Ecosyste.ms: Issues

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GitHub / rothamsted/knetminer issues and pull requests

#810 - Bump jakarta.xml.bind:jakarta.xml.bind-api from 4.0.1 to 4.0.2

Pull Request - State: open - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#809 - Bump com.sun.xml.bind:jaxb-impl from 4.0.4 to 4.0.5

Pull Request - State: open - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#808 - Bump org.apache.lucene:lucene-analyzers-common from 6.6.0 to 8.11.3

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

#807 - Bump org.eclipse.jetty:jetty-maven-plugin from 11.0.19 to 11.0.20

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

#806 - Bump org.eclipse.jetty:jetty-maven-plugin from 11.0.18 to 11.0.19

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies

#805 - "Cite Us" link leads to 404

Issue - State: closed - Opened by marco-brandizi about 1 year ago - 4 comments
Labels: bug, project:client

#804 - Can't search when the configured dataset has one specie only.

Issue - State: open - Opened by marco-brandizi over 1 year ago
Labels: bug

#803 - Define manual tests for user management

Issue - State: open - Opened by marco-brandizi over 1 year ago - 3 comments
Labels: UI-testing

#802 - Gene List Search, when the no of genes returns to a permitted value, the search button remains disabled

Issue - State: open - Opened by marco-brandizi over 1 year ago
Labels: bug, project:client, UX & UI, UI-testing

#801 - [InfiniteScrollingLocal UI Test] Filter reset button doesn't work in evidence table

Issue - State: open - Opened by marco-brandizi over 1 year ago - 1 comment
Labels: bug, project:client, UI-testing

#800 - Bump org.eclipse.jetty:jetty-maven-plugin from 11.0.17 to 11.0.18

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#799 - Bump org.codehaus.mojo:properties-maven-plugin from 1.2.0 to 1.2.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#798 - Bump com.sun.xml.bind:jaxb-impl from 4.0.0 to 4.0.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#797 - Javascript review on 20231018

Issue - State: open - Opened by marco-brandizi over 1 year ago
Labels: code review, project:client, code quality

#796 - Bump org.springframework:spring-test from 6.0.11 to 6.0.13

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#795 - Bump org.eclipse.jetty:jetty-maven-plugin from 11.0.15 to 11.0.17

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#794 - Bump org.springframework:spring-test from 6.0.11 to 6.0.12

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#793 - Bump jakarta.xml.bind:jakarta.xml.bind-api from 4.0.0 to 4.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#792 - Replace /ksHost call in loginUtils.js::getKsAPI() with /dataset-info/knetspace-url

Issue - State: open - Opened by marco-brandizi over 1 year ago
Labels: project:client, upgrades, project:knetspace

#791 - Evidence view filtering no longer works

Issue - State: open - Opened by Arnedeklerk over 1 year ago
Labels: bug

#790 - Bump org.eclipse.jetty:jetty-maven-plugin from 11.0.15 to 11.0.16

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#789 - Infinite scrolling in Evidence view never reaches the bottom

Issue - State: open - Opened by Arnedeklerk over 1 year ago - 2 comments
Labels: bug, UX & UI

#788 - Bump com.sun.xml.bind:jaxb-impl from 4.0.0 to 4.0.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#787 - Bump org.apache.lucene:lucene-analyzers-common from 6.6.0 to 8.11.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#786 - Check the KnetScore computation

Issue - State: closed - Opened by marco-brandizi over 1 year ago - 1 comment
Labels: question, project:web service

#785 - Converting Js type text/javascript to ESM modules

Issue - State: open - Opened by lawal-olaotan over 1 year ago

#784 - Evidence Distance Selector wrong

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: UX & UI

#783 - Loading CI-Test throws "Invalid user role ''" error

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: bug, UX & UI

#782 - Changing Evidence Distance removes KnetScore filter

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 4 comments
Labels: bug, UX & UI

#781 - KnetSpace login from localhost/aratiny doesn't work in Chrome, works in Firefox

Issue - State: open - Opened by marco-brandizi over 1 year ago - 2 comments
Labels: bug, project:client, project:knetspace

#780 - Gene list downloader duplicated headers.

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 5 comments
Labels: bug, project:client, UX & UI

#779 - Searching with a gene list yeilding no results loads infinitely

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 9 comments
Labels: bug, project:client, UX & UI

#778 - Creating a network with >10 genes without an account freezes UI

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: bug, UX & UI

#777 - Gene table view, Evidence detail box doesn't work anymore

Issue - State: open - Opened by marco-brandizi over 1 year ago - 4 comments
Labels: bug, project:client

#775 - Fake feature test: LLM NLP for Querying Neo4j KG using an English->Cypher Translation Layer

Issue - State: open - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: new feature, UX & UI

#774 - Reviewing Sample Queries and updating them to highlight account upgrade benefits

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 5 comments
Labels: enhancement

#773 - [BasicLocal UI Test] Copy gene accessions does not work anymore

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: bug, project:client, UI-testing

#772 - [InfiniteScrollingLocal UI Test] Type filters in Evidence view have become slow

Issue - State: closed - Opened by marco-brandizi over 1 year ago - 2 comments
Labels: bug, project:client, UI-testing

#771 - [BasicLocal UI Test] The links in the gene list columns don't work anymore

Issue - State: closed - Opened by marco-brandizi over 1 year ago - 2 comments
Labels: bug, project:client, UI-testing

#770 - Possible refactoring of CSS

Issue - State: open - Opened by marco-brandizi over 1 year ago - 1 comment
Labels: code review, code quality

#769 - Fake feature test: Summarise results

Issue - State: open - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: Fake Feature Test

#768 - User access management in the client code

Issue - State: open - Opened by marco-brandizi over 1 year ago - 7 comments
Labels: project:client

#767 - Commits Introduces Json to Knetminer UI

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

#766 - Introducing unit tests for Javascript code

Issue - State: open - Opened by marco-brandizi over 1 year ago - 1 comment
Labels: project:client, chore/infrastructure, continuous integration, UI-testing

#765 - Gene List cannot copy to clipboard from evidence view

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 2 comments
Labels: bug

#764 - Genome Region Search modifications prevent Search working

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: bug, UX & UI

#763 - Genome Region Search: Genes count needs to update more frequently

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: bug, UX & UI

#761 - [BasicCI] Testing 5.6 release candidate

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 4 comments
Labels: UI-testing

#760 - ETL Pipeline/Java Parser Issue with Special Characters

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 3 comments
Labels: resolution:can't reproduce

#759 - Cannot create network from evidence filtered gene view using hyperlinked gene accession

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 2 comments
Labels: bug

#758 - Add a “Publication Search” option, similar to Gene List, but to search for keywords in papers

Issue - State: open - Opened by Arnedeklerk over 1 year ago - 2 comments
Labels: enhancement, new feature

#757 - Gene List popup to better indicate Species in table

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: quality, UX & UI

#756 - Enhance Evidence View with Species-specific Toggle

Issue - State: closed - Opened by Arnedeklerk over 1 year ago - 1 comment
Labels: enhancement, new feature, UX & UI, resolution:migrated

#755 - EvidenceTable Genes column popup tooltips are getting duplicated

Issue - State: closed - Opened by lawal-olaotan over 1 year ago - 1 comment

#754 - [BasicLocal UI Test], The chromosome region selection entry doesn't update counts

Issue - State: closed - Opened by marco-brandizi almost 2 years ago - 2 comments
Labels: bug, project:client

#753 - Making the data source ID optional in API URLs

Issue - State: closed - Opened by marco-brandizi almost 2 years ago
Labels: project:web service, new feature

#751 - [InfiniteScrollingLocal] UI Test failures

Issue - State: closed - Opened by marco-brandizi almost 2 years ago - 1 comment
Labels: bug, project:client

#750 - Google Analytics requires upgrades to GA4

Issue - State: closed - Opened by marco-brandizi almost 2 years ago - 3 comments
Labels: question, project:web service

#745 - Update major dependencies

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

#743 - Render Gene view using JSON

Issue - State: open - Opened by Arnedeklerk almost 2 years ago - 17 comments
Labels: code review, UX & UI

#738 - Update Concept Selector button

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 7 comments
Labels: quality, UX & UI

#737 - SNP and SNPEffect both visible in Network View Interactive Legend

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 14 comments
Labels: bug, UX & UI

#734 - Infinite Scrolling for Gene and Evidence Views with sorted tables

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 3 comments
Labels: enhancement, quality, UX & UI

#733 - Improve testing of KnetMiner frontend code using Selenium and unit tests

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 4 comments
Labels: continuous integration, code quality, UI-testing, resolution:migrated

#732 - Omit/Add in Evidence view is broken

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 1 comment
Labels: bug

#731 - Concept selector broken

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 1 comment
Labels: bug

#727 - Evidence Table, add an optional flag to sort results

Issue - State: closed - Opened by marco-brandizi almost 2 years ago - 2 comments
Labels: project:web service

#726 - Review the Javascript about the evidence table for performance and code quality.

Issue - State: closed - Opened by marco-brandizi almost 2 years ago - 2 comments
Labels: project:client, code quality

#723 - Make GenoMaps take up whole container in Map View

Issue - State: closed - Opened by Arnedeklerk almost 2 years ago - 2 comments
Labels: enhancement

#717 - Update KnetMiner Sparql Lodestar page

Issue - State: closed - Opened by Arnedeklerk about 2 years ago - 5 comments
Labels: enhancement, quality, website, UX & UI

#711 - Multispecies example queries auto change for Pro users

Issue - State: closed - Opened by Arnedeklerk about 2 years ago - 5 comments
Labels: enhancement, quality

#709 - Lazy load gene evidences (onclick event)

Issue - State: closed - Opened by Arnedeklerk about 2 years ago - 4 comments
Labels: enhancement, chore/infrastructure, upgrades, quality, UX & UI

#706 - Make all returned data species specific

Issue - State: closed - Opened by Arnedeklerk about 2 years ago - 3 comments
Labels: bug, chore/infrastructure, resolution:migrated

#692 - Gene Neighborhood and P-Value Filtering

Issue - State: open - Opened by Arnedeklerk over 2 years ago - 11 comments
Labels: new feature

#688 - Table header isn't pixel perfect at the top

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 1 comment
Labels: bug, UX & UI

#670 - Gene List API for fast-updating results

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 3 comments
Labels: enhancement, chore/infrastructure, new feature, upgrades, resolution:migrated

#667 - Add all available species to paid species list

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 4 comments
Labels: enhancement, upgrades, website, UX & UI, CELEART

#655 - Make the output of genome API as pure JSON

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 20 comments
Labels: enhancement, project:web service

#653 - /dataSource API call returns wrong results about TAX IDs

Issue - State: open - Opened by marco-brandizi over 2 years ago - 4 comments
Labels: bug, project:web service, project:client

#651 - Java 17 Upgrade

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 2 comments
Labels: chore/infrastructure

#646 - Filter label improvements

Issue - State: closed - Opened by Arnedeklerk over 2 years ago - 2 comments
Labels: website, UX & UI

#642 - New configuration infrastructure and Knetminer building workflow

Issue - State: closed - Opened by marco-brandizi over 2 years ago
Labels: project:web service, chore/infrastructure, new feature

#626 - Add backend support for searching over a specific specie

Issue - State: closed - Opened by KeywanHP almost 3 years ago - 14 comments
Labels: enhancement, epic

#617 - Search fails when a Genome region is given but no keywords or genes

Issue - State: closed - Opened by marco-brandizi almost 3 years ago - 2 comments
Labels: bug, resolution:outdated, resolution:can't reproduce

#611 - Select all & deselect button for gene and evidence view

Issue - State: closed - Opened by EA2106-Universite-Francois-Rabelais about 3 years ago - 5 comments
Labels: enhancement, project:client

#590 - Data model/format for saving the Semantic Motif Paths

Issue - State: open - Opened by marco-brandizi over 3 years ago - 2 comments
Labels: project:backend, new feature

#541 - search and API - visualize and filter the shortest and full (long) path between keyword and genes

Issue - State: closed - Opened by AjitPS about 4 years ago - 2 comments
Labels: epic, new feature

#479 - JBox modal failure on Safari

Issue - State: closed - Opened by josephhearnshaw about 5 years ago - 2 comments
Labels: bug, project:client

#450 - Colour coding for taxID

Issue - State: open - Opened by josephhearnshaw over 5 years ago - 2 comments
Labels: enhancement

#436 - Annotate strength or certainty of relationships

Issue - State: open - Opened by KeywanHP over 5 years ago - 2 comments
Labels: enhancement, project:client

#409 - Save and re-open user networks

Issue - State: closed - Opened by KeywanHP over 5 years ago - 4 comments
Labels: project:web service, project:client, epic, new feature, project:knetspace

#378 - Setup OpenAPI for API documentation

Issue - State: open - Opened by AjitPS over 5 years ago - 12 comments
Labels: enhancement, project:web service, chore/infrastructure, good first issue

#376 - Map View - genes not shown until first zoom

Issue - State: closed - Opened by KeywanHP over 5 years ago - 3 comments
Labels: bug, project:client

#370 - Develop a better AND search

Issue - State: closed - Opened by KeywanHP over 5 years ago - 10 comments
Labels: enhancement, project:web service, resolution:migrated

#368 - Network View - No network is shown first - but works after refresh

Issue - State: closed - Opened by KeywanHP over 5 years ago - 6 comments
Labels: bug, project:client, resolution:outdated, resolution:can't reproduce

#366 - Remove Javascript 3rd-party dependencies from the Knetminer codebase

Issue - State: closed - Opened by marco-brandizi over 5 years ago - 6 comments
Labels: enhancement, project:client

#304 - Search features/adding new options

Issue - State: closed - Opened by AjitPS about 6 years ago - 1 comment
Labels: enhancement

#213 - MapView - Make URLs for QTLs customizable for each KnetMiner instance

Issue - State: open - Opened by AjitPS over 7 years ago - 1 comment
Labels: enhancement

#31 - Add gene regulation data to knowledge networks

Issue - State: open - Opened by KeywanHP over 9 years ago - 3 comments
Labels: enhancement