Provided access to human split-out data. #296
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Previously no end-user access was provided to unconcented human split-out data. For each study a new iRODS group will be created. This pull request enables access to the nonconcented human data via this new group.
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| if (@groups == 1) { # Do not give access to nc human data to multiple groups. | ||
| my $give_human_subset_access = 0; | ||
| my @af_avus = $self->find_in_metadata($ALIGNMENT_FILTER); | ||
| if (not @af_avus and $self->str =~ /_human[.]/xms) { |
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Can you expand on why the path fallback check is needed? As this is in the base class the behaviour will be inherited broadly, including by legacy genotype code, which could be given incorrent permissions as a result.
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As far as I understand, there is an intention to create and store in iRODS split-out human data, which will or might originate from outside of the main NPG Illumina pipeline. This data might not belong to Illumina platform. The requirement for this task was to provide this scpecial level of access to files with names containing the _human string. There is not firm agreement at the moment that fies like this will have the alignment_filter metadata set. Therefore, the code covers both eventualities.
As far as I understand, the requirement is to inherit the behaviour broadly. Personally, I prefer the version of this implementation in #297 and a sibling wtsi-npg/npg_irods#439. It ishould also be possible, though I have not tried this, to move the expected_groups method as it is in #297 to the npg_irods package if it has a seq platform independent part.
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I'll mark this as approved, but this change must not break https://github.com/wtsi-npg/genotyping which also depends on this package.
Previously no end-user access was provided to
unconcented human split-out data. For each study a new iRODS group will be created. This pull request enables access to the nonconcented human data via this new group.