Ecosyste.ms: Issues

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GitHub / phyloref/jphyloref issues and pull requests

#104 - Bump json from 20180130 to 20230227

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#103 - Bump spotless-maven-plugin from 1.15.0 to 1.20.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#102 - Add JOSS URL to README

Pull Request - State: closed - Opened by gaurav almost 3 years ago - 1 comment

#101 - Release of JPhyloRef v1.1.1

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

#100 - Fixes minor errors resulting from previous edits

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

#99 - Minor fixes to paper/paper.md

Issue - State: closed - Opened by jcoliver almost 3 years ago

#98 - Updated Cellinese 2021 citation to "accepted"

Pull Request - State: closed - Opened by gaurav almost 3 years ago - 6 comments

#97 - JPhyloRef v1.1.0 release

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

#96 - Introduces Statement of Need section

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

#95 - Remove "phylogenetic" when referring to clade definitions

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

#93 - Consider use of term "clade" vs. "phylogenetic clade"

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

#92 - Update README execution example

Issue - State: closed - Opened by jcoliver almost 3 years ago

#91 - Rearrange paper as per reviewer comment

Pull Request - State: closed - Opened by gaurav about 3 years ago - 6 comments

#90 - Fix IntelliJ settings

Pull Request - State: open - Opened by gaurav about 3 years ago

#89 - Improve documentation

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

#88 - Documentation: Example usage

Issue - State: closed - Opened by iimog about 3 years ago

#87 - Documentation: statement of need

Issue - State: closed - Opened by iimog about 3 years ago

#86 - Fix XML/Markdown/JSON formatting

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

#85 - Remove JFact as a supported reasoner

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

#84 - Improvements made in response to JOSS reviewer suggestions

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

#83 - Illegal reflective access in com.google.inject.internal.cglib.core.$ReflectUtils$2

Issue - State: closed - Opened by iimog about 3 years ago - 2 comments

#82 - Lots of WARNINGs when building jphyloref

Issue - State: closed - Opened by iimog about 3 years ago - 2 comments

#81 - Need to set JAVA_HOME to build jphyloref

Issue - State: closed - Opened by iimog about 3 years ago - 2 comments

#80 - Clarify readme

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

#79 - Added JOSS paper to submit

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

#78 - Removed FaCT++ JNI as a built-in reasoner

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

#77 - JPhyloRef v1.0.0

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

#76 - Add build/execute instructions and Maven Central badge to README

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

#75 - Add javadoc.io badge

Pull Request - State: closed - Opened by gaurav over 3 years ago - 2 comments

#73 - JPhyloRef v0.4.0

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

#72 - Switch to Github Actions

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

#71 - Skip phyloreferences without expected resolution during testing

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

#70 - Add the explicit import for OWL API

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

#69 - Write up manuscript to submit to JOSS

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

#68 - Release v0.3.1

Pull Request - State: closed - Opened by gaurav about 4 years ago - 1 comment

#67 - Fix bug in return value

Pull Request - State: closed - Opened by gaurav about 4 years ago

#66 - Release v0.3 of JPhyloRef

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

#65 - Add the filename to the testing output

Pull Request - State: closed - Opened by gaurav about 4 years ago

#63 - Added support for receiving JSON-LD files compressed with Gzip

Pull Request - State: closed - Opened by gaurav over 4 years ago - 1 comment

#62 - Make WebserverCommand work on macOS

Pull Request - State: closed - Opened by gaurav over 4 years ago

#60 - Use model 2.0 expected resolution information

Pull Request - State: closed - Opened by gaurav almost 5 years ago - 1 comment

#59 - Document how we execute JPhyloRef on our backend server

Pull Request - State: closed - Opened by gaurav almost 5 years ago - 1 comment

#58 - Update TestCommand to use Model 2.0 expectations

Issue - State: closed - Opened by gaurav almost 5 years ago
Labels: programming only

#57 - Improve testing of false negatives and resolving to multiple nodes

Issue - State: open - Opened by gaurav almost 5 years ago
Labels: programming only

#56 - Replace System.err with SLF4J calls

Pull Request - State: closed - Opened by gaurav almost 5 years ago

#55 - Update README with instructions on use

Pull Request - State: closed - Opened by gaurav almost 5 years ago

#54 - Moved Phyloref resolution code into PhylorefHelper

Pull Request - State: closed - Opened by gaurav almost 5 years ago

#53 - Centralize code for identifying resolved nodes

Issue - State: closed - Opened by gaurav almost 5 years ago

#52 - Created a ResolveCommand to resolve phylorefs from the command line

Pull Request - State: closed - Opened by gaurav almost 5 years ago

#51 - Replace information and error messages written to STDERR with calls to SLF4J

Issue - State: closed - Opened by gaurav about 5 years ago
Labels: programming only

#50 - Publish JPhyloRef to the Maven Central Repository

Issue - State: closed - Opened by gaurav about 5 years ago
Labels: programming only

#49 - Add tests for WebserverCommand

Issue - State: open - Opened by gaurav over 5 years ago
Labels: programming only, testing

#48 - Remove ReasonerCommand

Pull Request - State: closed - Opened by gaurav over 5 years ago

#47 - Switch to model 2.0 and add support for the Elk reasoner

Pull Request - State: closed - Opened by gaurav over 5 years ago

#46 - Updated phyx.js context URI in test files

Pull Request - State: closed - Opened by gaurav over 5 years ago

#45 - Add support for Model 2.0

Issue - State: closed - Opened by gaurav over 5 years ago - 1 comment

#44 - Replaced Phyloref Ontology URIs with version URIs in tests

Pull Request - State: closed - Opened by gaurav over 5 years ago

#43 - Replace method for identifying testable Phyloreferences

Issue - State: closed - Opened by gaurav over 5 years ago - 1 comment

#42 - Replace ontology.phyloref.org URLs with version IRIs

Issue - State: closed - Opened by gaurav over 5 years ago - 1 comment

#41 - Update README

Issue - State: closed - Opened by gaurav over 5 years ago
Labels: programming only

#40 - Eliminate reporting 'skipped' phyloreferences

Issue - State: closed - Opened by gaurav over 5 years ago - 1 comment
Labels: programming only

#39 - Modifies .travis.yml to cache Maven downloads.

Pull Request - State: closed - Opened by gaurav over 5 years ago

#38 - Add support for Whelk

Pull Request - State: closed - Opened by gaurav over 5 years ago

#37 - Set up hosting JPhyloRef on a server

Issue - State: closed - Opened by gaurav over 5 years ago - 2 comments

#36 - Allow TestCommand to read ontologies from STDIN

Pull Request - State: closed - Opened by gaurav over 5 years ago

#35 - Add support for JSON-LD to TestCommand

Pull Request - State: closed - Opened by gaurav over 5 years ago

#34 - Eliminated getReasonerNameAndVersion() crash when a JNI is not linked

Pull Request - State: closed - Opened by gaurav over 5 years ago - 1 comment

#33 - Updated .gitignore to ignore .DS_Store files

Pull Request - State: closed - Opened by gaurav over 5 years ago

#32 - Added Spotless as a code style enforcer

Pull Request - State: closed - Opened by gaurav over 5 years ago - 1 comment

#31 - Add a verbose mode for improved debugging

Issue - State: open - Opened by gaurav over 5 years ago - 1 comment
Labels: programming only

#30 - Add basic test suite

Pull Request - State: closed - Opened by gaurav over 5 years ago - 2 comments

#29 - Fixed incorrect code merged in #17

Pull Request - State: closed - Opened by gaurav over 5 years ago

#28 - Add support for OASIS XML Catalog files

Issue - State: open - Opened by gaurav over 5 years ago - 1 comment
Labels: programming only

#27 - Write out reasoner information during TestCommand/WebserverCommand

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#26 - Adds support for JSON-LD files with relative URIs

Pull Request - State: closed - Opened by gaurav almost 6 years ago - 6 comments

#25 - Updated WebserverCommand to use local ontologies if available

Pull Request - State: closed - Opened by gaurav almost 6 years ago - 1 comment

#23 - Fixes bug in running JPhyloRef without specifying which reasoner to use

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#21 - Add support for rule-based reasoners

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

#20 - Add support for FaCT++ as an alternate reasoner

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#19 - Added slf4j-simple as a dependency to close #18

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#18 - SLJ4F warnings when running JPhyloRef

Issue - State: closed - Opened by gaurav almost 6 years ago

#17 - Refactored Phyloref status checking code

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#16 - Updated Phyloref ontology IRI as per phyloref/phyloref-ontology#21

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#15 - JPhyloRef should ignore errors in phyloreferences marked deprecated

Issue - State: open - Opened by gaurav almost 6 years ago - 2 comments
Labels: programming only

#14 - Updated CHANGELOG as should have been carried out in PR #12 and #13

Pull Request - State: closed - Opened by gaurav almost 6 years ago

#13 - Removed some Eclipse files that shouldn't be in Git; added to .gitignore

Pull Request - State: closed - Opened by hlapp almost 6 years ago - 1 comment

#12 - Added a "webserver" command that provides an HTTP API for reasoning

Pull Request - State: closed - Opened by gaurav almost 6 years ago - 1 comment

#11 - Get rid of RDFHandler hack

Issue - State: closed - Opened by gaurav almost 6 years ago
Labels: programming only

#10 - Upgrade JFact to 5.0.1

Pull Request - State: closed - Opened by gaurav about 6 years ago - 1 comment

#7 - Phyloreference without expected resolution appears to resolve correctly

Issue - State: closed - Opened by gaurav about 6 years ago - 1 comment
Labels: bug

#5 - Add support for ignoring unnecessary specifiers

Issue - State: open - Opened by gaurav over 6 years ago - 1 comment
Labels: programming only

#4 - Add support for switching reasoners

Issue - State: closed - Opened by gaurav over 6 years ago - 3 comments

#3 - Add a test suite

Issue - State: closed - Opened by gaurav over 6 years ago