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  1. IGB
  2. IGBF-2948

Attempt to convert and load each track hub featured in the table interface

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          The goal of this issue is to identify unknown bugs or usability issues in the current implementation of the track hub facade interface and back end.

          Check at least one genome (ideally all of them) for each track hub.

          Also, make note of any odd behavior in the genome and species menus. (These are populated from "species" and "synonyms" and "contents" endpoints and are therefore vulnerable to bugs in those endpoints.)

            Attachments

              Issue Links

              is cloned by

              Task - A task that needs to be done. IGBF-3079 CLONE - Attempt to convert and load each track hub featured in the table interface

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-2964 Investigate: “This feature is not reachable” error

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2961 Investigate: Prolonged startup and genome loading times

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2962 Investigate: Removing data sources causes IGB to hang

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2963 Investigate: Rearranging data source order doesn’t behave as expected

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
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                ann.loraine Ann Loraine added a comment - - edited

                Philip Badzuh - please indicate what was done thus far.

                Show
                ann.loraine Ann Loraine added a comment - - edited Philip Badzuh - please indicate what was done thus far.
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2021 Sep 13 - Sep 24 [ 129 ] Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8 [ 129, 130 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                The current testing progress is listed below. Stopping now to report what seems to be a recurring issue.

                hg38 and hg19 genomes tested:

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - The current testing progress is listed below. Stopping now to report what seems to be a recurring issue. hg38 and hg19 genomes tested: http://127.0.0.1:8000/rest_api/?hubUrl=https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/20200227123210/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. e.g. https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ALFA_EUR.bb http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/current_release/homo_sapiens/hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://krishna.gs.washington.edu/download/CADD/bigWig/CADD-browserTracks/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. http://127.0.0.1:8000/rest_api/?hubUrl=http://www.bcgsc.ca/downloads/edcc/data/CEMT/hub/bcgsc_datahub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://s3.us-east-2.amazonaws.com/brainepigenome/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/Iuliana-Ionita-Laza/Colocalization_tracks/master/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://cotneylab.cam.uchc.edu/~jcotney/CRANIOFACIAL_HUB/Craniofacial_Data_Hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://cotneylab.cam.uchc.edu/~jcotney/HEART_HUB/heart_hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://openslice.fenyolab.org/tracks/CPTAC/cptac/v1/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://lisanwanglab.org/DASHR/tracks/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://dashr2.lisanwanglab.org/tracks/DASHR2_hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. http://127.0.0.1:8000/rest_api/?hubUrl=http://dbrip.org/dbRIPHub/hub.txt&fileName=/ Doesn’t show as data source for hg19 http://127.0.0.1:8000/rest_api/?hubUrl=https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=http://smithlab.usc.edu/trackdata/methylation/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/dna20/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/rna22/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ensembl.org/pub/papers/regulation/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://epd.epfl.ch/ucsc/epdHub/epdHub.txt&fileName=/ Trust following certificate? Warning/confirmation “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/AndyMSSMLab/UCSC_exp_meth_VNTR/main/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://www.facebase.org/trackhub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://fantom.gsc.riken.jp/5/datahub/hub.txt&fileName=/ java.lang.RuntimeException: Error reading BBFile header for: http://fantom.gsc.riken.jp/5/datahub/hg19/enhancers/Human_FANTOM-NET_enhancers.bb at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:147) http://127.0.0.1:8000/rest_api/?hubUrl=http://fantom.gsc.riken.jp/5/suppl/Ohmiya_et_al_2014/data/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://genecards.weizmann.ac.il/geneloc/gh_hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://bx.psu.edu/~yuzhang/Roadmap_ideas/ideas_hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://s3.amazonaws.com/DLPFC_n36/humanDLPFC/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://www.lncipedia.org/trackhub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://epigenomesportal.ca/hub/hub.txt&fileName=/
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                pbadzuh Philip Badzuh (Inactive) added a comment - - edited

                Observed IGB usability issues:

                • Prolonged startup and genome loading times
                  • Loading data sources is blocking.
                    • Make asynchronous
                    • Cache data source metadata files
                • Removing data sources causes IGB to hang
                  • Sometimes temporarily
                  • Sometimes entirely due to:
                    • Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: unable to create new native thread
                • Rearranging data source order doesn’t behave as expected
                    • Sometimes it isn’t the selected data source that is moved when the arrow buttons are used
                    • Not free to move custom data sources below some defaults

                Loraine note: Rearrange data source order is a known bug. No need to re-test in the cloned issue.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - - edited Observed IGB usability issues: Prolonged startup and genome loading times Loading data sources is blocking. Make asynchronous Cache data source metadata files Removing data sources causes IGB to hang Sometimes temporarily Sometimes entirely due to: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: unable to create new native thread Rearranging data source order doesn’t behave as expected Sometimes it isn’t the selected data source that is moved when the arrow buttons are used Not free to move custom data sources below some defaults Loraine note: Rearrange data source order is a known bug. No need to re-test in the cloned issue.
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2954 [ IGBF-2954 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2961 [ IGBF-2961 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2962 [ IGBF-2962 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2963 [ IGBF-2963 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2964 [ IGBF-2964 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                I forgot to push the changes I added to improve testing and fix a minor issue with the annots.xml endpoint. Please see them here.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - I forgot to push the changes I added to improve testing and fix a minor issue with the annots.xml endpoint. Please see them here .
                pbadzuh Philip Badzuh (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
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                ann.loraine Ann Loraine added a comment -

                Please submit PR.
                attn: Philip Badzuh

                Show
                ann.loraine Ann Loraine added a comment - Please submit PR. attn: Philip Badzuh
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Please see PR here.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Please see PR here .
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                PR merged and new code is deployed to translate.bioviz.org.

                Show
                ann.loraine Ann Loraine added a comment - PR merged and new code is deployed to translate.bioviz.org.
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                Link This issue is cloned by IGBF-3079 [ IGBF-3079 ]

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: