Ecosyste.ms: Issues

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GitHub / linkml/schema-automator issues and pull requests

#100 - Trouble installing schema-automator into semantic-synbio/synbio-schema

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

#99 - Help with `AttributeError: 'NoneType' object has no attribute 'classes'`

Issue - State: open - Opened by matentzn about 2 years ago - 6 comments

#98 - OMOP test case: generalize-tsv

Pull Request - State: closed - Opened by matentzn about 2 years ago - 4 comments

#97 - update oaklib to help with main branch test failures

Issue - State: closed - Opened by sierra-moxon about 2 years ago
Labels: bug

#96 - update dependencies fixes #95 fixes #97

Pull Request - State: closed - Opened by sierra-moxon about 2 years ago

#94 - Using inflect library to depluralize class names when generalizing.

Pull Request - State: closed - Opened by cmungall about 2 years ago

#92 - Improved docs for annotator

Pull Request - State: closed - Opened by cmungall about 2 years ago

#91 - poetry cli target for import-sql

Pull Request - State: closed - Opened by sujaypatil96 about 2 years ago - 1 comment
Labels: enhancement

#90 - Added toml generalizer

Pull Request - State: closed - Opened by cmungall about 2 years ago

#89 - Use json2python-models as a generalizer

Issue - State: open - Opened by cmungall about 2 years ago

#88 - Write a pydantic-importer (pydantic class -> LinkML YAML)

Issue - State: open - Opened by cmungall about 2 years ago - 1 comment
Labels: good first issue

#87 - Write an XML Schema importer

Issue - State: open - Opened by cmungall about 2 years ago - 1 comment
Labels: generator-misc

#86 - Additional tests and documentation

Pull Request - State: closed - Opened by cmungall about 2 years ago

#85 - `convert_dicts` throws a TypeError with nested lists

Issue - State: open - Opened by ialarmedalien about 2 years ago
Labels: bug

#84 - Added generalization using panderas

Pull Request - State: closed - Opened by cmungall about 2 years ago

#83 - Add ability to import a schema from an HTML table

Issue - State: open - Opened by cmungall about 2 years ago
Labels: convert

#82 - Re committing sql_importer.

Pull Request - State: closed - Opened by cmungall about 2 years ago

#81 - doc-fixes-bullets

Pull Request - State: closed - Opened by cmungall about 2 years ago

#80 - Enhancing sphinx docs

Pull Request - State: closed - Opened by cmungall about 2 years ago

#79 - Added frictionless importer

Pull Request - State: closed - Opened by cmungall about 2 years ago

#78 - First pass at SQL Importer. See #67

Pull Request - State: closed - Opened by cmungall about 2 years ago

#77 - Schema enricher and Docker config

Pull Request - State: closed - Opened by cmungall about 2 years ago

#76 - Dockerize this package

Issue - State: closed - Opened by cmungall about 2 years ago

#75 - refactoring

Pull Request - State: closed - Opened by cmungall over 2 years ago

#73 - pypi

Pull Request - State: closed - Opened by cmungall over 2 years ago

#72 - update pypi release action

Pull Request - State: closed - Opened by cmungall over 2 years ago

#71 - removing unused files

Pull Request - State: closed - Opened by cmungall over 2 years ago

#70 - Refactored package layout and command line interface

Pull Request - State: closed - Opened by cmungall over 2 years ago

#69 - Small fixes to automator

Pull Request - State: closed - Opened by matentzn over 2 years ago

#68 - set version to 0.0.0 and added authors

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

#67 - Add ability to bootstrap a linkml schema from a SQL DDL

Issue - State: closed - Opened by cmungall over 2 years ago - 1 comment

#66 - Make README concise and change documentation theme.

Pull Request - State: closed - Opened by hrshdhgd over 2 years ago

#65 - Sphinx docs

Pull Request - State: closed - Opened by hrshdhgd over 2 years ago

#64 - create a site using sphinx

Issue - State: closed - Opened by cmungall over 2 years ago

#63 - add commands for jsonschema translator to pyproject.toml

Pull Request - State: closed - Opened by sierra-moxon over 2 years ago

#62 - add working token for pypi

Pull Request - State: closed - Opened by sierra-moxon over 2 years ago

#61 - refactor code to use new name in prep for release on pypi

Pull Request - State: closed - Opened by sierra-moxon over 2 years ago

#60 - owlimports schemaorg

Pull Request - State: closed - Opened by cmungall over 2 years ago

#59 - Address issues from PR #47

Issue - State: open - Opened by cmungall over 2 years ago - 1 comment

#58 - uses schema.org rangeincludes/domain includes

Pull Request - State: closed - Opened by cmungall over 2 years ago

#57 - docs(readme): update installation section

Pull Request - State: closed - Opened by noelmcloughlin over 2 years ago - 1 comment

#56 - General repo maintenance

Issue - State: open - Opened by sujaypatil96 over 2 years ago - 5 comments
Labels: enhancement, backlog, low priority

#55 - rename this repo

Issue - State: closed - Opened by cmungall over 2 years ago - 1 comment

#54 - EBI OLS started returning XMLHttpRequest instead of JSON?!

