Ecosyste.ms: Issues

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GitHub / PATRIC3/patric3_website issues and pull requests

#100 - strangeness with toolbar

Issue - State: closed - Opened by jimdavis1 over 9 years ago - 4 comments

#99 - Source ID in drug target database table

Issue - State: closed - Opened by cshenry over 9 years ago - 1 comment

#98 - figfam id.

Issue - State: closed - Opened by jimdavis1 over 9 years ago - 2 comments

#97 - How do you download a whole genome?

Issue - State: closed - Opened by jimdavis1 over 9 years ago - 2 comments

#96 - searching with seed/taxonomy ids

Issue - State: closed - Opened by jimdavis1 over 9 years ago - 1 comment
Labels: UI

#95 - Differential Expression App job failures using the provided data set

Issue - State: closed - Opened by rkenyon over 9 years ago - 3 comments

#94 - problem with import of experiments?

Issue - State: closed - Opened by rwill1 over 9 years ago - 6 comments

#93 - Need flyovers for icons in workspace

Issue - State: closed - Opened by rkenyon over 9 years ago

#92 - Get error when trying to download Excel file of Transcriptomics Gene List

Issue - State: closed - Opened by rkenyon over 9 years ago - 4 comments
Labels: Fixed, UI

#91 - file list dialog is too narrow

Issue - State: closed - Opened by hyoo over 9 years ago - 1 comment

#90 - Banner menu in Workspace does not navigate to correct pages

Issue - State: closed - Opened by rkenyon over 9 years ago - 2 comments

#89 - ID mapping to UniProtKB-Accession is empty

Issue - State: closed - Opened by hyoo over 9 years ago - 1 comment
Labels: Bug

#88 - annotation app - can't put in a tax id

Issue - State: closed - Opened by olsonanl over 9 years ago - 2 comments

#87 - Red text in upload makes me thing I've already made an error

Issue - State: closed - Opened by olsonanl over 9 years ago - 1 comment

#86 - Column size issue in upload

Issue - State: closed - Opened by olsonanl over 9 years ago - 1 comment

#85 - Workspace UI sorting includes "Parent Folder"

Issue - State: open - Opened by hyoo over 9 years ago - 3 comments
Labels: UI: Workspace

#84 - RASTtk files lack column heads

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#83 - RASTtk files that I get from PATRIC are corrupted

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#82 - Experiment Groups Workspace headers don't match the column contents

Issue - State: closed - Opened by rwill1 over 9 years ago - 1 comment

#81 - In my workspace Experiment Group folder, some groups were empty

Issue - State: closed - Opened by chmao1 over 9 years ago - 2 comments

#80 - Logged in to beta many times and it won't show my workspace

Issue - State: closed - Opened by ARWattam over 9 years ago

#79 - From heatmap view, when I save proteins to group, the dialog box doesn't go away

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#78 - Major issue with pathways

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#77 - ID Mapping not returning results from workspace

Issue - State: closed - Opened by ARWattam over 9 years ago
Labels: Fixed

#76 - In my workspace, ID mapping for features returned one one record

Issue - State: closed - Opened by chmao1 over 9 years ago - 2 comments

#75 - MSA not loading from workspace

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#74 - MSA not working from workspace

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#73 - When clicking sort in an empty column in Workspace, all records disappear

Issue - State: closed - Opened by rkenyon over 9 years ago - 2 comments
Labels: Fixed

#72 - Genome metadata missing from workspace download

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#70 - Need download to Excel in Workspace

Issue - State: closed - Opened by rkenyon over 9 years ago - 1 comment

#69 - Excel option missing from download table in workspace

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#68 - Clicking twice on genome group doesn't work consistently.

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#67 - Can't remove data in workspace group any longer

Issue - State: closed - Opened by ARWattam over 9 years ago

#66 - Have to re-enter keyword in filter when picking something else in metadata

Issue - State: closed - Opened by ARWattam over 9 years ago - 3 comments

#65 - Once logged in, website insists on my logging in again

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#64 - Logout while still in workspace leaves confused state?

Issue - State: closed - Opened by rwill1 over 9 years ago - 4 comments

#63 - Login on Chrome / Mac doesn't display WORKSPACE: HOME>

Issue - State: closed - Opened by rwill1 over 9 years ago - 2 comments

#61 - HTTP Status 404 on IE 11

Issue - State: closed - Opened by rwill1 over 9 years ago - 1 comment
Labels: Infrastructure, Obsolete

#59 - changes needed in Workspace header

Issue - State: closed - Opened by rwill1 over 9 years ago

#58 - Getting java.lang.NullPointerException error in some pages

Issue - State: closed - Opened by rkenyon over 9 years ago - 1 comment

#57 - typo (KiB) for size in workspace

Issue - State: closed - Opened by chmao1 over 9 years ago - 1 comment

#56 - Change in Genome Annotation page language

Issue - State: closed - Opened by ARWattam over 9 years ago

#55 - genome annotation fails when file of proteins is uploaded

Issue - State: closed - Opened by olsonanl over 9 years ago - 5 comments
Labels: Service: Annotation

#54 - Top section of App Forms cut off

Issue - State: closed - Opened by rkenyon over 9 years ago - 1 comment

#53 - Ensure Logged in when visiting app pages

Issue - State: closed - Opened by dmachi over 9 years ago - 1 comment

#52 - Negative Genome counts in pathway tool

Issue - State: closed - Opened by bparrello over 9 years ago - 2 comments

#51 - feature_data table generated by annotation app has no headings

Issue - State: closed - Opened by cshenry over 9 years ago - 1 comment

#50 - Buttons for navigation in workspace are sometimes unresponsive

Issue - State: closed - Opened by cshenry over 9 years ago - 1 comment

#49 - Need obvious message that only faa files supported in genome annotation upload

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#48 - Strange behavior on Safari after logging in during initial account creation

Issue - State: closed - Opened by cshenry over 9 years ago - 2 comments
Labels: UI: Workspace

#47 - Need better error message about non-supportive GenBank file

Issue - State: closed - Opened by ARWattam over 9 years ago

#46 - NA sequence not found when clicking on protein in compare regions

Issue - State: closed - Opened by olsonanl over 9 years ago - 2 comments
Labels: Enhancement, UI, Obsolete, Tool: Compare Regions

#45 - Null Pointer Exception when exploring pathways

Issue - State: closed - Opened by bparrello over 9 years ago - 1 comment

#44 - Time represented in log

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#43 - 404 not found on Interactions link

Issue - State: closed - Opened by olsonanl over 9 years ago - 1 comment

#42 - Genes on the reverse strand need the start and stop indicators switched

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#41 - Can't load genomes from phylogeny viewer

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#40 - single pathway table is not working

Issue - State: closed - Opened by hyoo over 9 years ago - 1 comment

#39 - Workspace now requires login

Issue - State: closed - Opened by olsonanl over 9 years ago - 1 comment

#37 - typo "recieved" in the user registration process

Issue - State: closed - Opened by sebhtml over 9 years ago - 1 comment

#36 - Differential Expression - job gets suspended

Issue - State: closed - Opened by chmao1 over 9 years ago - 3 comments

#35 - Pathway summary in tool bar does not appear to be working

Issue - State: closed - Opened by ARWattam over 9 years ago - 3 comments

#34 - Literature tab doesn't work

Issue - State: closed - Opened by chmao1 over 9 years ago - 1 comment

#33 - search / add to workspace / login issue?

