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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.)

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            Hide
            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.
            Hide
            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=/
            Hide
            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.
            Hide
            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 .
            Hide
            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
            Hide
            pbadzuh Philip Badzuh (Inactive) added a comment -

            Please see PR here.

            Show
            pbadzuh Philip Badzuh (Inactive) added a comment - Please see PR here .
            Hide
            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.

              People

              • Assignee:
                pbadzuh Philip Badzuh (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: