geneontology/amigo issues and pull requests

#721 - Add taxon constraints to display (redux)

Issue - State: open - Opened by kltm 3 months ago - 5 comments
Labels: enhancement

#720 - Add never_in_taxon

Pull Request - State: open - Opened by cmungall 5 months ago

#719 - Fix URL-encoding issues in GOlr searches

Pull Request - State: closed - Opened by pkalita-lbl 6 months ago

#718 - Annotation filter GO class (direct) not working

Issue - State: closed - Opened by raymond91125 7 months ago - 9 comments
Labels: bug (B: affects usability)

#717 - Evidence filters no longer working

Issue - State: closed - Opened by kltm 8 months ago - 2 comments
Labels: bug (A: showstopper), duplicate

#716 - Filter annotations by evidence is not working

Issue - State: closed - Opened by vanaukenk 8 months ago - 16 comments
Labels: bug (B: affects usability)

#715 - Remove stats page from AmiGO

Issue - State: open - Opened by ValWood 10 months ago - 5 comments
Labels: bug (C: surface issue)

#714 - searching on gene name

Issue - State: open - Opened by ValWood 10 months ago - 2 comments
Labels: enhancement

#713 - Closure should be used when querying the genes biotype

Issue - State: open - Opened by cmungall 10 months ago - 2 comments

#712 - Taxon info displays "none" when there are constraints

Issue - State: closed - Opened by suzialeksander 10 months ago - 25 comments
Labels: bug (B: affects usability)

#711 - Update dates on AmiGO

Issue - State: closed - Opened by pgaudet 11 months ago - 1 comment

#710 - Support node > 8

Issue - State: open - Opened by nathanweeks 11 months ago - 1 comment
Labels: bug (B: affects usability)

#709 - Change "data health" to "feedback" on ontology pages

Issue - State: closed - Opened by kltm 12 months ago - 1 comment
Labels: bug (C: surface issue)

#708 - Update term_details_main.tmpl

Pull Request - State: closed - Opened by cmungall 12 months ago - 1 comment

#707 - Remove link to GOnuts

Issue - State: open - Opened by pgaudet 12 months ago - 2 comments
Labels: enhancement, bug (C: surface issue)

#706 - Display logical definitions and reaction participants in AmiGO

Issue - State: open - Opened by pgaudet 12 months ago - 15 comments
Labels: enhancement

#705 - Definitions of molecular_function and cellular_component do not match in AmiGO and QuickGO

Issue - State: closed - Opened by addiehl about 1 year ago - 4 comments
Labels: duplicate

#704 - AmiGO does not display the current definition of biological_process

Issue - State: open - Opened by addiehl about 1 year ago - 2 comments

#703 - Upgrade pathway widget to version 1.0.0

Pull Request - State: closed - Opened by pkalita-lbl about 1 year ago

#702 - BUG when including "regulates"

Issue - State: closed - Opened by ValWood about 1 year ago - 2 comments
Labels: question

#701 - Make PMID search more visible

Issue - State: closed - Opened by kltm about 1 year ago - 2 comments
Labels: enhancement

#700 - Change PANTHER enrichment correction param to match GO site

Pull Request - State: closed - Opened by dustine32 about 1 year ago - 1 comment

#699 - Update pantherdb enrichment form URLs to HTTPS

Pull Request - State: closed - Opened by dustine32 about 1 year ago

#697 - Improve amigo xrefs page to better clarify the nature of the synonyms

Issue - State: open - Opened by kltm about 1 year ago - 1 comment
Labels: enhancement

#696 - Switch AmiGO production to master once refactored GO API is in production

Issue - State: closed - Opened by kltm about 1 year ago - 2 comments

#695 - managing golr and amigo dns records

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

#694 - Add update pathway widget to AmiGO (prod)

Issue - State: closed - Opened by kltm over 1 year ago - 3 comments

#693 - Rationalize main production and noctua / NEO autocomplete index creation (and codebase)

Issue - State: open - Opened by kltm over 1 year ago
Labels: bug (B: affects usability)

