Ecosyste.ms: Issues

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GitHub / fair-workflows/nanopub issues and pull requests

#167 - Integrate Local Blazegraph SPARQL Endpoint

Pull Request - State: open - Opened by rahules24 about 1 month ago

#166 - `np setup` fails to parse newly-generated keypair

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

#165 - Fix nanopub-java version to 1.47

Pull Request - State: closed - Opened by vemonet 10 months ago

#164 - np setup fails

Issue - State: open - Opened by ronentk 11 months ago - 1 comment

#163 - NanopubClient server recon fails on timeouts

Issue - State: open - Opened by Ostrzyciel about 1 year ago

#162 - Fix searching for nanopubs example in docs

Pull Request - State: closed - Opened by Ostrzyciel about 1 year ago - 2 comments

#161 - nanopub.org not working

Issue - State: open - Opened by nicola883 over 1 year ago - 7 comments

#160 - Improve dependencies versioning

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

#159 - Yatiml dependencies creates conflicts

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

#158 - Fix how introduces_concept is handled

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

#157 - Add RSD badge for nanopub

Pull Request - State: closed - Opened by raar1 about 2 years ago

#156 - Major update to the nanopub API, adding signing in python, removing java dependency

Pull Request - State: closed - Opened by vemonet about 2 years ago - 7 comments

#155 - Bump version to 1.2.11

Pull Request - State: closed - Opened by raar1 about 2 years ago

#154 - Add new author new release 1.2.11

Pull Request - State: closed - Opened by raar1 about 2 years ago

#153 - Delete azure-devops-sync.yml

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

#152 - Allow rdflib v5 and v6

Pull Request - State: closed - Opened by raar1 about 2 years ago

#149 - Making the addition of `prov:generatedAtTime` and `prov:wasAttributedTo` optional

Issue - State: closed - Opened by vemonet about 2 years ago - 5 comments

#148 - Error due to `.decode('utf-8')`

Issue - State: closed - Opened by vemonet about 2 years ago - 4 comments

#147 - typo fix

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

#146 - Automatic validation of your citation metadata

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

#145 - Update requirements

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

#144 - Include LICENSE in manifest

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

#143 - Also publish sdist to pypi

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

#141 - Add license for nanopub-java

Pull Request - State: closed - Opened by svenvanderburg over 3 years ago - 1 comment

#140 - Use 3-arg click callback for `validate_orcid_id`

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

#139 - Adding / changing provenance_rdf information doesn't do any changes

Issue - State: closed - Opened by evaevertovna over 3 years ago - 6 comments
Labels: bug

#138 - Issue135 no overwrite keys

Pull Request - State: closed - Opened by raar1 over 3 years ago

#137 - Pin click to 7.1.2 until we work out why click 8 is breaking setup_na…

Pull Request - State: closed - Opened by raar1 over 3 years ago

#136 - setup_nanopub_profile broken by click 8.0.0

Issue - State: closed - Opened by raar1 over 3 years ago - 1 comment

#135 - setup_nanopub_profile should not overwrite keys

Issue - State: closed - Opened by raar1 over 3 years ago

#134 - Fetching DisGeNET, neXtProt, and WikiPathways nanopublications fail

Issue - State: closed - Opened by ImranAsif48 over 3 years ago - 6 comments
Labels: bug

#133 - Fix overwriting of pubinfo and prov rdf

Pull Request - State: closed - Opened by raar1 over 3 years ago

#132 - Issue131 nanopub mutating rdf

Pull Request - State: closed - Opened by raar1 over 3 years ago

#131 - Nanopub mutates user rdf when publishing

Issue - State: closed - Opened by raar1 over 3 years ago
Labels: bug

#130 - Make a conda package for nanopub

Issue - State: closed - Opened by raar1 over 3 years ago - 3 comments

#129 - Issue128 pubinfo wasattributedto

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#127 - Fix FileAlreadyExists bug in setup_nanopub_profile

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#126 - Fix FileAlreadyExistsException when reusing old RSA keys

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

#125 - Add azure devops sync github action

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#124 - Add more tests 20210122

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#123 - Validate orcid should also calculate checksum

Issue - State: open - Opened by raar1 almost 4 years ago - 1 comment
Labels: low priority

#122 - Add utf8 flags to java call in nanopub-java

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#121 - Issue119 orcid regex

Pull Request - State: closed - Opened by raar1 almost 4 years ago
Labels: bug

#120 - Deprecation warning coming from click

Issue - State: closed - Opened by raar1 almost 4 years ago

#119 - Some valid ORCIDs do not match the regex check

Issue - State: closed - Opened by raar1 almost 4 years ago - 1 comment
Labels: bug

#118 - Add CI for Windows

Issue - State: closed - Opened by svenvanderburg almost 4 years ago
Labels: low priority

#117 - Issue111 json decode error empty search result

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#116 - Issue115 rename setup profile

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#115 - Rename setup_profile to setup_nanopub_profile

Issue - State: closed - Opened by raar1 almost 4 years ago

#114 - Potential problem with Nanopub in use with Nanotate

Issue - State: closed - Opened by raar1 almost 4 years ago - 6 comments

#113 - Rename tox.ini to setup.cfg to avoid confusion

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#112 - Searching with spaces results in error

Issue - State: open - Opened by svenvanderburg almost 4 years ago - 4 comments
Labels: low priority

#111 - JSONDecodeError when search result is empty

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

#110 - Fetching a publication, modifying, and republishing fails

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 5 comments
Labels: bug, wontfix

#109 - Bump version to v1.2.0

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#108 - Nanopub release blog post

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#107 - Add bin/nanopub-java.bat and include it in installation for windows

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#106 - ModuleNotFoundError: No module named 'ruamel'

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 13 comments
Labels: question, wontfix

#105 - Add pagination of search results

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#104 - Update CHANGELOG.md

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#103 - Bin lib java dependency

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#102 - nanopub-java installed upon installation instead of runtime

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#101 - Add zenodo badge

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#100 - Bump version to 1.1.0

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#99 - Add conditional skip of publishing coverage when token is not there

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#97 - Check if nanopub works on Windows?

Issue - State: closed - Opened by raar1 almost 4 years ago - 1 comment

#96 - Add .zenodo.json

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago - 2 comments

#95 - Fix publish coverage error

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 3 comments

#94 - Add find signed valid nanopublications calls

Pull Request - State: closed - Opened by vemonet almost 4 years ago

#93 - Expand functionality on knowing about retractions

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#92 - Add methods to NanopubClient for 'valid_signed' endpoints

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#91 - Catch FileNotFoundError when profile file does not exist

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#90 - Fix link to what are nanopubs documentation

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#89 - Pagination of search results

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#88 - permission denied when creating nanopub-java jar file

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 3 comments

#87 - Catch FileNotFoundError if profile is not setup yet

Issue - State: closed - Opened by svenvanderburg almost 4 years ago

#86 - Link to documentation in README is broken

Issue - State: closed - Opened by raar1 almost 4 years ago

#85 - max_num_results default is unclear/confusing

Issue - State: closed - Opened by raar1 almost 4 years ago - 1 comment

#83 - Expand functionality on knowing about retractions

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 8 comments

#82 - Bump to version 1.0.0

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#81 - Issue80 increase test coverage

Pull Request - State: closed - Opened by raar1 almost 4 years ago

#80 - Get test coverage up before release

Issue - State: closed - Opened by raar1 almost 4 years ago - 1 comment

#79 - Fix search result and add documentation on it.

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#78 - Disemmination of nanopub library upon release

Issue - State: closed - Opened by raar1 almost 4 years ago - 5 comments

#77 - Fix and document search result

Issue - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#76 - Add software quality checklist

Issue - State: closed - Opened by raar1 almost 4 years ago - 4 comments

#75 - Update CONTRIBUTING.md for having flake configuration in tox.ini

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#74 - Update CONTRIBUTIONS to reflect tox usage

Issue - State: closed - Opened by raar1 almost 4 years ago

#73 - Add a changelog

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago - 1 comment

#72 - Use provenance_rdf arg for from_assertion in claim method

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#71 - Fix flake8 complaints, and make it fail on builds in github action

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#70 - Fix small stuf

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#69 - Add documentation about the different nanopub elements

Pull Request - State: closed - Opened by svenvanderburg almost 4 years ago

#63 - Add a changelog

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