miga-base 0.2.3.1 → 0.2.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8204affac00281361567c3a597321dd3ab5a5145
-  data.tar.gz: 62fbd4daf6698b317e9f76b89b352b7bf33d3b54
+  metadata.gz: e9353efac39e230da0d999efff1f3839dd5d0c1e
+  data.tar.gz: 2860e3b8c6ee0bb18bfb5f8ff753754762253eb6
 SHA512:
-  metadata.gz: f1d1b5e052e91e176529a6cec60736f2c21bca0591ba4b184485e59f6d906204ae34c1dba0464f1d5b1d01ed691e599cf15f63b3e1760f89c222187030a2a830
-  data.tar.gz: 1611ac19a30c23bb7fd79c7acc2d1b0559b03ae3d179dd8881c10d0a828ba447f4546e1ce18b9907a277260656bcb85120054e739395922a505e93f9a84efe70
+  metadata.gz: 66086e7e08f1ca5cb27986ebd206d65c71562fe0b9c026673c08c20f543772b015dfe23fd6c1792e9747d1334d331b2feade1ea9225e579c9b4e691575bb16b2
+  data.tar.gz: b7801121cb4f332eebe6e88c907c9e68c0f6e3851cd445eb2467cdf84a9091243a0303fecad6505ae6efba7efa5287f4f5c3efc6b9bd44d54ce4af653e8ddc11

data/actions/create_dataset.rb

@@ -6,7 +6,7 @@
 o = {q:true, ref:true, update:false}
 OptionParser.new do |opt|
   opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset, :dataset_type])
+  opt_object(opt, o, [:project, :dataset, :dataset_type_req])
   opt.on("-q", "--query",
     "If set, the dataset is registered as a query, not a reference dataset."
     ){ |v| o[:ref]=!v }
@@ -43,6 +43,7 @@ end.parse!
 
 ##=> Main <=
 opt_require(o)
+opt_require(o, type:"-t")
 
 $stderr.puts "Loading project." unless o[:q]
 p = MiGA::Project.load(o[:project])

data/actions/create_project.rb

@@ -6,7 +6,7 @@
 o = {q:true, update:false}
 OptionParser.new do |opt|
   opt_banner(opt)
-  opt_object(opt, o, [:project, :project_type])
+  opt_object(opt, o, [:project, :project_type_req])
   opt.on("-n", "--name STRING",
     "Name of the project."){ |v| o[:name]=v }
   opt.on("-d", "--description STRING",
@@ -20,7 +20,7 @@ OptionParser.new do |opt|
 end.parse!
 
 ##=> Main <=
-opt_require(o, project:"-P")
+opt_require(o, project:"-P", type:"-t")
 
 unless File.exist? "#{ENV["HOME"]}/.miga_rc" and
       File.exist? "#{ENV["HOME"]}/.miga_daemon.json"

data/actions/daemon.rb

@@ -22,6 +22,10 @@ OptionParser.new do |opt|
   opt.separator ""
   opt.separator "MiGA options:"
   opt_object(opt, o, [:project])
+  opt.on("--shutdown-when-done",
+    "If passed, the daemon will exit when all processing is done.",
+    "Otherwise (default), it will stay idle awaiting for new data."
+    ){ |v| o[:shutdown_when_done] = v }
   opt.on("--latency INT",
     "Number of seconds the daemon will be sleeping."
     ){ |v| o[:latency]=v.to_i }
@@ -45,7 +49,7 @@ opt_require(o, project:"-P")
 raise "Project doesn't exist, aborting." unless MiGA::Project.exist? o[:project]
 p = MiGA::Project.new(o[:project])
 d = MiGA::Daemon.new(p)
-[:latency, :maxjobs, :ppn].each do |k|
+[:latency, :maxjobs, :ppn, :shutdown_when_done].each do |k|
   d.runopts(k, o[k]) unless o[k].nil?
 end
 d.daemon(task, o[:daemon_opts])