#692 - Term matrix issue

Issue - State: open - Opened by Antonialock over 1 year ago - 2 comments
Labels: question

#691 - Minor fixes: health checks, httpd golr conf, qos

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

#690 - Syntax error in load_ontology_purge_safe

Issue - State: open - Opened by nathanweeks over 1 year ago - 3 comments
Labels: bug (B: affects usability)

#689 - Need redirects from old http to new https pages

Issue - State: closed - Opened by pgaudet over 1 year ago - 5 comments

#688 - In some environments, the xrefs page (Xrefs.pm) fails with a server error

Issue - State: closed - Opened by kltm over 1 year ago - 1 comment
Labels: bug (B: affects usability)

#687 - Set babel's sourceType option to avoid injecting "use strict" statement

Pull Request - State: closed - Opened by pkalita-lbl over 1 year ago - 1 comment

#686 - Filter for large facet sets has disappeared

Issue - State: closed - Opened by kltm over 1 year ago - 1 comment
Labels: bug (B: affects usability)

#685 - Removes JXON use for native DOMParser for Pubmed abstract parsing

Pull Request - State: open - Opened by AlexanderNull over 1 year ago - 4 comments

#684 - Add data download to matrix tool

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

#683 - Add GO-CAMs tab to term pages

Issue - State: open - Opened by pkalita-lbl over 1 year ago - 2 comments

#682 - XSS vulnerability in search (medial_search) with q parameter

Issue - State: closed - Opened by kltm over 1 year ago - 3 comments
Labels: bug (A: showstopper)

#681 - Add Models tab to gene product pages

Pull Request - State: closed - Opened by pkalita-lbl over 1 year ago - 13 comments

#680 - Refresh JS build system

Pull Request - State: closed - Opened by pkalita-lbl over 1 year ago - 4 comments

#679 - Give feedback on improvements or changes necessary for AmiGO use case of pathway widget

Issue - State: closed - Opened by kltm over 1 year ago - 7 comments
Labels: enhancement

#678 - Add a top-level /model/ route to AmiGO and populate it with pathway widget and model metadata

Issue - State: closed - Opened by kltm over 1 year ago - 1 comment
Labels: enhancement

#677 - Add "model" tab to gene product pages

Issue - State: closed - Opened by kltm over 1 year ago - 4 comments
Labels: enhancement

#676 - Refresh the build system in AmiGO to better support modern JS/widgetry

Issue - State: closed - Opened by kltm over 1 year ago - 2 comments
Labels: enhancement

#675 - load_details pages no longer display any information

Issue - State: open - Opened by kltm over 1 year ago
Labels: bug (B: affects usability)

#674 - amigo now uses ssl and redirects http to https

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

#673 - Test ssl off

Pull Request - State: closed - Opened by abessiari over 1 year ago - 1 comment

#672 - Experiment: take a look at generating a limited ontology for AmiGO load

Issue - State: open - Opened by kltm almost 2 years ago - 1 comment

#671 - Experiment: take a look at scope of general index use and how it is wired in

Issue - State: closed - Opened by kltm almost 2 years ago - 5 comments

#670 - Using jammy

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

#669 - Using jammy

Pull Request - State: closed - Opened by abessiari almost 2 years ago - 1 comment

#668 - Using jammy

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

#667 - Amigo often supplies non-GO terms (confusing for users)

Issue - State: closed - Opened by ValWood almost 2 years ago - 1 comment

#665 - Bump json5 and rc-config-loader

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#664 - Bump json5 and rc-config-loader in /javascript/npm/bbop-widget-set

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#664 - Bump json5 and rc-config-loader in /javascript/npm/bbop-widget-set

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#663 - Bump json5 and rc-config-loader

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, javascript

#662 - Bump json5 and rc-config-loader in /javascript/npm/bbop-widget-set

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, javascript

#662 - Bump json5 and rc-config-loader in /javascript/npm/bbop-widget-set

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, javascript

#661 - AmiGO stats count differently than geneontology.org and release.go statistics

