ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2018-09-06T10:50:07Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/64[ENSCORESW-2690]. Close only if we've really got an iterator, can get…2018-09-06T10:50:07ZMarek Szuba[ENSCORESW-2690]. Close only if we've really got an iterator, can get…*Created by: sanjay-boddu*
… an empty hash ref under special cases.
## Requirements
- Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed ...*Created by: sanjay-boddu*
… an empty hash ref under special cases.
## Requirements
- Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
- Review the [Ensembl contributing guidelines](https://github.com/Ensembl/ensembl/blob/release/90/CONTRIBUTING.md#why-could-my-pull-request-be-rejected); remember in particular:
- do not modify code without testing for regression
- provide simple unit tests to test the changes
- the PR must not fail unit testing
## Description
This is a request to cherry pick one of the commits from release/93 to release/92.
## Use case
_Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place._
## Benefits
_If applicable, describe the advantages the changes will have._
## Possible Drawbacks
_If applicable, describe any possible undesirable consequence of the changes._
## Testing
_Have you added/modified unit tests to test the changes?_
_If so, do the tests pass/fail?_
_Have you run the entire test suite and no regression was detected?_
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/77Check response status code instead of message for file fetch requests (for e96)2019-02-14T16:28:12ZMarek SzubaCheck response status code instead of message for file fetch requests (for e96)*Created by: imransl*
This is the same as #74 for e96.*Created by: imransl*
This is the same as #74 for e96.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/75Check response status code instead of message for file fetch requests (for e95)2019-02-15T11:00:30ZMarek SzubaCheck response status code instead of message for file fetch requests (for e95)*Created by: imransl*
This is the same as #74 for e95.*Created by: imransl*
This is the same as #74 for e95.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/61Improvements to error reporting - ENSWEB-20522018-08-01T11:58:15ZMarek SzubaImprovements to error reporting - ENSWEB-2052*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files
## Use case
Mainly for use when attaching trackhubs and parsing their files. See JIRA ENSWEB-2052.
## Benefits
Improve...*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files
## Use case
Mainly for use when attaching trackhubs and parsing their files. See JIRA ENSWEB-2052.
## Benefits
Improved usability
## Possible Drawbacks
None.
## Testing
Tested in browser. No applicable unit tests.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/45[ENSWEB-2126] Extra param size_limit added to avoid loading bix files2018-12-17T16:17:48ZMarek Szuba[ENSWEB-2126] Extra param size_limit added to avoid loading bix files*Created by: ens-hsr*
*Created by: ens-hsr*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/31'defined' will return 1 if compression is provided2018-12-17T16:17:52ZMarek Szuba'defined' will return 1 if compression is provided*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/49EnsEMBL::Web::Tree changed2018-12-17T16:17:44ZMarek SzubaEnsEMBL::Web::Tree changed*Created by: ens-hsr*
*Created by: ens-hsr*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/67Allow .bgz/.bgz.tbi files to be read in TabixParser2018-09-19T16:12:19ZMarek SzubaAllow .bgz/.bgz.tbi files to be read in TabixParser*Created by: ima23*
## Description
Some resources use _.bgz_ as ending for a BGZF-compressed vcf files (example gnomAD). Currently TabixParser allows only _.gz_ files to be read.
## Use case
The current changes will allow user...*Created by: ima23*
## Description
Some resources use _.bgz_ as ending for a BGZF-compressed vcf files (example gnomAD). Currently TabixParser allows only _.gz_ files to be read.
## Use case
The current changes will allow users to use _.vcf.bgz_ files for VEP custom annotations.
## Benefits
TabixParser will be able to process .bgz files and allow extended VEP custom annotations.
## Possible Drawbacks
_If applicable, describe any possible undesirable consequence of the changes._
## Testing
_Have you added/modified unit tests to test the changes?_
Yes.
_If so, do the tests pass/fail?_
Tests pass.
_Have you run the entire test suite and no regression was detected?_
Yes, tests passed.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/80Reinstate line deleted by accident2019-02-22T13:27:14ZMarek SzubaReinstate line deleted by accident*Created by: ens-ap5*
As per discussion with Mark & Tiago on 21/02/19*Created by: ens-ap5*
As per discussion with Mark & Tiago on 21/02/19https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/66Allow .bgz/.bgz.tbi files to be read in TabixParser2018-09-19T16:16:18ZMarek SzubaAllow .bgz/.bgz.tbi files to be read in TabixParser*Created by: ima23*
## Description
Some resources use _.bgz_ as ending for a BGZF-compressed vcf files (example gnomAD). Currently TabixParser allows only _.gz_ files to be read.
## Use case
The current changes will allow user...*Created by: ima23*
## Description
Some resources use _.bgz_ as ending for a BGZF-compressed vcf files (example gnomAD). Currently TabixParser allows only _.gz_ files to be read.
## Use case
The current changes will allow users to use _.vcf.bgz_ files for VEP custom annotations.
## Benefits
TabixParser will be able to process .bgz files and allow extended VEP custom annotations.
## Possible Drawbacks
_If applicable, describe any possible undesirable consequence of the changes._
## Testing
_Have you added/modified unit tests to test the changes?_
Yes.
_If so, do the tests pass/fail?_
Tests pass.
_Have you run the entire test suite and no regression was detected?_
Yes, tests passed.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/19Respect the html parameter in trackDb file2015-10-07T12:53:18ZMarek SzubaRespect the html parameter in trackDb file*Created by: brucebolt*
I have noticed the UCSC TrackHub specification has a html parameter for the description file URL (see https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#html), which appears not to be used by Ensembl...*Created by: brucebolt*
I have noticed the UCSC TrackHub specification has a html parameter for the description file URL (see https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#html), which appears not to be used by Ensembl. Instead, Ensembl generates its own description URL based on the track name.
This modification looks for a html parameter before using Ensembl’s default assumed URL. It also deals with inheritance of the parent's description if a parent value is specified.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/76Check response status code instead of message for file fetch requests (for e94)2019-02-14T16:22:37ZMarek SzubaCheck response status code instead of message for file fetch requests (for e94)*Created by: imransl*
This is the same as #74 for e94.*Created by: imransl*
This is the same as #74 for e94.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/24Remove unnecessary dependencies2015-12-11T16:12:20ZMarek SzubaRemove unnecessary dependencies*Created by: davidrichardson*
Removed unused import of assert_ref and changed throw to confess
*Created by: davidrichardson*
Removed unused import of assert_ref and changed throw to confess
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/74Check response status code instead of message for file fetch requests2019-02-14T15:21:39ZMarek SzubaCheck response status code instead of message for file fetch requests*Created by: imransl*
This fixes responses that have a message other than 'OK' (e.g. Gatewaying) failing. An example issue is, the Allele Frequency Calculator stopped submitting jobs to the hive as the FTP files fetched for it always re...*Created by: imransl*
This fixes responses that have a message other than 'OK' (e.g. Gatewaying) failing. An example issue is, the Allele Frequency Calculator stopped submitting jobs to the hive as the FTP files fetched for it always return 'Gatewaying' as the reponse message. However, the status code was always 200 and the file was successfully fetched too.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/62Changes required to support bigInteract format - ENSWEB-47512018-08-14T09:33:03ZMarek SzubaChanges required to support bigInteract format - ENSWEB-4751*Created by: ens-ap5*
## Description
Extend the BED/bigBed parsers to allow location data to be retrieved by column index.
## Use case
UCSC have introduced another variation on bigBed format, designed for use with long-range in...*Created by: ens-ap5*
## Description
Extend the BED/bigBed parsers to allow location data to be retrieved by column index.
## Use case
UCSC have introduced another variation on bigBed format, designed for use with long-range interactions. However as part of their specification they encourage their users to set their own column names in the AutoSQL for the source and target locations, meaning that our web code cannot rely on using the default column names to fetch this data. See https://genome.ucsc.edu/goldenpath/help/interact.html
We must therefore rely on the column index alone, which is not currently supported by the bed-like parsers.
## Benefits
Enables us to support this new format in the browser.
## Possible Drawbacks
Perhaps not the most elegant solution, but the changes to the BED parser are mainly to keep things DRY. We need to convert UCSC chromosome names into Ensembl ones, and zero-based coordinates into Ensembl coordinates, so being able to do this for any arbitrary column saves repeating code in the bigBed parser.
## Testing
I've run the bed.t and bigbed.t tests, which passed successfully. I'm not aware of any other tests that would be affected by this change since it's specific to these formats.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/18Fix for bug in GTF get_attribute_by_name2015-08-21T15:34:47ZMarek SzubaFix for bug in GTF get_attribute_by_name*Created by: davidrichardson*
The method get_attribute_by_name in modules/Bio/EnsEMBL/IO/Parser/GTF.pm fails for ensembl GTF files, due to a space between ; and the attribute key. Test case for GTF files is included.
Also removed the ...*Created by: davidrichardson*
The method get_attribute_by_name in modules/Bio/EnsEMBL/IO/Parser/GTF.pm fails for ensembl GTF files, due to a space between ; and the attribute key. Test case for GTF files is included.
Also removed the last use of throw from modules/Bio/EnsEMBL/IO/TextParser.pm
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/111ENSCORESW-3526 updated metakey provider.* to assembly.provider_*2020-08-17T14:56:48ZMarek SzubaENSCORESW-3526 updated metakey provider.* to assembly.provider_**Created by: ameya1981*
Changes made for 102:
Same as https://github.com/Ensembl/ensembl-io/pull/110.
Change in metakey from provider.* to assembly.provider_**Created by: ameya1981*
Changes made for 102:
Same as https://github.com/Ensembl/ensembl-io/pull/110.
Change in metakey from provider.* to assembly.provider_*https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/113104 version bump in testdbs2020-09-18T15:46:16ZMarek Szuba104 version bump in testdbs*Created by: ameya1981*
version bump in testdbs for 104. Part of release SOP.*Created by: ameya1981*
version bump in testdbs for 104. Part of release SOP.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/103add try::tiny2020-07-08T11:30:07ZMarek Szubaadd try::tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tinyhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/110ENSCORESW-3526 updated provider.* metakeys to assembly.proivder_*2020-08-17T14:56:20ZMarek SzubaENSCORESW-3526 updated provider.* metakeys to assembly.proivder_**Created by: ameya1981*
Same as https://github.com/Ensembl/ensembl/pull/504*Created by: ameya1981*
Same as https://github.com/Ensembl/ensembl/pull/504