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Consolidate #120

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dba2e36
consilidate 7 apps into 4
qzzhang Jun 6, 2023
0b9c821
remove scientific_name, genetic_code and domain from the input parame…
qzzhang Jun 7, 2023
4f2a909
removing ncbi_taxon_id as well
qzzhang Jun 7, 2023
91c4058
convert genomeset name to ref before fetch object data to avoid error…
qzzhang Jun 8, 2023
7b44e2e
updated RELEASE_NOTES.md and bumped up the version to 1.9.6
qzzhang Jun 8, 2023
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8 changes: 5 additions & 3 deletions RAST_SDK.spec
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Expand Up @@ -247,7 +247,7 @@ module RAST_SDK {


/*
For RAST annotating genomes/assemblies
For RAST annotating genomes/assemblies in bulk

Reference to a set of annotated Genome and/or Assembly objects in the workspace
@id ws KBaseSearch.GenomeSet
Expand All @@ -259,10 +259,12 @@ module RAST_SDK {
list<data_obj_ref> input_assemblies;
genomeSet_ref input_genomeset;
string input_text;
string scientific_name;

/*string scientific_name;
int genetic_code;
string domain;
int ncbi_taxon_id;
int ncbi_taxon_id;*/

int relation_engine_timestamp_ms;
string output_workspace;
string output_GenomeSet_name;
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4 changes: 4 additions & 0 deletions RELEASE_NOTES.md
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@@ -1,6 +1,10 @@
### OVERVIEW
This module wraps the RAST annotation pipeline for KBase.

### Version 1.9.6
__Changes__
Consolidated apps by combining 2 apps "Annotate Microbial Assembly with RASTtk - v1.073" and "Annotate Microbial Genome with RASTtk - v1.073" into "Annotate Genome/Assembly with RASTtk - v1.073"; another 2 apps "Annotate Multiple Microbial Assemblies with RASTtk - v1.073" and "Annotate Multiple Microbial Genomes with RASTtk - v1.073" into "Annotate Multiple Genomes/Assemblies with RASTtk - v1.073". After the consolidation, RETIRED the previousl 4 apps.

### Version 1.9.5
__Changes__
Added code to correct many errors in genomes created by RAST: added DNA sequence length to mRNA, added DNA sequence to non-coding genes, corrected repeat noncoding genes, fixed noncoding gene IDs, added md5 to noncoding genes
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2 changes: 1 addition & 1 deletion kbase.yml
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Expand Up @@ -10,7 +10,7 @@ service-language:
perl

module-version:
1.9.5
1.9.6

owners:
[chenry, scanon, olson, jjeffryes, umaganapathyswork, landml, gaprice, qzhang, ialarmedalien]
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7 changes: 5 additions & 2 deletions lib/RAST_SDK/AnnotationUtils.pm
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Expand Up @@ -3317,7 +3317,7 @@ sub _get_bulk_rast_parameters {
my $ws = $params->{output_workspace};
my $in_assemblies = $params->{input_assemblies};
my $in_genomes = $params->{input_genomes};
my $in_genomeset_ref = $params->{input_genomeset};
my $in_genomeset = $params->{input_genomeset};
my $in_text = $params->{input_text};

print "*********Input genomes------\n".Dumper($in_genomes)."\n";
Expand All @@ -3327,7 +3327,10 @@ sub _get_bulk_rast_parameters {

# If a genomeSet object is given in the input, fetch the genome refs and add them to
# the $in_genomes array first.
if ($in_genomeset_ref) {
if ($in_genomeset) {
my $chk = $self->_validate_KB_objref_name($in_genomeset);
my $gnmset_info = $self->_fetch_object_info($in_genomeset, $chk, $ws);
my $in_genomeset_ref = $gnmset_info->[6].'/'.$gnmset_info->[0].'/'.$gnmset_info->[4];
my $genomeset_data = $self->_fetch_object_data($in_genomeset_ref);
my $genomeset_elements = $genomeset_data->{elements};
for my $ele_key (keys(%{$genomeset_elements})) {
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24 changes: 4 additions & 20 deletions lib/RAST_SDK/RAST_SDKImpl.pm
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Expand Up @@ -3,9 +3,9 @@ use strict;
use Bio::KBase::Exceptions;
# Use Semantic Versioning (2.0.0-rc.1)
# http://semver.org
our $VERSION = '1.9.3';
our $GIT_URL = 'https://github.com/kbaseapps/RAST_SDK';
our $GIT_COMMIT_HASH = '5e51d931af209b9ffda681301703e03cf5868e02';
our $VERSION = '1.9.5';
our $GIT_URL = 'https://github.com/kbaseapps/RAST_SDK.git';
our $GIT_COMMIT_HASH = '0b9c821d171634c9ea4ea1bf108b31cbc3401e66';

=head1 NAME

Expand Down Expand Up @@ -2183,10 +2183,6 @@ BulkRastGenomesAssembliesParams is a reference to a hash where the following key
input_assemblies has a value which is a reference to a list where each element is a RAST_SDK.data_obj_ref
input_genomeset has a value which is a RAST_SDK.genomeSet_ref
input_text has a value which is a string
scientific_name has a value which is a string
genetic_code has a value which is an int
domain has a value which is a string
ncbi_taxon_id has a value which is an int
relation_engine_timestamp_ms has a value which is an int
output_workspace has a value which is a string
output_GenomeSet_name has a value which is a string
Expand All @@ -2211,10 +2207,6 @@ BulkRastGenomesAssembliesParams is a reference to a hash where the following key
input_assemblies has a value which is a reference to a list where each element is a RAST_SDK.data_obj_ref
input_genomeset has a value which is a RAST_SDK.genomeSet_ref
input_text has a value which is a string
scientific_name has a value which is a string
genetic_code has a value which is an int
domain has a value which is a string
ncbi_taxon_id has a value which is an int
relation_engine_timestamp_ms has a value which is an int
output_workspace has a value which is a string
output_GenomeSet_name has a value which is a string
Expand Down Expand Up @@ -3150,7 +3142,7 @@ report_ref has a value which is a string

=item Description

For RAST annotating genomes/assemblies
For RAST annotating genomes/assemblies in bulk

Reference to a set of annotated Genome and/or Assembly objects in the workspace
@id ws KBaseSearch.GenomeSet
Expand Down Expand Up @@ -3192,10 +3184,6 @@ input_genomes has a value which is a reference to a list where each element is a
input_assemblies has a value which is a reference to a list where each element is a RAST_SDK.data_obj_ref
input_genomeset has a value which is a RAST_SDK.genomeSet_ref
input_text has a value which is a string
scientific_name has a value which is a string
genetic_code has a value which is an int
domain has a value which is a string
ncbi_taxon_id has a value which is an int
relation_engine_timestamp_ms has a value which is an int
output_workspace has a value which is a string
output_GenomeSet_name has a value which is a string
Expand All @@ -3211,10 +3199,6 @@ input_genomes has a value which is a reference to a list where each element is a
input_assemblies has a value which is a reference to a list where each element is a RAST_SDK.data_obj_ref
input_genomeset has a value which is a RAST_SDK.genomeSet_ref
input_text has a value which is a string
scientific_name has a value which is a string
genetic_code has a value which is an int
domain has a value which is a string
ncbi_taxon_id has a value which is an int
relation_engine_timestamp_ms has a value which is an int
output_workspace has a value which is a string
output_GenomeSet_name has a value which is a string
Expand Down
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