RubyGems - rbbt-sources - Versions diffs - 3.3.0 → 3.4.1 - Mend

rbbt-sources 3.3.0 → 3.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (26) hide show

checksums.yaml +4 -4
data/etc/allowed_biomart_archives +2 -4
data/etc/biomart/missing_in_archive +2 -0
data/etc/build_organism +4 -4
data/etc/organisms +1 -0
data/lib/rbbt/sources/biomart.rb +48 -13
data/lib/rbbt/sources/ensembl_ftp.rb +31 -15
data/lib/rbbt/sources/entrez.rb +13 -0
data/lib/rbbt/sources/go.rb +2 -2
data/lib/rbbt/sources/mesh.rb +26 -0
data/lib/rbbt/sources/organism.rb +45 -24
data/lib/rbbt/sources/pubmed.rb +13 -2
data/share/install/Organism/{Hsa/Rakefile → Hsa.rake} +23 -15
data/share/install/Organism/{Mmu/Rakefile → Mmu.rake} +3 -20
data/share/install/Organism/{Rno/Rakefile → Rno.rake} +3 -8
data/share/install/Organism/Sce.rake +38 -0
data/share/install/Organism/organism_helpers.rb +126 -53
data/share/install/lib/rake_helper.rb +2 -2
data/test/rbbt/sources/test_biomart.rb +44 -6
data/test/rbbt/sources/test_ensembl_ftp.rb +11 -0
data/test/rbbt/sources/test_entrez.rb +5 -0
data/test/rbbt/sources/test_mesh.rb +10 -0
data/test/rbbt/sources/test_organism.rb +15 -15
data/test/rbbt/sources/test_pubmed.rb +18 -8
metadata +12 -7
data/share/install/Organism/Sce/Rakefile +0 -52

metadata CHANGED Viewed

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.3.0
+  version: 3.4.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-12-21 00:00:00.000000000 Z
+date: 2025-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -95,6 +95,7 @@ files:
 - lib/rbbt/sources/jochem.rb
 - lib/rbbt/sources/kegg.rb
 - lib/rbbt/sources/matador.rb
+- lib/rbbt/sources/mesh.rb
 - lib/rbbt/sources/oncodrive_role.rb
 - lib/rbbt/sources/oreganno.rb
 - lib/rbbt/sources/organism.rb
@@ -119,10 +120,10 @@ files:
 - share/install/KEGG/Rakefile
 - share/install/Matador/Rakefile
 - share/install/NCI/Rakefile
-- share/install/Organism/Hsa/Rakefile
-- share/install/Organism/Mmu/Rakefile
-- share/install/Organism/Rno/Rakefile
-- share/install/Organism/Sce/Rakefile
+- share/install/Organism/Hsa.rake
+- share/install/Organism/Mmu.rake
+- share/install/Organism/Rno.rake
+- share/install/Organism/Sce.rake
 - share/install/Organism/organism_helpers.rb
 - share/install/PharmaGKB/Rakefile
 - share/install/Pina/Rakefile
@@ -132,11 +133,13 @@ files:
 - share/install/lib/rake_helper.rb
 - test/rbbt/sources/test_HPRD.rb
 - test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_ensembl_ftp.rb
 - test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_gscholar.rb
 - test/rbbt/sources/test_kegg.rb
 - test/rbbt/sources/test_matador.rb
+- test/rbbt/sources/test_mesh.rb
 - test/rbbt/sources/test_organism.rb
 - test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_pina.rb
@@ -164,18 +167,20 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.0.dev
+rubygems_version: 3.5.23
 signing_key:
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
 - test/rbbt/sources/test_HPRD.rb
 - test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_ensembl_ftp.rb
 - test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_gscholar.rb
 - test/rbbt/sources/test_kegg.rb
 - test/rbbt/sources/test_matador.rb
+- test/rbbt/sources/test_mesh.rb
 - test/rbbt/sources/test_organism.rb
 - test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_pina.rb

data/share/install/Organism/Sce/Rakefile DELETED Viewed

@@ -1,52 +0,0 @@
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__),'..', '..', '..', '..', 'lib'))
-require 'rbbt/sources/biomart'
-require 'rbbt/sources/entrez'
-require File.join(File.dirname(__FILE__), '../../lib/helpers')
-$taxs = [559292,4932]
-$scientific_name = "Saccharomyces cerevisiae"
-#$ortholog_key = "yeast_ensembl_gene"
-$biomart_db = 'scerevisiae_gene_ensembl'
-$biomart_lexicon = [
-  [ 'Associated Gene Name' , "external_gene_id"],
-]
-$biomart_protein_identifiers = [
-  [ 'Protein ID', "protein_id"  ],
-  [ 'RefSeq Protein ID', "refseq_peptide"  ],
-  [ 'Unigene ID', "unigene"  ],
-  [ 'UniProt/SwissProt ID', "uniprot_swissprot"  ],
-  [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession"  ],
-]
-$biomart_probe_identifiers = [
-]
-$biomart_identifiers = [
-  [ 'Entrez Gene ID', "entrezgene"],
-  [ 'Ensembl Protein ID', "ensembl_peptide_id"  ],
-  [ 'Associated Gene Name', "external_gene_id"  ],
-  [ 'Protein ID', "protein_id"  ],
-  [ 'RefSeq Protein ID', "refseq_peptide"  ],
-  [ 'UniProt/SwissProt ID', "uniprot_swissprot"  ],
-  [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession"  ],
-  [ 'EMBL (Genbank) ID' , "embl"] ,
-  [ 'RefSeq mRNA' , "refseq_mrna"] ,
-]
-$biomart_go= [
-  ["GO ID", 'go_id'],
-  ["GO Namespace", 'namespace_1003'],
-]
-$biomart_go_2009= [
-  ["GO BP ID", 'go_biological_process_id'],
-  ["GO MF ID", 'go_molecular_function_id'],
-  ["GO CC ID", 'go_cellular_component_id'],
-]
-$namespace = File.basename(File.dirname(File.expand_path(__FILE__)))
-Thread.current["namespace"] = File.basename(File.dirname(File.expand_path(__FILE__)))
-load File.join(File.dirname(__FILE__), '../organism_helpers.rb')