalue string delimiter from `|` to `!` ?

Issue - State: open - Opened by turbomam almost 2 years ago - 3 comments
Labels: yq

#22 - generated excel file includes a DhInterface tab with no populated columns

Issue - State: closed - Opened by turbomam almost 2 years ago - 1 comment

#21 - can't update to sheets-and-friends 0.2.0

Issue - State: closed - Opened by turbomam almost 2 years ago

#20 - oxy_stat_samp failing validation in WaterInterface

Issue - State: closed - Opened by turbomam almost 2 years ago

#19 - Validations for WaterInterface, inc. patterns, applied with yq

Pull Request - State: closed - Opened by turbomam almost 2 years ago - 2 comments

#18 - patterns for WaterInterface

Issue - State: closed - Opened by turbomam almost 2 years ago

#17 - Standardize multiple examples

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#16 - Pin slot imports to latest main schema release

Pull Request - State: closed - Opened by pkalita-lbl almost 2 years ago

#15 - Generate submission schema from specific version of main schema

Issue - State: closed - Opened by pkalita-lbl almost 2 years ago - 1 comment

#14 - examples/output instead of src/data/output

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#13 - add rdf/ttl output to run-linkml-examples

Issue - State: closed - Opened by turbomam almost 2 years ago - 2 comments

#12 - don't write to src/data/output

Issue - State: closed - Opened by turbomam almost 2 years ago

#11 - start adding patterns back

Issue - State: closed - Opened by turbomam almost 2 years ago

#10 - apply schema fixer

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

#9 - add linkml-rendering of example data

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

#8 - add SQLite dump of some sample data

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#7 - check-jsonschema

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#6 - closed jsonschema take two

Pull Request - State: closed - Opened by turbomam almost 2 years ago

#5 - add check-jsonschema

Issue - State: closed - Opened by turbomam almost 2 years ago

#4 - add sqldb dumping

Issue - State: closed - Opened by turbomam almost 2 years ago

#3 - eliminate need for --no-validate re elev = numeric?

Issue - State: closed - Opened by turbomam almost 2 years ago

#2 - closed jsonschema

Pull Request - State: closed - Opened by turbomam almost 2 years ago