rbbt-util 5.40.4 → 5.41.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 8d0ee0a0942be2cf07259baed09d2c2feb98a67b314adc70bd0ac1e03ecba4f9
+  metadata.gz: 5f8c020988e2d5df3aa710ce88fe4d92a2a754363d924a580fcc31b138330258
+  data.tar.gz: b6ee155b7bfb819baa21fac27c8561a3e1332bd9677a081abbe811bbb45c7973
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+  metadata.gz: 16d876542942fd0a0e1982dee1e7bf94ccd7bf8c8f4e3bb5310588a2f4587a3abe6d56fb101e1e1352c12225de507d46c18fa6b9109b2328079a999142479fa9
+  data.tar.gz: 6d135e37aa6151b68552a5c9f32f3cc1f1fef20a3f26695c9a033a09e0541a31a60de9b2fac33aea4c69e89a1acff54296264ba8435e9fecdaed5dcd5ee868fb

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/resource/path.rb

@@ -359,7 +359,16 @@ module Path
   end
 
   def list
-    Open.read(self.produce.find).split "\n"
+    begin
+      path = self.produce
+    rescue Resource::ResourceNotFound => e
+      begin
+        path = self.set_extension('list').produce
+      rescue Resource::ResourceNotFound 
+        raise e
+      end
+    end
+    Open.read(path).split("\n")
   end
 
   def keys(field = 0, sep = "\t")

data/lib/rbbt/util/migrate.rb

@@ -26,6 +26,7 @@ puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
       if original_path.located?
         paths = [original_path]
       else
+        path = Path.setup(path) unless Path === path
         paths = (path.directory? ? path.glob_all : path.find_all)
       end
 

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/dependencies.rb

@@ -165,7 +165,8 @@ module Workflow
                    workflow, dep_task, options = dependency
 
                    if override_dependencies[workflow.to_s] && value = override_dependencies[workflow.to_s][dep_task]
-                     overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                      setup_override_dependency(value, workflow, dep_task)
                    else
 
@@ -189,21 +190,23 @@ module Workflow
                      job = workflow._job(dep_task, jobname, _inputs)
                      ComputeDependency.setup(job, compute) if compute
 
-                     overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                     overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
 
                      job
                    end
                  when Step
                    job = dependency
-                   overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                   overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                    job
                  when Symbol
                    if override_dependencies[self.to_s] && value = override_dependencies[self.to_s][dependency]
-                     overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                     #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                      setup_override_dependency(value, self, dependency)
                    else
                      job = _job(dependency, jobname, _inputs)
-                     overriden = true if TrueClass === job.overriden && (options.nil? || ! options[:not_overriden])
+                     overriden = true if Symbol === job.overriden && (options.nil? || ! options[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
+
                      job
                    end
                  when Proc
@@ -212,7 +215,8 @@ module Workflow
                      wf, task_name, options = orig_dep
 
                      if override_dependencies[wf.to_s] && value = override_dependencies[wf.to_s][task_name]
-                       overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                       overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                       #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                        dep = setup_override_dependency(value, wf, task_name)
                      else
 
@@ -243,7 +247,8 @@ module Workflow
                            d[:task] ||= task_name
                            _override_dependencies = override_dependencies.merge(override_dependencies(d[:inputs] || {}))
                            d = if _override_dependencies[d[:workflow].to_s] && value = _override_dependencies[d[:workflow].to_s][d[:task]]
-                                 overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                                 overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                                 #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                                  setup_override_dependency(value, d[:workflow], d[:task])
                                else
                                  task_info = d[:workflow].task_info(d[:task])
@@ -251,7 +256,7 @@ module Workflow
                                  _inputs = assign_dep_inputs({}, options.merge(d[:inputs] || {}), real_dependencies, task_info) 
                                  _jobname = d.include?(:jobname) ? d[:jobname] : jobname
                                  job = d[:workflow]._job(d[:task], _jobname, _inputs) 
-                                 overriden = true if TrueClass === job.overriden && (d.nil? || ! d[:not_overriden])
+                                 overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                                  job
                                end
                          end
@@ -267,14 +272,15 @@ module Workflow
                        dep[:workflow] ||= wf || self
                        _override_dependencies = override_dependencies.merge(override_dependencies(dep[:inputs] || {}))
                        if _override_dependencies[dep[:workflow].to_s] && value = _override_dependencies[dep[:workflow].to_s][dep[:task]]
-                         overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                         overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
+                         #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                          setup_override_dependency(value, dep[:workflow], dep[:task])
                        else
                          task_info = (dep[:task] && dep[:workflow]) ? dep[:workflow].task_info(dep[:task]) : nil
                          _inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, task_info)
                          _jobname = dep.include?(:jobname) ? dep[:jobname] : jobname
                          job = dep[:workflow]._job(dep[:task], _jobname, _inputs)
-                         overriden = true if TrueClass === job.overriden && (d.nil? || ! d[:not_overriden])
+                         overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                          job
                        end
                      end

