Details
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Type:
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: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9
Description
The Quickload converter site will read metadata configuration files from a Track Hub site and translate the information over to the IGB Quickload specification.
Before we can write the converter code, we first must define the structure of an IGB quickload site, which includes the following resources:
- listing of genome versions supported by the site
- for those genomes, a listing of their sequence names and sizes
- file resources associated with each genome version, and where IGB can find them on the Internet (or on the user's local system)
Review the specification for an IGB Quickload site. Also, browse the existing Quickload sites using their Web interfaces.
Using this info, develop a first draft description of how the different entities related to a Quickload site map onto a Track Hub site.
IGB quickload documentation:
Quickloads already available in IGB:
- Quickload main: http://igbquickload.org/quickload/
- RNA-Seq quickload: http://igbquickload.org/rnaseq
- ChIP-Seq quickload: http://igbquickload.org/dnaseq
- BAR quickload: http://igbquickload.org/bar
- Quickload main subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2831 [ 19524 ] |
| Summary | Create a first draft of database tables representing an IGB Quickload site | Create a first draft of database table design representing an IGB Quickload site |
| Description |
The Quickload converter site will read metadata configuration files from a Track Hub site and translate the information over to the IGB Quickload specification, ultimately storing the data as Django models in a Django-managed database.
Before we can write the converter code, we first must define the structure of an IGB quickload site, which includes the following resources: * listing of genome versions supported by the site * for those genomes, a listing of their sequence names and sizes * file resources associated with each genome version, and where IGB can find them on the Internet (or on the user's local system) Review the specification for an IGB Quickload site. Also, browse the existing Quickload sites using their Web interfaces. Using this info, develop a first draft description of how the different entities related to a Quickload site should be represented in a database. Create a database table diagram that can be edited and updated as we iterate the system. Once we have a design we're happy with, we will translate into Django models. |
The Quickload converter site will read metadata configuration files from a Track Hub site and translate the information over to the IGB Quickload specification, ultimately storing the data as Django models in a Django-managed database.
Before we can write the converter code, we first must define the structure of an IGB quickload site, which includes the following resources: * listing of genome versions supported by the site * for those genomes, a listing of their sequence names and sizes * file resources associated with each genome version, and where IGB can find them on the Internet (or on the user's local system) Review the specification for an IGB Quickload site. Also, browse the existing Quickload sites using their Web interfaces. Using this info, develop a first draft description of how the different entities related to a Quickload site should be represented in a database. Create a database table diagram that can be edited and updated as we iterate the system. Once we have a design we're happy with, we will translate into Django models. IGB quickload documetation: * https://wiki.transvar.org/display/igbman/Sharing+data+using+QuickLoad+sites Quickloads already avaialable in IGB: * Quickload main: http://igbquickload.org/quickload/ * RNA-Seq quickload: http://igbquickload.org/rnaseq * ChIP-Seq quickload: http://igbquickload.org/dnaseq * BAR quickload: http://igbquickload.org/bar * Quickload main subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload |
| Security | Hidden [ 10001 ] |
| Sprint | Spring 2 2021 Apr 5 - Apr 16 [ 118 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 118, 119 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 118, 119 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14 [ 118, 119, 120 ] |
| Rank | Ranked higher |
| Summary | Create a first draft of database table design representing an IGB Quickload site | Understand IGB Quickload |
| Description |
The Quickload converter site will read metadata configuration files from a Track Hub site and translate the information over to the IGB Quickload specification, ultimately storing the data as Django models in a Django-managed database.
Before we can write the converter code, we first must define the structure of an IGB quickload site, which includes the following resources: * listing of genome versions supported by the site * for those genomes, a listing of their sequence names and sizes * file resources associated with each genome version, and where IGB can find them on the Internet (or on the user's local system) Review the specification for an IGB Quickload site. Also, browse the existing Quickload sites using their Web interfaces. Using this info, develop a first draft description of how the different entities related to a Quickload site should be represented in a database. Create a database table diagram that can be edited and updated as we iterate the system. Once we have a design we're happy with, we will translate into Django models. IGB quickload documetation: * https://wiki.transvar.org/display/igbman/Sharing+data+using+QuickLoad+sites Quickloads already avaialable in IGB: * Quickload main: http://igbquickload.org/quickload/ * RNA-Seq quickload: http://igbquickload.org/rnaseq * ChIP-Seq quickload: http://igbquickload.org/dnaseq * BAR quickload: http://igbquickload.org/bar * Quickload main subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload |
The Quickload converter site will read metadata configuration files from a Track Hub site and translate the information over to the IGB Quickload specification.
Before we can write the converter code, we first must define the structure of an IGB quickload site, which includes the following resources: * listing of genome versions supported by the site * for those genomes, a listing of their sequence names and sizes * file resources associated with each genome version, and where IGB can find them on the Internet (or on the user's local system) Review the specification for an IGB Quickload site. Also, browse the existing Quickload sites using their Web interfaces. Using this info, develop a first draft description of how the different entities related to a Quickload site map onto a Track Hub site. IGB quickload documentation: * https://wiki.transvar.org/display/igbman/Sharing+data+using+QuickLoad+sites Quickloads already available in IGB: * Quickload main: http://igbquickload.org/quickload/ * RNA-Seq quickload: http://igbquickload.org/rnaseq * ChIP-Seq quickload: http://igbquickload.org/dnaseq * BAR quickload: http://igbquickload.org/bar * Quickload main subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload |
| Assignee | Irvin Naylor [ inaylor ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Irvin Naylor [ inaylor ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14 [ 118, 119, 120 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 118, 119, 120, 121 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 118, 119, 120, 121 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 118, 119, 120, 121, 122 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 118, 119, 120, 121, 122 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 118, 119, 120, 121, 122, 123 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 118, 119, 120, 121, 122, 123 ] | Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 118, 119, 120, 121, 122, 123, 124 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Notes on Quickload vs. UCSC structure: https://docs.google.com/document/d/1BV5biFJnLKkSzYYtLg_D9rtxbRi5PASNuD311GEC2TM/edit?usp=sharing