rbbt-sources 3.2.16 → 3.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0745fa19486f2c9c8c86b24ddf5f44689aa010c500db0bf7fadfc67e03072bf8
-  data.tar.gz: b6d5f1481202d3f191b725f5c0021c371a4f044e14661d3534d31a260ffb480e
+  metadata.gz: b10dbe140b4c0733476823e5f5d94e57a3d9a755fc370f6b9640d1e7b8efc368
+  data.tar.gz: 38aaf56670a07537ad0ef0c025d17e655fc5d7fb87d97ee1c08d0af82c44fbbd
 SHA512:
-  metadata.gz: 1241babce1692c616242e1ef5a501c5e337f3b042110fca932ee3e320ade576538be40723968eabac97ea02133d58144275f5949c3288926d87fc03192417522
-  data.tar.gz: 53b45cbb861f44f2f4f51f4e14a36c3f70210d729f45138228ac06a542857162e94f736b0b43a107af413da0ff68247061e4d99a774932fa5b4f65b3547205c3
+  metadata.gz: a8ac9df1da30fc7aec3c54a5a200a0c7a9629807b9238089a1e8064e78b0ecd5bad36c4b6a77fac7e7cfdf332ad56be06149b12d0e0fd7f6506b0b82d2e03bcf
+  data.tar.gz: acff50e8bdb0d4443c3e1dbd237539953206b7d5dcb886db64ec0677f7bba43cf3a9782e4147985a9b3fc1b34df692e89fb2b7185f2aa0f93ccd196a4d19d54a

data/etc/allowed_biomart_archives

@@ -1,6 +1,7 @@
 may2009
 feb2014
 may2017
+oct2018
 apr2019
 feb2021
 feb2023

data/lib/rbbt/sources/biomart.rb

@@ -15,7 +15,7 @@ module BioMart
 
   BIOMART_URL = 'http://www.ensembl.org/biomart/martservice?query='
 
-  MISSING_IN_ARCHIVE = Rbbt.etc.biomart.missing_in_archive.exists? ? Rbbt.etc.biomart.missing_in_archive.yaml : {}
+  MISSING_IN_ARCHIVE = Rbbt.etc.biomart.missing_in_archive.exists? ? Rbbt.etc.biomart.missing_in_archive.find.yaml : {}
 
   private
 
@@ -33,7 +33,7 @@ module BioMart
    
   def self.set_archive(date)
     if defined? Rbbt and Rbbt.etc.allowed_biomart_archives.exists?
-      raise "Biomart archive #{ date } is not allowed in this installation" unless Rbbt.etc.allowed_biomart_archives.read.split("\n").include? date
+      raise "Biomart archive #{ date } is not allowed in this installation" unless Rbbt.etc.allowed_biomart_archives.find.read.split("\n").include? date
     end
     Thread.current['archive'] = date
     Thread.current['archive_url'] = BIOMART_URL.sub(/www/, date + '.archive')

data/lib/rbbt/sources/pubmed.rb

@@ -241,11 +241,13 @@ module PubMed
     pmids = [pmids] unless Array === pmids
     pmids = pmids.compact.collect{|id| id}
 
+    chunk_size = 50
     result_files = FileCache.cache_online_elements(pmids, 'pubmed-{ID}.xml') do |ids|
       result = {}
       values = []
-      chunks = Misc.divide(ids, (ids.length / 20) + 1)
+      chunks = Misc.divide(ids, (ids.length / chunk_size) + 1)
       Log::ProgressBar.with_bar(chunks.length, :desc => "Downloading articles from PubMed") do |bar|
+        bar.init
         chunks.each do |list|
           begin
             Misc.try3times do

data/lib/rbbt/sources/signor.rb

@@ -19,7 +19,11 @@ module Signor
   end
   
   Signor.claim Signor.data, :proc do
-    Signor[".source/all.csv"].tsv :header_hash => '', :merge => true, :zipped => true
+    begin
+      Signor[".source/all.csv"].tsv :header_hash => '', :merge => true, :zipped => true
+    rescue
+      Signor[".source/all.csv"].tsv :header_hash => '', :merge => true, :one2one => true
+    end
   end
 
   Signor.claim Signor.protein_protein, :proc do 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.2.16
+  version: 3.3.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-18 00:00:00.000000000 Z
+date: 2023-12-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -164,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.19
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)