Ecosyste.ms: Issues

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GitHub / microbiomedata/submission-schema issues and pull requests

#293 - Bump `nmdc-schema` version from `11.3.0rc1` to `11.3.0`

Pull Request - State: closed - Opened by eecavanna 17 days ago

#292 - Build process leaves residual `temp_target` file on file system

Issue - State: open - Opened by eecavanna 17 days ago
Labels: x small

#291 - Update submission schema to use `nmdc-schema` version `11.3.0`

Issue - State: closed - Opened by eecavanna 17 days ago
Labels: x small

#288 - non-oak discovery of EnvO class/subset relations

Pull Request - State: open - Opened by turbomam 22 days ago

#287 - builds at @turbomam's Ubuntu command prompt, but not within PyCharm

Issue - State: closed - Opened by turbomam 24 days ago - 10 comments

#285 - build robot templates for ENVO subset membership

Issue - State: open - Opened by turbomam 24 days ago - 1 comment

#284 - Ensure all examples in schema validate

Pull Request - State: closed - Opened by pkalita-lbl about 1 month ago - 5 comments

#283 - Notebooks for `Water` environmental context value sets

Pull Request - State: closed - Opened by turbomam about 1 month ago - 2 comments

#282 - DNA sample name doesn't allow "." in names, but it should

Issue - State: open - Opened by mslarae13 about 2 months ago - 5 comments

#281 - Upgrade to `nmdc-schema` v11.2.1

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

#280 - post-voting env triad value set serialization

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

#279 - Update submission schema to use `nmdc-schema` version `11.2.1`

Issue - State: closed - Opened by eecavanna 2 months ago - 2 comments
Labels: help wanted, x small

#277 - Containerize the build process and fill in developer documentation

Pull Request - State: closed - Opened by eecavanna 3 months ago - 7 comments

#276 - Write test output to temp file instead of back to input file

Pull Request - State: closed - Opened by pkalita-lbl 3 months ago

#275 - Implement a Docker-based build environment for the submission schema

Issue - State: closed - Opened by eecavanna 3 months ago - 1 comment
Labels: x small

#274 - Upgrade nmdc-schema to 11.1.0

Pull Request - State: closed - Opened by pkalita-lbl 3 months ago - 1 comment

#273 - Developer documentation does not say to install `yq` before running `make all`

Issue - State: closed - Opened by eecavanna 3 months ago - 9 comments
Labels: bug, documentation, x small

#272 - Update submission schema to use `nmdc-schema` version `11.1.0`

Issue - State: closed - Opened by eecavanna 3 months ago - 1 comment

#271 - Developer documentation does not say to run `poetry install` before running `make all`

Issue - State: closed - Opened by eecavanna 3 months ago
Labels: documentation, x small

#270 - new voting sheets, generated in Python (notebook) not Makefile

Pull Request - State: closed - Opened by turbomam 3 months ago - 4 comments

#268 - quick prototype of voting sheet generation in notebook in this repo

Issue - State: closed - Opened by turbomam 3 months ago - 1 comment

#266 - add new water, sediment TSVs to the enum population scripts

Issue - State: closed - Opened by sierra-moxon 3 months ago - 1 comment

#262 - re-emphasize voting and GOLD mappings

Pull Request - State: closed - Opened by turbomam 3 months ago

#260 - add PV terms from env triad to schema

Pull Request - State: closed - Opened by sierra-moxon 3 months ago - 2 comments

#259 - Syntax error in graph mermaid version 8.8.0 on SoilInterface docs page

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

#257 - notebook re-articulations of environmental triad google sheets consensus

Pull Request - State: closed - Opened by turbomam 3 months ago - 2 comments

#254 - Makefile etc cleanup

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

#253 - makefile cleanup: identify out-dated code; extract todos into issues

Issue - State: open - Opened by turbomam 3 months ago - 1 comment

#252 - Add validation to EMSL and JGI project IDs

Issue - State: open - Opened by mslarae13 3 months ago

#251 - re-synchronized .PHONY lists

Pull Request - State: closed - Opened by turbomam 3 months ago

#250 - removed incomplete/buggy oak enums workflow

Pull Request - State: closed - Opened by turbomam 3 months ago

#249 - remove OAK/enums stuff

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

#248 - audit phony targets

Issue - State: closed - Opened by turbomam 3 months ago

#247 - templated schema-as-yaml modifier

Pull Request - State: open - Opened by turbomam 3 months ago - 1 comment

#244 - delete `rules_test/`

Pull Request - State: closed - Opened by turbomam 3 months ago

#243 - Don't generate Excel schema artifact

Pull Request - State: closed - Opened by turbomam 3 months ago

#241 - remove `rules_test/` ?

Issue - State: closed - Opened by turbomam 3 months ago

#240 - no placeholder descriptions

Pull Request - State: closed - Opened by turbomam 3 months ago

#239 - remove placeholder descriptions from enums, etc.

Issue - State: closed - Opened by turbomam 3 months ago

#238 - what schema derivatives do we really want to generate?

Issue - State: closed - Opened by turbomam 3 months ago

#237 - create post-clean target

Pull Request - State: closed - Opened by turbomam 3 months ago

#236 - remove test-like conversions and dumps

Pull Request - State: closed - Opened by turbomam 3 months ago

#235 - move scripts to src/scripts

Pull Request - State: closed - Opened by turbomam 3 months ago

#233 - eliminate some testing like `linkml-sqldb` dump ?

Issue - State: closed - Opened by turbomam 3 months ago - 1 comment

#232 - delete generated local files etc. before and after build?

Issue - State: closed - Opened by turbomam 3 months ago - 1 comment

#230 - Identify which types of schema modifications are currently performed by `yq`

Issue - State: open - Opened by pkalita-lbl 4 months ago - 5 comments
Labels: yq

#228 - Upgrade to `nmdc-schema` v11.0.1

Pull Request - State: closed - Opened by pkalita-lbl 4 months ago - 1 comment

#224 - Update 'data set' DOI to award DOI, multivalued, capture source/authority

Issue - State: closed - Opened by mslarae13 5 months ago - 17 comments

#223 - add guidance for study description (no links)

Issue - State: open - Opened by mslarae13 5 months ago - 2 comments

#222 - Upgrade to nmdc-schema v11.0.0rc20

Pull Request - State: closed - Opened by pkalita-lbl 5 months ago

#221 - Review NMDC submission schema for berkeley-schema needed changes

Issue - State: closed - Opened by mslarae13 5 months ago - 2 comments

#220 - Create submission-schema using Berkeley-schema

Issue - State: closed - Opened by mslarae13 5 months ago - 16 comments

#219 - Documentation and devOps maintenance

Pull Request - State: open - Opened by sujaypatil96 6 months ago - 4 comments

#218 - nmdc-schema v10.8.0

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

#216 - Upgrade to nmdc-schema 1.7.0

Pull Request - State: closed - Opened by pkalita-lbl 7 months ago

#215 - Add excel_worksheet_name annotations to DhInterface subclasses

Pull Request - State: closed - Opened by pkalita-lbl 7 months ago - 3 comments

#214 - Upgrade to nmdc-schema 10.6.0

Pull Request - State: closed - Opened by pkalita-lbl 7 months ago

#212 - Consolidate storage condition terms

Issue - State: open - Opened by pvangay almost 3 years ago - 3 comments
Labels: GSP2023, documentation, enhancement

#211 - Make description and guidance for "sample linkage" consistent

Issue - State: open - Opened by pvangay almost 3 years ago - 1 comment
Labels: GSP2023, documentation

#210 - sample shipped amount: add validation of units

Issue - State: open - Opened by pvangay almost 3 years ago
Labels: question

#209 - Provide improved guidance for “experimental factor- other"

Issue - State: open - Opened by pvangay almost 3 years ago - 1 comment
Labels: GSP2023, question

#208 - “DNA Sample ID” should be unique

Issue - State: open - Opened by pvangay almost 3 years ago - 2 comments
Labels: enhancement

#207 - Add GOLD treeviewer to GOLD term guidance

Issue - State: open - Opened by pvangay almost 3 years ago - 1 comment
Labels: enhancement

#206 - implicit units should go in column header

Issue - State: open - Opened by turbomam about 3 years ago

#204 - create `examples/output/` again

Pull Request - State: closed - Opened by turbomam 7 months ago - 1 comment

#203 - Filled in missing modifications

Pull Request - State: closed - Opened by bmeluch 7 months ago

#199 - Find a home for these notes about yq rule injection

Issue - State: open - Opened by turbomam 9 months ago
Labels: yq

#198 - moved most yq commands and comments

Pull Request - State: open - Opened by turbomam 9 months ago - 2 comments
Labels: yq

#194 - Missing actions in modifications_long.tsv

Issue - State: closed - Opened by bmeluch 10 months ago - 5 comments
Labels: yq

#180 - remove everything from src/data besides valid and invalid

Pull Request - State: closed - Opened by turbomam about 1 year ago - 17 comments
Labels: backlog

#178 - move yq commands out of project.Makefile and into a configuration file

Issue - State: open - Opened by turbomam about 1 year ago - 5 comments
Labels: yq

#172 - The headers of the NMDC website don't match the products

Issue - State: closed - Opened by mslarae13 about 1 year ago - 8 comments