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

@@ -16,6 +16,17 @@ class Step
                        end
                      end
 
+  def relocated
+    if @relocated.nil?
+      if Open.exists?(info_file) and (info[:path] != path)
+        @relocated = true
+      else
+        @relocated = false
+      end
+    end
+    @relocated
+  end
+
   def self.serialize_info(info)
     info = info.clean_version if IndiferentHash === info
     INFO_SERIALIZER.dump(info)
@@ -417,4 +428,8 @@ class Step
              end
   end
 
+  def inspect
+    Misc.fingerprint(self)
+  end
+
 end

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

@@ -48,7 +48,11 @@ class Step
         IndiferentHash.setup info_inputs
         @inputs = NamedArray.setup info_inputs.values_at(*task.inputs.collect{|name| name.to_s}), task.inputs
       else
-        @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
+        if Hash === info_inputs
+          @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
+        else
+          @inputs = info_inputs
+        end
       end
     else
       nil

data/lib/rbbt/workflow/step.rb

@@ -51,9 +51,6 @@ class Step
     @info_mutex = Mutex.new
     @inputs = inputs 
     NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs
-    if Open.exists?(info_file) and (info[:path] != path)
-      @relocated = true
-    end
   end
 
   def workflow

data/lib/rbbt/workflow.rb

@@ -495,7 +495,8 @@ module Workflow
       end
     end
 
-    overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
+    #overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
+    overriden = true if dependencies.select{|d| Symbol === d.overriden }.any?
 
     input_values = task.take_input_values(inputs)
     if real_inputs.empty? && Workflow::TAG != :inputs && ! overriden #&& ! dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
@@ -665,6 +666,7 @@ module Workflow
     step = Step.new path
     relocated = false
     dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
+      dep_path = task if dep_path.nil?
       if Open.exists?(dep_path) || Open.exists?(dep_path + '.info') || Open.remote?(dep_path) || Open.ssh?(dep_path)
         Workflow._load_step dep_path
       else

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/write_excel

@@ -7,11 +7,12 @@ $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_c
 
 options = SOPT.setup <<EOF
 
-Description
+Write a Excel file with the contents of a TSV
 
-$ rbbt tsv write_excel [options] <filename.tsv|-> <filename.xls|filename.xlsx>
+$ rbbt tsv write_excel [options] <filename.tsv|-> [<filename.xls|filename.xlsx>]
 
-Use - to read from STDIN
+If no target file is specified it uses the same input files but replaces extension. Specifying
+the extension of the excel file select the excel format to use.
 
 -k--key_field* Key field
 -f--fields* Fields

data/share/rbbt_commands/workflow/cmd

@@ -70,9 +70,14 @@ begin
       exit 0
     else
       if command == 'bootstrap'
-        Log.info "No bootstrap for #{ workflow }, running examples instead"
-        puts `rbbt workflow example #{ workflow }`
-        exit 0
+        if wf.libdir["test_workflow.rb"].exists?
+          Log.info "No bootstrap for #{ workflow }, running test_workflow.rb instead"
+          CMD.cmd_log('ruby', wf.libdir["test_workflow.rb"].find)
+        else
+          Log.info "No bootstrap for #{ workflow }, running examples instead"
+          CMD.cmd_log("rbbt workflow example #{ workflow }")
+          exit 0
+        end
       end
 
       raise ParameterException, "Error: Command not understood: #{command}"

data/share/rbbt_commands/workflow/info

@@ -114,6 +114,7 @@ end
 if dependencies and dependencies.any?
   puts Log.color(:magenta, "Dependencies") << ": "
   dependencies.each do |name,task,file|
+    file = name if file.nil?
     puts "  " << file
   end 
 end

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: 5.40.4
+  version: 5.41.0
 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: 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
@@ -584,7 +584,7 @@ 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: Utilities for the Ruby Bioinformatics Toolkit (rbbt)