rbbt-util 5.40.5 → 5.41.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 84c1669d61fce9e4a239ec7865aee04b67684f99911cc9e378b569517b819388
+  metadata.gz: 4bd731f2fb8604116f9baf947e8e0b5f5e8bd1b252773864f5a76e9c4b52126d
+  data.tar.gz: 82c364cc76d5921e49197c410d05a919e8b71a96d0499827b0546bf402c401ae
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-  data.tar.gz: 3e5c396193a6423d7c8afbb381c623844bf457d0a34ef329b7bfe6ac29f6a13841f23b9ce7c3bb051fdeeb35a2e72bfed16279aff52fb3a0ff1484b1587bb841
+  metadata.gz: 655e499e17ea4806f278ecaf83521c200aa978ace61c27f5aac0490bc99a40cac42498f323155ee3c547a2a98d23271a8fa6d3b424180c87b249b50219fb7235
+  data.tar.gz: c3ef8cc5790db9bb5df6d0853542355b267e2f8f26c4b6bc8305729b793eff8832a33479a53339605bcaf8b450a500dc58a9bd5557e1d993f8c8b72228ab1793

data/lib/rbbt/persist.rb

@@ -412,9 +412,9 @@ module Persist
         repo.delete path if persist_options[:update]
         repo[path] ||= yield
 
-      when (type.to_sym == :annotations and persist_options.include? :annotation_repo)
+      when (type.to_sym == :annotations and (persist_options.include?(:annotation_repo) || persist_options.include?(:repo)))
 
-        repo = persist_options[:annotation_repo]
+        repo = persist_options[:annotation_repo] || persist_options[:repo]
 
         keys = nil
         subkey = name + ":"

data/lib/rbbt/tsv.rb

@@ -69,6 +69,7 @@ module TSV
     options = TSV.str2options(options) if String === options and options.include? "~"
     options ||= {}
     options[:type] ||= type unless type.nil?
+    options[:zipped] = true if options[:one2one]
 
     persist_options = Misc.pull_keys options, :persist
 

data/lib/rbbt/util/misc/omics.rb

@@ -251,12 +251,20 @@ module Misc
   end
 
   def self.translate_prot_mutation_hgvs2rbbt(mutation)
+    mutation.sub!('p.', '')
+    if m = mutation.match(/([a-z]{3})(\d+)([a-z]{3})/i)
+      ref = m[1]
+      num = m[2]
+      alt = m[3]
+      ref = THREE_TO_ONE_AA_CODE[ref.downcase]
+      alt = THREE_TO_ONE_AA_CODE[alt.downcase]
+      mutation = [ref, num, alt] * ""
+    end
     one_aa_code = THREE_TO_ONE_AA_CODE.values
     one_aa_code << "X" << "B" << "Z" << "J" << "*" << "?"
     one_aa_code_re = one_aa_code*""
     subs = Regexp.new("^[#{one_aa_code_re}]\\d+[#{one_aa_code_re}]")
     f_aa = Regexp.new("^[#{one_aa_code_re}]\\d+")
-    mutation.sub!('p.', '')
     mutation = case
                when mutation =~ subs
                  mutation

data/lib/rbbt/workflow/doc.rb

@@ -30,7 +30,7 @@ module Workflow
     title = doc_parse_first_line doc
     description, task_info = doc_parse_up_to doc, /^# Tasks/i
     task_description, tasks = doc_parse_up_to task_info, /^##/, true
-    tasks = doc_parse_chunks tasks, /## (.*)/ 
+    tasks = doc_parse_chunks tasks, /^## (.*)/ 
     {:title => title.strip, :description => description.strip, :task_description => task_description.strip, :tasks => tasks}
   end
 

data/lib/rbbt/workflow/step/accessor.rb

@@ -428,4 +428,8 @@ class Step
              end
   end
 
+  def inspect
+    Misc.fingerprint(self)
+  end
+
 end

data/python/{rbbt.py → rbbt/__init__.py}

@@ -1,24 +1,53 @@
 import warnings
 import sys
 import os
+import subprocess
 
-def rbbt():
-    print("Rbbt")
+def rbbt(cmd = None):
+    if cmd is None:
+        print("Rbbt")
+    else:
+        return subprocess.run('rbbt_exec.rb', input=cmd.encode('utf-8'), capture_output=True).stdout.decode()
+
+def libdir():
+    return rbbt('puts Rbbt.find(:lib)').rstrip()
+
+def add_libdir():
+    pythondir = os.path.join(libdir(), 'python')
+    sys.path.insert(0, pythondir)
 
 def path(subdir = None, base_dir = None):
     from pathlib import Path
     import os
 
-    if (base_dir == None):
+    if (base_dir == 'base'):
         base_dir = os.path.join(Path.home(), ".rbbt")
+    elif (base_dir == 'lib'):
+        base_dir = libdir()
+    else:
+        for base_dir in ('lib', 'base'):
+            file = path(subdir, base_dir)
+            if os.path.exists(file):
+                return file
+        return path(subdir, 'base')
+
     if (subdir == None):
         return base_dir
     else:
         return os.path.join(base_dir, subdir)
 
+def read(subdir, base_dir = None, encoding='utf-8'):
+    file = path(subdir, base_dir)
+    with open(file, encoding=encoding) as f:
+        return f.read()
+
 def inspect(obj):
     print(dir(obj))
 
+def rich(obj):
+    import rich
+    rich.inspect(obj)
+
 def log_tsv(tsv):
     print(tsv)
     print(tsv.keys())

data/share/rbbt_commands/tsv/get

@@ -7,9 +7,10 @@ options = SOPT.setup <<EOF
 
 Query a TSV value
 
-$ rbbt tsv get [options] <filename.tsv|-> <key>
+$ rbbt tsv get [options] <filename.tsv|-> [<key>]
 
-Use - to read from STDIN
+Use - to read from STDIN, 'key' can be the key string or a number representing
+its position. If not specified 'key' defaults to 0, the first entry.
 
 -tch--tokyocabinet File is a tokyocabinet hash database
 -tcb--tokyocabinet_bd File is a tokyocabinet B database
@@ -26,7 +27,7 @@ rbbt_usage and exit 0 if options[:help]
 
 file, key = ARGV
 
-raise ParameterException, "Please specify file and key" if key.nil?
+raise ParameterException, "Please specify file" if file.nil?
 
 file = STDIN if file == '-'
 
@@ -48,7 +49,15 @@ key_field = options[:key_field]
 fields = fields.split(/[,|]/, -1) unless fields.nil?
 
 if TSV === tsv
+  case key
+  when nil
+    key = tsv.keys.first if key.nil?
+  when /^\d+$/
+    key = tsv.keys[key.to_i] unless tsv.include?(key)
+  end
+
   v = tsv[key]
+
   fields ||= tsv.fields
   puts Log.color(:blue, "Key: #{ key }")
   if fields
@@ -72,8 +81,15 @@ end
 parser = TSV::Parser.new tsv, :key_field => key_field,  :fields => fields, :type => options[:type], :header_hash => options[:header_hash], :sep => options[:sep]
 fields ||= parser.fields
 
+i = 0
 TSV.traverse(parser) do |k,v|
-  next unless k.include? key
+  if key== "#{i}"
+    key = k.first
+  elsif key.nil?
+    key = k.first
+  end
+  i += 1
+  next unless k.include?(key)
   k = k.first if Array === k
   puts Log.color(:blue, "Key: #{ k }")
   if fields

data/share/workflow_config.ru

@@ -46,6 +46,7 @@ app.get '/' do
   begin
     template_render('main', params, 'main', :cache_type => :asynchronous)
   rescue TemplateMissing
+    Log.exception $!
     redirect to(File.join('/', wf.to_s))
   end
 end
@@ -88,7 +89,16 @@ load_file Rbbt.etc['app.d/semaphores.rb'].find_all
 if etc_dir['target_workflow_exports'].exists?
   exports = etc_dir['target_workflow_exports'].read.split("\n")
   exports.each do |task|
-    wf.export task.to_sym
+    if task.include?('#')
+      wf_name, task_name = task.split("#")
+      begin
+        task_wf = Kernel.const_get wf_name
+        task_wf.export task_name.to_sym
+      rescue
+      end
+    else
+      wf.export task.to_sym
+    end
   end
 end
 

data/test/rbbt/util/misc/test_omics.rb

@@ -35,6 +35,7 @@ class TestMiscOmics < Test::Unit::TestCase
   end
 
   def test_translate_prot_mutation_hgvs2rbbt
+    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.Arg2459Gly"), "R2459G"
     assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E255K"), "E255K"
     assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E279Z"), "E279Z"
     assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.R132?"), "R132?"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.40.5
+  version: 5.41.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-26 00:00:00.000000000 Z
+date: 2024-01-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -338,7 +338,7 @@ files:
 - lib/rbbt/workflow/util/orchestrator.rb
 - lib/rbbt/workflow/util/provenance.rb
 - lib/rbbt/workflow/util/trace.rb
-- python/rbbt.py
+- python/rbbt/__init__.py
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R