rbbt-sources 3.1.17 → 3.1.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: bf8a7403301523a87252057d4be1ac9e0f348708
-  data.tar.gz: '0939814d7b68cb713e05b5f1af2a572a8fffee75'
+  metadata.gz: d6a24c95d852df442ed303fe4fdc57b47b2fd0f2
+  data.tar.gz: ea6a37e44a97d4a8659a8d07ee58f7264fa50062
 SHA512:
-  metadata.gz: 779c0aa427ee0335a2533533179e05ef0c42c543316ea7cd9eb3c5b793f6603ea46cf63bffba71df9aed9cec0fc08df984255c1c3a83fe85c9bb5b51048395d1
-  data.tar.gz: 8a78a7bc1e4ba4819849c0375a1d6744e20bce89cdaf91e1c21cd26d4541f2ff91bd1d5aa9bed05e38b211051cc51774df2b0d2eb198bd4500d94c95196d48ac
+  metadata.gz: a78985096754ac5d3689f06306c470b2f82334c9e427cb5efe05a88d78051fab07644e656f646079903eb2811642274039b6b71b8c233ef9e2f7fa45dd672add
+  data.tar.gz: 99004a5e7c6bc624f371f70306600cca13f915a13c2021c7ac50705206b6cc8df678d757843ab6e969c0b5dd4b453ce3e8f58d9ad0b9b766162e9042cb108842

data/etc/allowed_biomart_archives

@@ -1,9 +1,7 @@
 may2009
 may2012
-sep2013
-jan2013
-feb2014
 dec2013
+feb2014
 dec2014
 dec2015
 oct2016

data/etc/biomart/missing_in_archive

@@ -1,10 +1,13 @@
+">dec2016":
+    - uniprot_swissprot_accession~uniprotswissprot
+    - uniprot_swissprot~uniprotswissprot
+    - codelink
 "<jun2009":
     - refseq_mrna
     - refseq_ncrna
     - refseq_mrna_predicted
     - refseq_ncrna_predicted 
 ">jun2015":
-    - uniprot_swissprot
     - uniprot_swissprot_accession~uniprot_swissprot
 <aug2014:
     - external_gene_name~external_gene_id

data/lib/rbbt/sources/biomart.rb

@@ -209,8 +209,12 @@ module BioMart
       orig,_sep, new = str.partition "~"
       changes[orig] = new
     end
-    attrs = attrs.collect{|n,k| [n, changes[k] || k] }
-    attrs
+    changed = true
+    while changed
+      new_attrs = attrs.collect{|n,k| [n, changes[k] || k] }
+      changed = new_attrs != attrs
+      attrs = new_attrs
+    end
 
 
     codes = attrs.collect{|attr| attr[1]}

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.17
+  version: 3.1.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-10 00:00:00.000000000 Z
+date: 2017-08-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -181,24 +181,24 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.6
+rubygems_version: 2.6.12
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/sources/test_pubmed.rb
-- test/rbbt/sources/test_string.rb
-- test/rbbt/sources/test_gscholar.rb
-- test/rbbt/sources/test_biomart.rb
 - test/rbbt/sources/test_go.rb
+- test/rbbt/sources/test_pubmed.rb
 - test/rbbt/sources/test_pina.rb
-- test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_organism.rb
-- test/rbbt/sources/test_matador.rb
-- test/rbbt/sources/test_tfacts.rb
-- test/rbbt/sources/test_kegg.rb
 - test/rbbt/sources/test_synapse.rb
+- test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_stitch.rb
+- test/rbbt/sources/test_biomart.rb
 - test/rbbt/sources/test_HPRD.rb
+- test/rbbt/sources/test_string.rb
+- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_tfacts.rb
+- test/rbbt/sources/test_matador.rb
+- test/rbbt/sources/test_gscholar.rb
+- test/test_helper.rb