Issue - State: open - Opened by suzialeksander almost 2 years ago - 1 comment

#660 - Bump express from 4.16.3 to 4.17.3

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#659 - Bump decode-uri-component from 0.2.0 to 0.2.2

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#659 - Bump decode-uri-component from 0.2.0 to 0.2.2

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#658 - Bump decode-uri-component from 0.2.0 to 0.2.2 in /javascript/npm/bbop-widget-set

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, javascript

#657 - PMID eutilities has changed their API breaking AmiGO pub pages

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

#656 - Bump minimatch and gulp

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#656 - Bump minimatch and gulp

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#655 - Reference page not correctly displaying article title.

Issue - State: open - Opened by malcolmfisher103 about 2 years ago - 8 comments
Labels: bug (C: surface issue)

#654 - Bump bootstrap from 4.0.0 to 4.3.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#654 - Bump bootstrap from 4.0.0 to 4.3.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, javascript

#653 - XSS vulnerability in visualize

Issue - State: closed - Opened by kltm over 2 years ago - 2 comments
Labels: bug (A: showstopper)

#652 - Draft:Using existing vpc

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

#651 - 'Download' should be a real downlod

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

#650 - Gauge amount of work necessary to embed AGR pathway and/or ribbon widgets into AmiGO

Issue - State: closed - Opened by kltm over 2 years ago - 8 comments
Labels: question

#649 - confusing search results

Issue - State: closed - Opened by ValWood over 2 years ago - 5 comments
Labels: duplicate

#648 - term matrix should report counts for genes in aspect that do not slim up

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

#647 - Possible self-XSS vulnerability in matrix tool

Issue - State: open - Opened by kltm over 2 years ago
Labels: enhancement

#640 - Bump minimist from 1.2.0 to 1.2.6

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#639 - AmiGO browse not showing number of annotations anymore

Issue - State: closed - Opened by pgaudet over 2 years ago - 4 comments
Labels: bug (B: affects usability)

#639 - AmiGO browse not showing number of annotations anymore

Issue - State: closed - Opened by pgaudet over 2 years ago - 4 comments
Labels: bug (B: affects usability)

#638 - Searching AmiGO by PubMed ID

Issue - State: open - Opened by ValWood over 2 years ago - 7 comments
Labels: enhancement, question

#637 - create elastic ip instead of pointing to existing one

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

#637 - create elastic ip instead of pointing to existing one

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

#636 - Bump marked from 0.3.19 to 4.0.10

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies, javascript

#635 - using custom image. using temp amigo.yaml file as it is modified when…

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

#634 - Refresh interface for term pages to allow switching relation closures

Issue - State: closed - Opened by kltm almost 3 years ago - 12 comments
Labels: bug (B: affects usability)

#634 - Refresh interface for term pages to allow switching relation closures

Issue - State: closed - Opened by kltm almost 3 years ago - 12 comments
Labels: bug (B: affects usability)

#633 - Issue 620 change default closure

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

#632 - Using s3 credfile

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

#632 - Using s3 credfile

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

#631 - using shell command for docker compose

Pull Request - State: closed - Opened by abessiari almost 3 years ago - 4 comments

#630 - added monit to golr container and log rotation monit, of amigo logs and golr jetty process

Pull Request - State: closed - Opened by abessiari almost 3 years ago - 5 comments

#629 - S3logs

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

#629 - S3logs

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

#628 - using pigz. added starting services using ansible. no more warnin…

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

#628 - using pigz. added starting services using ansible. no more warnin…

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

#627 - handling production and development mode.

Pull Request - State: closed - Opened by abessiari about 3 years ago - 9 comments

#627 - handling production and development mode.

Pull Request - State: closed - Opened by abessiari about 3 years ago - 9 comments

#626 - Untraceable annotation for ZDB-GENE-060818-1

Issue - State: closed - Opened by pgaudet about 3 years ago - 7 comments
Labels: question

GitHub / geneontology/amigo issues and pull requests