data/bin/miga

@@ -53,18 +53,24 @@ end
 def opt_object(opt, o, what=[:project, :dataset])
   opt.on("-P", "--project PATH", "(Mandatory) Path to the project."
     ){ |v| o[:project]=v } if what.include? :project
-  opt.on("-D", "--dataset PATH", "(Mandatory) Name of the dataset."
-    ){ |v| o[:dataset]=v } if what.include? :dataset
-  opt.on("-D", "--dataset PATH", "Name of the dataset."
+  opt.on("-D", "--dataset STRING",
+    (what.include?(:dataset) ? "(Mandatory) " : "") +
+    "Name of the dataset."){ |v| o[:dataset]=v } if what.include? :dataset or
+      what.include? :dataset_opt
+  opt.on("-D", "--dataset STRING", "Name of the dataset."
     ){ |v| o[:dataset]=v } if what.include? :dataset_opt
   opt.on("-t", "--type STRING",
+    (what.include?(:dataset_type_req) ? "(Mandatory) " : "")+
     "Type of dataset. Recognized types include:",
     *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}" }
-    ){ |v| o[:type]=v.to_sym } if what.include? :dataset_type
+    ){ |v| o[:type]=v.to_sym } if what.include? :dataset_type or
+      what.include? :dataset_type_req
   opt.on("-t", "--type STRING",
+    (what.include?(:project_type_req) ? "(Mandatory) " : "") +
     "Type of dataset. Recognized types include:", 
     *MiGA::Project.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
-    ){ |v| o[:type]=v.to_sym } if what.include? :project_type
+    ){ |v| o[:type]=v.to_sym } if what.include? :project_type or
+      what.include? :project_type_req
   opt.on("-r", "--result STRING",
     "(Mandatory) Name of the result to add.",
     "Recognized names for dataset-specific results include:",

data/lib/miga/daemon.rb

@@ -66,6 +66,7 @@ class MiGA::Daemon < MiGA::MiGA
       v = v.to_i if [:latency, :maxjobs, :ppn].include? k
       raise "Daemon's #{k} cannot be set to zero." if
         !force and v.is_a? Integer and v==0
+      v = !!v if [:shutdown_when_done].include? k
       @runopts[k] = v
     end
     @runopts[k]
@@ -83,6 +84,11 @@ class MiGA::Daemon < MiGA::MiGA
   # Returns Integer indicating the number of CPUs per job.
   def ppn() runopts(:ppn) ; end
 
+  ##
+  # Returns Boolean indicating if the daemon should shutdown when processing is
+  # complete.
+  def shutdown_when_done?() !!runopts(:shutdown_when_done) ; end
+
   ##
   # Initializes the daemon with +opts+.
   def start(opts=[]) daemon("start", opts) ; end
@@ -106,7 +112,9 @@ class MiGA::Daemon < MiGA::MiGA
     options = default_options
     opts.unshift(task)
     options[:ARGV] = opts
-    Daemons.run_proc("MiGA:#{project.name}", options) { loop { in_loop } }
+    Daemons.run_proc("MiGA:#{project.name}", options) do
+      loop { break unless in_loop }
+    end
   end
 
   ##
@@ -205,12 +213,12 @@ class MiGA::Daemon < MiGA::MiGA
       # Launch job
       if runopts(:type) == "bash"
         job[:pid] = spawn job[:cmd]
-        Process.detach job[:pid] unless job[:pid].nil? or job[:pid].empty?
+        Process.detach job[:pid] unless [nil, "", 0].include? job[:pid]
       else
         job[:pid] = `#{job[:cmd]}`.chomp
       end
       # Check if registered
-      if job[:pid].nil? or job[:pid].empty?
+      if [nil, "", 0].include? job[:pid].nil?
         job[:pid] = nil
         @jobs_to_run << job
         say "Unsuccessful #{job[:task_name]}, rescheduling."
@@ -230,7 +238,7 @@ class MiGA::Daemon < MiGA::MiGA
   end
 
   ##
-  # Run one loop step.
+  # Run one loop step. Returns a Boolean indicating if the loop should continue.
   def in_loop
     if loop_i == -1
       say "-----------------------------------"
@@ -250,6 +258,10 @@ class MiGA::Daemon < MiGA::MiGA
       purge!
     end
     sleep(latency)
+    if shutdown_when_done? and jobs_running.size+jobs_to_run.size == 0
+      return false
+    end
+    true
   end
 
   ##

data/lib/miga/dataset.rb

@@ -43,9 +43,10 @@ class MiGA::Dataset < MiGA::MiGA
     metagenome: {description: "A metagenome (excluding viromes).",
       multi: true},
     virome: {description: "A viral metagenome.", multi: true},
-    scgenome: {description: "A genome from a single cell.", multi: false},
-    popgenome: {description: "The genome of a population (including " +
-      "microdiversity).", :multi=>false}
+    scgenome: {description: "A Single-cell Genome Amplification (SGA).",
+      multi: false},
+    popgenome: {description: "A population genome (including " +
+      "metagenomic bins).", :multi=>false}
   }
 
   ##
@@ -108,6 +109,8 @@ class MiGA::Dataset < MiGA::MiGA
     metadata[:ref] = is_ref
     @metadata = MiGA::Metadata.new(
       File.expand_path("metadata/#{name}.json", project.path), metadata )
+    raise "Unrecognized dataset type: #{type}." if
+      !type.nil? and @@KNOWN_TYPES[type].nil?
   end
   
   ##
@@ -118,6 +121,10 @@ class MiGA::Dataset < MiGA::MiGA
     self.metadata.save
   end
   
+  ##
+  # Get the type of dataset as Symbol.
+  def type ; metadata[:type] ; end
+  
   ##
   # Delete the dataset with all it's contents (including results) and returns
   # nil.

data/lib/miga/project.rb

@@ -65,7 +65,7 @@ class MiGA::Project < MiGA::MiGA
       single: true, multi: true},
     genomes: {description: "Collection of genomes.",
       single: true, multi: false},
-    clade: {description: "Collection of closely-related genomes (ANI <= 90%).",
+    clade: {description: "Collection of closely-related genomes (ANI >= 90%).",
       single: true, multi: false},
     metagenomes: {description: "Collection of metagenomes and/or viromes.",
       single: false, multi: true}
@@ -115,6 +115,8 @@ class MiGA::Project < MiGA::MiGA
     self.create if not update and not Project.exist? self.path
     self.load if self.metadata.nil?
     self.load_plugins
+    self.metadata[:type] = :mixed if type.nil?
+    raise "Unrecognized project type: #{type}." if @@KNOWN_TYPES[type].nil?
   end
 
   ##

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.2, 3, 1]
+  VERSION = [0.2, 4, 0]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2017, 3, 14)
+  VERSION_DATE = Date.new(2017, 3, 23)
   
   ##
   # Reference of MiGA.

data/scripts/_distances_functions.bash

@@ -56,7 +56,7 @@ fx_exists miga-haai || function miga-haai {
   local HAAI=$(MIGA_AAI_SAVE_RBM="no-save-rbm" miga-aai "$F1" "$F2" "$TH" "$DB")
   if [[ "$HAAI" != "" && $(perl -e "print 1 if '$HAAI' <= 90") == "1" ]] ; then
     local AAI=$(perl -e "print (100-exp(2.435076 + 0.4275193*log(100-$HAAI)))")
-    [[ ! -s $AAI_DB ]] && make_empty_aai_db "$AAI_DB"
+    [[ ! -s $AAI_DB ]] && miga-make_empty_aai_db "$AAI_DB"
     echo "insert into aai values('$N1','$N2','$AAI',0,0,0);" | sqlite3 "$AAI_DB"
     echo "$AAI"
   fi

data/scripts/init.bash

@@ -162,7 +162,7 @@ case "$dtype" in
       dmaxjobs=$(ask_user "How many jobs can I launch at once?" "6")
       dppn=$(ask_user "How many CPUs can I use per job?" "2")
       echo "Setting up internal daemon defaults, if you don't understand this just leave default values:" >&2
-      dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, %3\$d for CPUs, %4\$s for log file, and %5\$s for task name." "%2\$s '%1\$s' &> '%4\$s'")
+      dcmd=$(ask_user "How should I launch tasks? Use %1\$s for script path, %2\$s for variables, %3\$d for CPUs, %4\$s for log file, and %5\$s for task name." "%2\$s '%1\$s' > '%4\$s' 2>&1")
       dvar=$(ask_user "How should I pass variables? Use %1\$s for keys and %2\$s for values." "%1\$s=%2\$s")
       dsep=$(ask_user "What should I use to separate variables?" " ")
       dalive=$(ask_user "How can I know that a process is still alive? Use %1\$s for PID, output should be 1 for running and 0 for non-running." "ps -p '%1\$s'|tail -n+2|wc -l|awk '{print \$1}'")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.2.3.1
+  version: 0.2.4.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-03-14 00:00:00.000000000 Z
+date: 2017-03-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -192,9 +192,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14.1
+rubygems_version: 2.0.14
 signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []
-has_rdoc: true