ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2015-08-20T15:21:12Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/17Support parsing from an already open file handle.2015-08-20T15:21:12ZMarek SzubaSupport parsing from an already open file handle.*Created by: andrewyatz*
This changes the code in TextParser to check if the given filename was a file handle. If it is a file handle the code just assigns it and assumes you know what you are doing.
There was also some cleaning up of ...*Created by: andrewyatz*
This changes the code in TextParser to check if the given filename was a file handle. If it is a file handle the code just assigns it and assumes you know what you are doing.
There was also some cleaning up of the open_content() method to delegate to open() once it had created the in-memory filehandle. It seemed odd not to do once open() could support open filehandles.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/16Keeping core API dependencies to a minimum2015-08-20T11:37:57ZMarek SzubaKeeping core API dependencies to a minimum*Created by: andrewyatz*
It seems we have others within the team that would like to use ensembl-io but will not because of the core dependency. This commit attempts to
1. Remove any use of Utils::Exception and replace it with Carp
2. Re...*Created by: andrewyatz*
It seems we have others within the team that would like to use ensembl-io but will not because of the core dependency. This commit attempts to
1. Remove any use of Utils::Exception and replace it with Carp
2. Remove any use of Utils::IO work_with_file and replace it with an open
3. Remove any unused/unnecessary imports (there were a lot)
Also this commit pulls up that simple_list.t is no longer a valid test because its dependencies are broken.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/15Adding travis-ci tests2015-08-20T11:38:15ZMarek SzubaAdding travis-ci tests*Created by: andrewyatz*
This brings in a lot of changes to support Travis-CI's running of the test suite. Reading through the tests I believe they've fallen into disrepair due to their infrequent running. Once this change is integrated...*Created by: andrewyatz*
This brings in a lot of changes to support Travis-CI's running of the test suite. Reading through the tests I believe they've fallen into disrepair due to their infrequent running. Once this change is integrated we will need to switch on the Travis-CI webhook.
It has also caused a few changes to the tests run already to remove any code which should be using alternative TAP compatible solutions.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/14License was not correct. This is an Apache2 project.2015-08-20T11:38:20ZMarek SzubaLicense was not correct. This is an Apache2 project.*Created by: andrewyatz*
In a number of places the Apache2 license was not applied, the older
Apache-like license was applied or dates were wrong. A header LICENSE
file was not present. It has now been added to all files.
*Created by: andrewyatz*
In a number of places the Apache2 license was not applied, the older
Apache-like license was applied or dates were wrong. A header LICENSE
file was not present. It has now been added to all files.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/13ENSWEB-1560: Overzealous caching of sample ids.2015-08-14T10:51:02ZMarek SzubaENSWEB-1560: Overzealous caching of sample ids.*Created by: ens-ds23*
If an array then key by contents of array not the ref which we might be unlucky and have cached before and it been reused.
This bug affects display of multiple puplation LD views on live site.
*Created by: ens-ds23*
If an array then key by contents of array not the ref which we might be unlucky and have cached before and it been reused.
This bug affects display of multiple puplation LD views on live site.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/9Duplicate all methods that relate to individual data in a VCF file.2015-05-19T15:27:35ZMarek SzubaDuplicate all methods that relate to individual data in a VCF file.*Created by: at7*
For the duplicated methods replace individual by sample to match
the new sample schema in the variation API. The plan is to store all genotype information on sample level. For now leave methods that relate to individua...*Created by: at7*
For the duplicated methods replace individual by sample to match
the new sample schema in the variation API. The plan is to store all genotype information on sample level. For now leave methods that relate to individual. But deprecate them first and then remove them from the parser.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/10add non_ref_only option when fetching genotypes2015-06-02T07:59:43ZMarek Szubaadd non_ref_only option when fetching genotypes*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/8Non-extended summary retrieval for BigWigs.2015-04-23T14:08:06ZMarek SzubaNon-extended summary retrieval for BigWigs.*Created by: ens-ds23*
Saves us having to do the computation ourselves.
*Created by: ens-ds23*
Saves us having to do the computation ourselves.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/7Fix trackDb absolute url bug.2015-04-08T06:59:33ZMarek SzubaFix trackDb absolute url bug.*Created by: ens-ds23*
Typo in regex.
*Created by: ens-ds23*
Typo in regex.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/11fix for slightly clumsy passing of args to synonym methods2015-06-02T09:41:19ZMarek Szubafix for slightly clumsy passing of args to synonym methods*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/6fix when individual_ids not defined2015-03-30T13:09:14ZMarek Szubafix when individual_ids not defined*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/4don't assume diploid2014-10-29T09:29:13ZMarek Szubadon't assume diploid*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/2Add some new features and fixes for the VCF backend code in the Variation API2014-10-08T10:06:45ZMarek SzubaAdd some new features and fixes for the VCF backend code in the Variation API*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/3fix misuse of get_alternatives in get_start2014-10-24T15:13:31ZMarek Szubafix misuse of get_alternatives in get_start*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/1Feature/blast parser2018-12-17T16:18:00ZMarek SzubaFeature/blast parser*Created by: avullo*
This is a parser of BLAST+ applications (e.g. blast_formatter) formatted outputs.
WARNING:
Support is only provided for a LIMITED number of ouptut formats, the column based ones.
In other words, this parser will ...*Created by: avullo*
This is a parser of BLAST+ applications (e.g. blast_formatter) formatted outputs.
WARNING:
Support is only provided for a LIMITED number of ouptut formats, the column based ones.
In other words, this parser will only correctly parse output files which have been
produced by a BLAST+ application by specifying one of the following "alignment view options":
- 6: tabular
- 7: tabular with comment lines
- 10: comma-separated values
The parser's "open" method understand two arguments, the first is the name of the file to
parse, and the second is the same string as the output format given to the BLAST+ application
with the option '-outfmt'.
Valid output formats are those containing just the alignment view option with no format specifiers,
e.g. '6', '7' or '10', in which case the parser will parse the columns as if they were in
the order of the blast_formatter default format specifiers:
'seqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore',
or will parse the columns as if they were in the order specified in the open method second
argument, e.g.:
'7 qacc sacc evalue score nident pident qstart qend sstart send length positive ppos qseq sseq'
will parse qacc, sacc, ... separated by tabs.
IMPORTANT:
The parser automatically generates get_raw_[field_name] and get_[field_name] accessor methods
for [field_name], where [field_name] is the name of a format specifier specified in the output
format string.
Invoking a getter method for a field which is not in the output format raises an exception.
Tests have been done for all three supported alignment view options (6, 7 and 10). Option 7 has
been tested with the output format used by Compara in Bio::EnsEMBL::Compara::RunnableDB::BlastAndParsePAF,
and with an output format as closely as possible to that used by the Ensembl Web team in their NCBIBLAST module in the private sanger-plugins repo.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/5fix when individual_ids not defined2015-03-30T13:09:02ZMarek Szubafix when individual_ids not defined*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/87Patch the variation test database to version 98 [release/98]2019-06-19T13:21:59ZMarek SzubaPatch the variation test database to version 98 [release/98]*Created by: mkszuba*
I forgot that patch_test_databases can only handle single-version bumps so with the test databases having only fully been sinced with 97 on the relevant release branch, the variation schema ended up remaining at 96...*Created by: mkszuba*
I forgot that patch_test_databases can only handle single-version bumps so with the test databases having only fully been sinced with 97 on the relevant release branch, the variation schema ended up remaining at 96 on master even when all other DBs got bumped to 98. Manually apply variation schema patches to bring that test DB up to date.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/88Travis: explicitly use Ubuntu Trusty for builds2019-06-25T12:08:02ZMarek SzubaTravis: explicitly use Ubuntu Trusty for builds*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
...*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
## Description
It has turned out that in spite of what the Travis documentation says, perl-5.14 is *not* available under the Xenial environment on Travis. We still require compatibility with that Perl version so it is necessary for us to make sure we continue to use Trusty even after the default Travis environment has been changed to Xenial, a change that is now in progress following the end of life of Ubuntu Trusty (see https://blog.travis-ci.com/2019-04-15-xenial-default-build-environment).
## Possible Drawbacks
Ubuntu Trusty has already reached end of life.
## Testing
_Have you added/modified unit tests to test the changes?_
No, changes affect Travis only.
_If so, do the tests pass/fail?_
N/A
_Have you run the entire test suite and no regression was detected?_
No, changes affect Travis only.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/84README: Use the same badge syntax as for 'ensembl'2019-06-17T14:45:50ZMarek SzubaREADME: Use the same badge syntax as for 'ensembl'*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branch*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branchhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/82[ENSCORESW-3077] Travis: Unify configuration of Slack notifications2019-04-23T08:40:50ZMarek Szuba[ENSCORESW-3077] Travis: Unify configuration of Slack notifications*Created by: mkszuba*
Use the same Slack access token as well as the same notification configuration for all Infrastructure repositories.*Created by: mkszuba*
Use the same Slack access token as well as the same notification configuration for all Infrastructure repositories.