Issue - State: closed - Opened by rwill1 over 9 years ago - 4 comments

#32 - PATRIC global search issue

Issue - State: closed - Opened by chmao1 over 9 years ago - 1 comment

#31 - RAST, GO Search, EC Search should be removed from Tool list page

Issue - State: closed - Opened by hyoo over 9 years ago - 2 comments

#30 - PPI is not working

Issue - State: closed - Opened by hyoo over 9 years ago - 3 comments

#29 - The up arrow for the Parent Folder doesn't work in workspace

Issue - State: closed - Opened by chmao1 over 9 years ago - 2 comments

#28 - Better default column widths in table in workspace

Issue - State: closed - Opened by rkenyon over 9 years ago - 1 comment
Labels: Enhancement

#27 - Two copies of "Genome Groups" are now in my workspace

Issue - State: closed - Opened by rkenyon over 9 years ago - 2 comments

#26 - Genomes missing from genome group

Issue - State: closed - Opened by rkenyon over 9 years ago - 4 comments

#25 - need to increase acceptable request size

Issue - State: closed - Opened by hyoo over 9 years ago

#24 - Links to Jmol generating error message

Issue - State: closed - Opened by ARWattam over 9 years ago - 3 comments

#23 - Blue highlight boxes not appearing when Pathway Summary tool is clicked

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments
Labels: Enhancement

#22 - More genomes missing strain names, although listed in metadata

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#21 - Reference genomes-Brucella pinnipedialis B2/94 has two different sequences

Issue - State: closed - Opened by ARWattam over 9 years ago - 2 comments

#20 - Data: Strain name not showing

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment
Labels: Fixed, Data

#19 - I can't log in

Issue - State: closed - Opened by ARWattam over 9 years ago - 1 comment

#18 - Modal changes needed for "forgot password" functionality

Issue - State: closed - Opened by rwill1 over 9 years ago - 3 comments

#17 - MSA/Tree doesn't work with more than 120-150 features

Issue - State: closed - Opened by mshukla1 almost 10 years ago - 1 comment

#16 - Feature level, genome browser tab shows zoomed out view

Issue - State: closed - Opened by mshukla1 almost 10 years ago

#15 - # of gene link from pathway map to the gene level list

Issue - State: closed - Opened by hyoo almost 10 years ago - 2 comments
Labels: Bug, Fixed

#14 - feature link in the gene list of user-uploaded experiment is broken

Issue - State: closed - Opened by hyoo almost 10 years ago - 1 comment
Labels: Bug

#13 - Download tool with genome selection is not working

Issue - State: closed - Opened by hyoo almost 10 years ago - 1 comment
Labels: Bug

#12 - PFS clustering is not working

Issue - State: closed - Opened by hyoo almost 10 years ago - 1 comment

#11 - PFS filter is not working

Issue - State: closed - Opened by hyoo almost 10 years ago - 1 comment

#10 - PFS with genome group

Issue - State: closed - Opened by mshukla1 almost 10 years ago

#9 - BYO transcriptomics, links from gene list

Issue - State: closed - Opened by mshukla1 almost 10 years ago

#8 - pathway heatmap problems

Issue - State: closed - Opened by mshukla1 almost 10 years ago - 3 comments
Labels: Bug

#7 - Performance of JBrowse in Solr-ized P3

Issue - State: closed - Opened by rwill1 almost 10 years ago - 2 comments
Labels: UI

#6 - Archaea phylogeny trees

Issue - State: closed - Opened by rwill1 almost 10 years ago - 1 comment

#5 - No Uniprot Accession in the ID mapping tool

Issue - State: closed - Opened by aswarren almost 10 years ago - 2 comments

#4 - DATA - Need to clean up some TB-ARC Mali genomes (different "genomes" have same GenBank Accession)

Issue - State: closed - Opened by rwill1 almost 10 years ago - 2 comments
Labels: Data

#3 - MINOR (IMHO) - should we check there is a "RefSeq" annotation before putting that on the genome browser

Issue - State: closed - Opened by rwill1 almost 10 years ago - 1 comment
Labels: UI

#2 - Need some work on Global Search results page in light of new IDs?

Issue - State: closed - Opened by rwill1 almost 10 years ago - 1 comment
Labels: UI, Obsolete

#1 - Error on PATRIC's RAST Tool landing page

Issue - State: closed - Opened by rwill1 almost 10 years ago - 1 comment