Details
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Type:
Sub-task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.1.0
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Labels:None
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Story Points:4
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Sprint:Fall 7, Fall 8, Spring 1, Spring 2, Spring 3
Description
Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=refGene;chrom=chrM API and load Data only for genePred file type for now.
Attachments
Issue Links
- relates to
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IGBF-3584 Fix UCSC data tracks disappearing
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- Closed
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Activity
Tested the code and it is working as expected. Able to see the data after clicking load data for the selected genome. Code is available at branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501
To test:
- Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501 and start the application.
- Select a particular genome, preferably one that doesn't have data in IGB quick load.
- Click on the load data button either from the top right corner or in the data management table.
I'm really enjoying looking through the commits and understanding Jaya Sravani Sirigineedi's implementation!
Nowlan Freese While testing the application I observed one thing, the list of chromosomes differs for each track, click on the below links to see the number of chromosomes returned for each. Right now in our implementations, we are calling the chromosomes API only once at the start without any track parameter. Because of this, when we are trying to load data for the chromosomes that are not present in the current track we are receiving empty response from the UCSC API.
API without track: https://api.genome.ucsc.edu/list/chromosomes?genome=allMis1 (this returns 14645 chromosomes),
while API with track: https://api.genome.ucsc.edu/list/chromosomes?genome=allMis1&track=refGene (returns 54 chromosomes)
1) If I download the same refGene from UCSC Table Browser (link) that should be equivalent to the API call above (link), the file that it produces has only 54 chromosomes. I think this is just a weird dataset, and there is nothing wrong with what we are doing.
2) When I tested loading data from the UCSC REST data source I was seeing the following error in some genomes, for example human:
14:39:36.095 ERROR o.l.i.u.r.a.s.u.UCSCRestServerUtils - Server returned HTTP response code: 400 for URL: https://api.genome.ucsc.edu/list/chromosomes?genome=H_sapiens_Dec_2013
The 400 is due to the genome name included in the request being in the IGB format (H_sapiens_Dec_2013) instead of the UCSC format (GRCh38/hg38). If you disable the IGB quickload data source before selecting a genome then IGB loads the "UCSC" genome instead, and the requests use the correct UCSC genome name. My guess is that when IGB quickload is enabled, and the user selects a genome that is available in both IGB quickload and UCSC REST the IGB genome name is being used. Need to update logic to map IGB genome name to UCSC genome name.
Fixed the issue and tested the API using two different genomes, working as expected. Code is available in the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501
I am now able to load the UCSC REST data for various genomes (mouse, human, chicken) while IGB Quickload is also active as a data source.
However, there is some odd behavior when adding the same tracks across different genomes. For example, if I add the UCSC REST refGene for mouse, select chromosome 1, click Load Data, then switch to chicken and follow the same steps (refGene, chromosome 1, Load Data), then go back to the mouse genome, the refGene track will appear with a gray background as if it had not been loaded previously, though the gene models remain. The refGene track will also have disappeared from the Data Management Table. However, as this behavior also exists in IGB 9.1.10 when loading UCSC DAS data, I have created the ticket IGBF-3584 to investigate this issue.
Closing ticket.
Developed the code to integrate the API to load data for the selected track. Using the existing UcscGeneSym class as the Symmetry class for the genePred track type. Right now, testing and fixing the issues.