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

#53 - Loss of non-ASCII characters in enum annotation

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

#52 - provide cleanup from enum annotation annotations

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

#51 - enum_annotator: title is not a recommended slot on permissible values

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

#49 - how to collapse multiple PVs mapped to the same meaning?

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

#48 - add ubiquity count to enums_to_curateable

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

#47 - Mark cumulative

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

#46 - Mark combined testing

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

#45 - Update check-pull-request.yaml

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

#44 - moved one failing test to pre_poetry #43

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

#43 - resinstate tests

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

#42 - Choose who owns linkml-model-enrichment in PyPI and what metadata should be used

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

#41 - test DF sizes #35

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

#40 - don't pin requirment versions so hard

Issue - State: closed - Opened by turbomam over 2 years ago - 2 comments
Labels: enhancement

#39 - TSV report of the enums and permissible values #38

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

#38 - simple TSV dump of enum and pv names

Issue - State: closed - Opened by turbomam over 2 years ago
Labels: enhancement

#37 - files for GH action #33 #23

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

#36 - Add documentation for post-annotation enum curation scripts

Issue - State: closed - Opened by turbomam over 2 years ago - 1 comment
Labels: documentation, enhancement

#35 - enum_annotator.py chokes on some of the enums from the NMDC DH model

Issue - State: closed - Opened by turbomam over 2 years ago - 1 comment
Labels: bug

#34 - Update README

Issue - State: closed - Opened by turbomam over 2 years ago - 1 comment
Labels: documentation, enhancement

#33 - shift GH actions to poetry instead of pip?

Issue - State: closed - Opened by turbomam over 2 years ago - 5 comments
Labels: enhancement

#32 - added trim_parentheticals to enum_annotator #31

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

#31 - truncate trailing parenthetical portions of enum queries

Issue - State: closed - Opened by turbomam over 2 years ago
Labels: enhancement

#30 - match_id annotation for #19

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

#29 - Issue 19

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

#28 - added jsonld context annotator

Pull Request - State: closed - Opened by cmungall over 2 years ago - 2 comments

#27 - possibly redundant with #22 from upstream repo?

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

#26 - tidying - may be redundant with latest version

Pull Request - State: closed - Opened by cmungall almost 3 years ago

#25 - schema annotator

Pull Request - State: closed - Opened by cmungall almost 3 years ago

#24 - Issue #22 enum anno evo

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

#23 - Try switching to poetry in this repo

Issue - State: closed - Opened by turbomam almost 3 years ago - 6 comments
Labels: enhancement, devops

#22 - PR for evolved enum annotator and manual review components

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

#21 - review annotator

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

#20 - consider a more conventional approach to http requests in annotate-enums

Issue - State: closed - Opened by cmungall almost 3 years ago - 1 comment

#19 - Annotate meanings

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment
Labels: enhancement

#18 - annotator

Pull Request - State: closed - Opened by cmungall almost 3 years ago

#17 - add a method to generate edge slots from a TSV

Pull Request - State: closed - Opened by sierra-moxon almost 3 years ago

#16 - biopax

Pull Request - State: closed - Opened by cmungall almost 3 years ago

#15 - document "requirement" for "pip install -e ."

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

#14 - rdflib and other pip incompatibilities

Issue - State: closed - Opened by turbomam almost 3 years ago - 8 comments
Labels: bug

#13 - json instance import

Pull Request - State: closed - Opened by cmungall about 3 years ago - 1 comment

#12 - General debugging in advance of ICBO 2021

Issue - State: closed - Opened by turbomam about 3 years ago - 1 comment
Labels: bug

#11 - jsonschema-and-dosdps

Pull Request - State: closed - Opened by cmungall about 3 years ago

#10 - Infer from owl

Pull Request - State: closed - Opened by cmungall about 3 years ago

#9 - Refactor all_enums_to_ols to avoid globals

Issue - State: closed - Opened by cmungall about 3 years ago - 3 comments

#8 - Adding inference from OWL schemas and RDF instance graphs

Pull Request - State: closed - Opened by cmungall about 3 years ago

#7 - infer_model.py intermittently has problems parsing dates in non date cols?

Issue - State: closed - Opened by turbomam about 3 years ago - 1 comment
Labels: bug

#5 - todo (before merging webmap code into main ?)

Issue - State: open - Opened by turbomam over 3 years ago - 3 comments

#4 - temporarily disabled test action

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

#3 - can't get infer_model.py started

Issue - State: closed - Opened by turbomam over 3 years ago - 1 comment
Labels: bug

#2 - web based term mapping

Pull Request - State: closed - Opened by turbomam over 3 years ago - 3 comments

#1 - Add bioportal annotator code

Issue - State: closed - Opened by cmungall over 3 years ago - 1 comment