rbbt-util 5.34.5 → 5.34.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '073587b420676db7c055e58dbabaecbf04a7b30ba9d7ea912f1c12df5a6d180d'
-  data.tar.gz: 6d263d07b85095fefb48c15692af0db66b56ef671ada83e98c66a4765d4ca416
+  metadata.gz: ec5860171e51e2e53a8383ae8ea1156b79c7f75194d384c5aa2c43efd759e129
+  data.tar.gz: a6ab8a782b3169eae1e475a2029e8a4f0ac2d12f375475ec70de9d97f513f21a
 SHA512:
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-  data.tar.gz: a8ba069b626b1a09d6da8e73eaa901119795ade4b4af33f1891b8581cfe80ccf48ca439a6a96b67f45e6bdf687ba7e90df263b8b4caabec18af45f6008e2b5d9
+  metadata.gz: 2fb6a8ac5abee267891f6bb0736b659f202019de75fa0ecef80e955838a54013eaeabb495c44daff45196a8706821b706bfae75b095ce3ca8b82e8351436d4ef
+  data.tar.gz: ab24e4ab588e75f94adfcd9a02e178511bd4471edadef18c6c49537974353b8b4d83c61438d8fe638acbc26101556637a92d5da325ebc135736da44558971334

data/lib/rbbt/tsv/accessor.rb

@@ -16,6 +16,9 @@ module TSV
 
   def annotate(tsv)
     TSV.setup(tsv, info)
+    tsv.entity_options = self.entity_options
+    tsv.entity_templates = self.entity_templates
+    tsv
   end
 
   def entity_options

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -389,7 +389,7 @@ module TSV
       when Set
         traverse_array(obj.to_a, options, &block)
       when String
-        if Open.remote?(obj) or Misc.is_filename?(obj)
+        if Open.remote?(obj) || Open.ssh?(obj) || Misc.is_filename?(obj)
           Open.open(obj) do |s|
             traverse_obj(s, options, &block)
           end

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

@@ -135,20 +135,25 @@ def self.add_libdir(dir=nil)
   end
 
   def self.insist(times = 4, sleep = nil, msg = nil)
-    if Array === times
-      sleep_array = times
-      times = sleep_array.length
-      sleep = sleep_array.shift
-    end
-    try = 0
-
-    if sleep.nil?
-      sleep_array = ([0] + [0.001, 0.01, 0.1, 0.5] * (times / 3)).sort[0..times-1]
-      sleep = sleep_array.shift
-    end
+    sleep_array = nil
 
+    try = 0
     begin
-      yield
+      begin
+        yield
+      rescue Exception
+        if Array === times
+          sleep_array = times
+          times = sleep_array.length
+          sleep = sleep_array.shift
+        end
+
+        if sleep.nil?
+          sleep_array = ([0] + [0.001, 0.01, 0.1, 0.5] * (times / 3)).sort[0..times-1]
+          sleep = sleep_array.shift
+        end
+        raise $!
+      end
     rescue TryAgain
       sleep sleep
       retry

data/lib/rbbt/util/open.rb

@@ -522,7 +522,7 @@ module Open
   # Questions
 
   def self.remote?(file)
-    !! (file =~ /^(?:https?|ftp):\/\//)
+    !! (file =~ /^(?:https?|ftp|ssh):\/\//)
   end
 
   def self.ssh?(file)

data/lib/rbbt/workflow/remote_workflow/driver/rest.rb

@@ -18,7 +18,24 @@ class RemoteWorkflow
       end
     end
 
+    def self.escape_url(url)
+      base, _sep, query = url.partition("?")
+      protocol, path = base.split("://") 
+      path = protocol if path.nil?
+      path = path.split("/").collect{|p| CGI.escape(p) }* "/"
+      base = protocol ? [protocol, path] * "://" : path
+
+      if query && ! query.empty?
+        query = query.split("&").collect{|e| e.split("=").collect{|pe| CGI.escape(pe) } * "=" } * "&"
+        [base, query] * "?"
+      else
+        base
+      end
+    end
+
     def self.encode(url)
+      # ToDo: Check this
+      return escape_url(url)
       begin
         URI::DEFAULT_PARSER.escape(url)
       rescue
@@ -135,7 +152,7 @@ class RemoteWorkflow
 
     def self.execute_job(base_url, task, task_params, cache_type)
       RemoteWorkflow.capture_exception do
-        task_url = URI.encode(File.join(base_url, task.to_s))
+        task_url = self.escape_url(File.join(base_url, task.to_s))
 
         sout, sin = Misc.pipe
 

data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb

@@ -132,7 +132,7 @@ class RemoteStep
     def _run_job(cache_type = :asynchronous)
       get_streams
 
-      task_url = URI.encode(File.join(base_url, task.to_s))
+      task_url = RemoteWorkflow::REST.escape_url(File.join(base_url, task.to_s))
       @adaptor.__prepare_inputs_for_restclient(inputs)
       task_params = inputs.merge(:_cache_type => cache_type, :jobname => base_name, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json)
 
@@ -147,6 +147,7 @@ class RemoteStep
 
     def produce(*args)
       @started = true
+      init_job
       _run_job
     end
 

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

@@ -177,7 +177,7 @@ class Step
 
     Log.debug "Saving job input #{name} (#{type}) into #{path}"
 
-    if value.respond_to? :filename
+    if IO === value && value.respond_to?(:filename) && value.filename
       Open.write(path, value.filename)
     elsif IO === value
       Open.write(path, value)

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

@@ -75,6 +75,7 @@ class Step
 
   def dirty?
     return true if Open.exists?(pid_file) && ! ( Open.exists?(info_file) || done? )
+    return true if done? && ! (status == :done || status == :noinfo)
     return false unless done? || status == :done
     return false unless ENV["RBBT_UPDATE"] == "true"
 

data/share/rbbt_commands/app/start

@@ -96,6 +96,8 @@ Misc.in_dir(app_dir) do
     system ENV, "env RBBT_LOG=0 passenger start -R '#{config_ru_file}' -p #{options[:Port] || "2887"}"
   when 'puma_alt'
     system ENV, "puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 3 -t 8:32 --preload"
+  when 'puma_production'
+    CMD.cmd_log("env RBBT_LOG=#{Log.severity.to_s} puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 20 -t 10:160 --preload")
   else
     options[:config] = config_ru_file
     options[:threads] = "8:8"

data/share/rbbt_commands/tsv/view

@@ -47,6 +47,7 @@ tsv = TSV.open(tsv) if IO === tsv
 
 
 begin
+  require 'rbbt/workflow'
   Workflow.require_workflow "Genomics"
   tsv = Genomics.job(:names, nil, :tsv => tsv).run
 rescue

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.5
+  version: 5.34.7
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-07-20 00:00:00.000000000 Z
+date: 2022-07-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake