Made changes to generate hub.txt and genomes.txt files.
Sample local url paths:
hub.txt: http://127.0.0.1:8000/api/igbTrackHubs?quickLoadUrl=http://igbquickload.org/quickload&filePath=/hub.txt
genomes.txt: http://127.0.0.1:8000/api/igbTrackHubs?quickLoadUrl=http://igbquickload.org/quickload&filePath=/genomes.txt

Branch : https://bitbucket.org/lorainelab_udaya/hub-facade/branch/IGBF-4105

Jaya Sravani Sirigineedi, Dr. Nowlan Freese, please verify the commit.

Reviewed the code and everything looks good, I only have two suggestions: "\n" add this to a string variable delimiter and use that when joining strings to make it more readable and add res.text not null condition as well to the status code check just to avoid any null pointer exceptions. Build the branch locally and ran it, was able to get both files. The content in the files is as expected, optional rows are only present for genomes that are not in UCSC for the genomes that are in UCSC we don't need those fields as those are retrieved from UCSC itself.

Commit 1: https://bitbucket.org/lorainelab_udaya/hub-facade/commits/e29c464e4cafe65da8717a06ddf170306d19d6dd
Created an endpoint that generates synonyms.txt (IGB genome name and UCSC genome name) file by fetching the genomes name from https://api.genome.ucsc.edu/list/ucscGenomes and checks the genome in IGB synonyms.txt
api : http://127.0.0.1:8000/api/generateUcscSynonyms

Endpoint: http://127.0.0.1:8000/api/generateUcscSynonyms

Commit 2: https://bitbucket.org/lorainelab_udaya/hub-facade/commits/919ec25600d592014f7e47d9e287744b79f240a9
changes to generate hub.txt and genomes.txt
hub.txt: http://127.0.0.1:8000/api/igbTrackHubs?quickLoadUrl=http://igbquickload.org/quickload&filePath=/hub.txt
genomes.txt: http://127.0.0.1:8000/api/igbTrackHubs?quickLoadUrl=http://igbquickload.org/quickload&filePath=/genomes.txt

Commit 3: https://bitbucket.org/lorainelab_udaya/hub-facade/commits/2ab4cdb4cf4813959b12586cf2249974a94d1231
changes to generate trackDb.txt
trackDb.txt : http://127.0.0.1:8000/api/igbTrackHubs?quickLoadUrl=http://igbquickload.org/quickload&filePath=/ce6/trackDb.txt

How to test changes :
Commit 1:

1. Hit the Ucsc genome endpoint - https://api.genome.ucsc.edu/list/ucscGenomes
2. Check the ucsc genomes are present in IGB synonyms.txt in IGB repository (path : core/synonym-lookup/src/main/resources/synonyms.txt). If ucsc genomes are present in IGB synonyms.txt, then IGB genome name(which is the first column in IGB synonyms.txt) and Ucsc genome name should be added in new Synonyms.txt in hub_facade repo (path :igb_trackhub/synonyms.txt).

Commit 2&3:

Api : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub2/hub.txt
Track hub Bitbucket : https://bitbucket.org/lorainelab_udaya/testquickload/src/main/trackHub2/
Quickload bitbucket : https://bitbucket.org/lorainelab_udaya/testquickload/src/main/quickload1/
Created the above folder in bitbuket after testing the changes in my local.

1. Hub.txt file is a static data. Check if the data generated is same as below.
   hub IGBQuickLoad
   shortLabel IGB Quick Load
   longLabel Track hub generated from IGB
   genomesFile genomes.txt
   email igbhelper@gmail.com
2. Genomes.txt

• genome - It is either igb genome name or ucsc genome name. The preference is ucsc genome name.
• trackDb - It is always {genome_name}/trackDb.txt
  The below three fields are present only when the genome name is IGB genome name
  * organism - we get this from IGB species.txt (the first column) by checking with igb genome name.
  * defaultPos - It is always the first row of {genome_name}

  /genome.txt

• twoBitPath - We get the twoBitPath from name field in {genome_name}/annots.xml whose reference value is true.
  # trackDb.txt - We get this data from {genome_name}

  /annots.xml

• track - the first word of title field whose reference is not true
• bigDataUrl - name field whose reference is not true
• shortLabel - the last word of title field whose reference is not true
• longLabel - description field whose reference is not true
• type - type is assigned depending on the extension of the bigDataUrl
• visibility - It is a fixed value. visibility = "dense"

1. Check if above fields are generated properly
2. Copy the hub.txt api provided above and paste in https://genome.ucsc.edu/cgi-bin/hgHubConnect and click add hub
3. Check if the genomes are visibile in ucsc

Dr. Nowlan Freese and Jaya Sravani Sirigineedi Please verify the changes.

update branch : https://bitbucket.org/lorainelab_udaya/hub-facade/branch/IGBF-4105

Tested following instructions above. Everything looks to be working. I think we should go ahead and deploy the changes so that we can test the changes on the UCSC genome browser.

Note that there are currently merge conflicts due to IGBF-4139. Once the conflicts are resolved, ready for PR and deployment.

Reviewed the latest code chagnes, everyhting looks good.

PR: https://bitbucket.org/lorainelab/hub-facade/pull-requests/40/overview
Dr. Ann Loraine, Please review and merge the PR. This ticket can be tested only after deployment.

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

Testing on Chrome:
The hub.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/hub.txt
The genomes.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/genomes.txt

However, this does not work when I add it as a UCSC Track Hub. I have created IGBF-4192 to further test this.

As the hub.txt and genomes.txt are being returned, closing ticket.

Latest PR is merged and new code is deployed to translate.bioviz.org as per usual.
Ready for testing.