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:5
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Epic Link:
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Sprint:Summer 2, Summer 3, Summer 4, Summer 5, Summer 6
Description
Implement logic to load the available genomes from Ensembl API:
To get the list of species (genomes) available in Ensembl:
GET info/divisions
Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/documentation/info/info_divisions
Example: https://rest.ensembl.org/info/divisions?content-type=application/json
GET info/species
Lists all available species, their aliases, available adaptor groups, and data release.
To get the species for that ensembl division, have to specify the division optional parameter.
API to get the list of all species: https://rest.ensembl.org/documentation/info/species
Example: https://rest.ensembl.org/info/species?content-type=application/json
Use name, display_name, and assembly from the API response as the species name, tooltip description, and version respectively.
To get all the available species we have to call the above info/species API for all the ensemble divisions that are returned from the first API.
Add the logic in the retrieveDataContainer() method to check whether the species that is being loaded by the Ensembl provider is already present in the species list, if it's present don't add it if not add the species to the list and also, write logic to get the species name for the provided versionName.
Attachments
Issue Links
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3555 [ 22774 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 2 | 3 |
| Description |
Implement logic to load the available genomes from Ensembl API:
*+To get the list of species (genomes) available in Ensembl:+* *GET info/divisions* Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/documentation/info/info_divisions Example: https://rest.ensembl.org/info/divisions?content-type=application/json *GET info/species* Lists all available species, their aliases, available adaptor groups, and data release. To get the species for that ensembl division, have to specify the division optional parameter. API to get the list of all species: https://rest.ensembl.org/documentation/info/species Example: https://rest.ensembl.org/info/species?content-type=application/json _Use name, display_name, and accession from the API response as the species name, tooltip description, and version respectively._ To get all the available species we have to call the above info/species API for all the ensemble divisions that are returned from the first API. |
Implement logic to load the available genomes from Ensembl API:
*+To get the list of species (genomes) available in Ensembl:+* *GET info/divisions* Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/documentation/info/info_divisions Example: https://rest.ensembl.org/info/divisions?content-type=application/json *GET info/species* Lists all available species, their aliases, available adaptor groups, and data release. To get the species for that ensembl division, have to specify the division optional parameter. API to get the list of all species: https://rest.ensembl.org/documentation/info/species Example: https://rest.ensembl.org/info/species?content-type=application/json _Use name, display_name, and accession from the API response as the species name, tooltip description, and version respectively._ To get all the available species we have to call the above info/species API for all the ensemble divisions that are returned from the first API. Add the logic in the retrieveDataContainer() method to check whether the species that is being loaded by the Ensembl provider is already present in the species list, if it's present don't add it if not add the species to the list and also, write logic to get the species name for the provided versionName. |
| Description |
Implement logic to load the available genomes from Ensembl API:
*+To get the list of species (genomes) available in Ensembl:+* *GET info/divisions* Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/documentation/info/info_divisions Example: https://rest.ensembl.org/info/divisions?content-type=application/json *GET info/species* Lists all available species, their aliases, available adaptor groups, and data release. To get the species for that ensembl division, have to specify the division optional parameter. API to get the list of all species: https://rest.ensembl.org/documentation/info/species Example: https://rest.ensembl.org/info/species?content-type=application/json _Use name, display_name, and accession from the API response as the species name, tooltip description, and version respectively._ To get all the available species we have to call the above info/species API for all the ensemble divisions that are returned from the first API. Add the logic in the retrieveDataContainer() method to check whether the species that is being loaded by the Ensembl provider is already present in the species list, if it's present don't add it if not add the species to the list and also, write logic to get the species name for the provided versionName. |
Implement logic to load the available genomes from Ensembl API:
*+To get the list of species (genomes) available in Ensembl:+* *GET info/divisions* Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/documentation/info/info_divisions Example: https://rest.ensembl.org/info/divisions?content-type=application/json *GET info/species* Lists all available species, their aliases, available adaptor groups, and data release. To get the species for that ensembl division, have to specify the division optional parameter. API to get the list of all species: https://rest.ensembl.org/documentation/info/species Example: https://rest.ensembl.org/info/species?content-type=application/json _Use name, display_name, and assembly from the API response as the species name, tooltip description, and version respectively._ To get all the available species we have to call the above info/species API for all the ensemble divisions that are returned from the first API. Add the logic in the retrieveDataContainer() method to check whether the species that is being loaded by the Ensembl provider is already present in the species list, if it's present don't add it if not add the species to the list and also, write logic to get the species name for the provided versionName. |
| Sprint | Summer 2 [ 196 ] | Summer 2, Summer 3 [ 196, 197 ] |
| Rank | Ranked higher |
| Sprint | Summer 2, Summer 3 [ 196, 197 ] | Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ] |
| Rank | Ranked higher |
| Story Points | 3 | 5 |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Sprint | Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ] | Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ] |
| Rank | Ranked higher |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Sprint | Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ] | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6 [ 196, 197, 198, 199, 200 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| 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 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |