Class: SeqtrimWorkManager
- Inherits:
-
ScbiMapreduce::WorkManager
- Object
- ScbiMapreduce::WorkManager
- SeqtrimWorkManager
- Defined in:
- lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb
Class Method Summary collapse
- .end_work_manager ⇒ Object
- .exit_status ⇒ Object
- .global_error_received(error_exception) ⇒ Object
- .init_work_manager(sequence_readers, params, chunk_size = 100, use_json = false, skip_output = false, write_in_gzip = true) ⇒ Object
- .work_manager_finished ⇒ Object
Instance Method Summary collapse
- #error_received(worker_error, obj) ⇒ Object
- #get_file(file_name) ⇒ Object
- #get_next_seq_from_file(file) ⇒ Object
- #load_user_checkpoint(checkpoint) ⇒ Object
- #next_work ⇒ Object
- #save_files(obj) ⇒ Object
- #save_user_checkpoint ⇒ Object
- #too_many_errors_received ⇒ Object
-
#trash_checkpointed_work ⇒ Object
read a work that will not be processed, only to skip until checkpoint.
- #work_received(obj) ⇒ Object
- #worker_initial_config ⇒ Object
Class Method Details
.end_work_manager ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 93 def self.end_work_manager # if initial files doesn't exists, create it if !File.exists?(File.join(OUTPUT_PATH,'initial_stats.json')) File.open(File.join(OUTPUT_PATH,'initial_stats.json'),'w') do |f| f.puts JSON.pretty_generate(@@ongoing_stats) end end # load stats #r=File.read(STATS_PATH) #stats=JSON::parse(r) stats=@@full_stats # make graphs gs=GraphStats.new(stats) #close all files if @@use_json @@json_output.close end @@errors_file.close @@files.each do |k,file| file.close end end |
.exit_status ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 89 def self.exit_status return @@exit_status end |
.global_error_received(error_exception) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 123 def self.global_error_received(error_exception) $LOG.error "Global error:\n" + error_exception. + ":\n" +error_exception.backtrace.join("\n") @@errors_file.puts "Global error:\n" + error_exception. + ":\n" +error_exception.backtrace.join("\n") @@errors_file.puts "="*60 @@exit_status=-1 SeqtrimWorkManager.controlled_exit end |
.init_work_manager(sequence_readers, params, chunk_size = 100, use_json = false, skip_output = false, write_in_gzip = true) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 16 def self.init_work_manager(sequence_readers, params, chunk_size = 100, use_json=false, skip_output=false, write_in_gzip=true) @@full_stats={} @@params= params @@exit = false @@exit_status=0 @@ongoing_stats={} @@ongoing_stats[:sequence_count] = 0 @@ongoing_stats[:smallest_sequence_size] = 900000000000000 @@ongoing_stats[:biggest_sequence_size] = 0 @@skip_output=skip_output @@write_in_gzip=write_in_gzip @@chunk_size = chunk_size checkpoint_exists=File.exists?(ScbiMapreduce::CHECKPOINT_FILE) # @@use_qual = !qual_path.nil? and File.exists?(qual_path) @@open_mode='w' if checkpoint_exists @@open_mode = 'a' end #open input file @@sequence_readers=sequence_readers # @@use_qual = @@fqr.with_qual? # @@use_json = use_json @@params.set_param('use_qual',@@sequence_readers.first.with_qual?) @@params.set_param('use_json',use_json) @@params.set_param('tuple_size',@@sequence_readers.count) @@use_json=use_json @@sequence_readers.each do |sequence_reader| sequence_reader.rewind end # open output files if !Dir.exists?(OUTPUT_PATH) Dir.mkdir(OUTPUT_PATH) end @@files={} # @@rejected_output_file=File.open(File.join(OUTPUT_PATH,'rejected.txt'),@@open_mode) # seqs_with_errors @@errors_file=File.open('errors.txt',@@open_mode) if @@use_json @@json_output=File.open('results.json',@@open_mode) end @@json_separator='' @@paired_output_files={} @@sequences_output_files={} @@low_complexity_output_files={} @@sffinfo_files={} @@low_sffinfo_files={} @@tuple_id=0 end |
.work_manager_finished ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 131 def self.work_manager_finished @@full_stats['scbi_mapreduce']=@@stats puts "FULL STATS:\n" +JSON.pretty_generate(@@full_stats) # create stats file f = File.open(STATS_PATH,'w') f.puts JSON.pretty_generate(@@full_stats) f.close end |
Instance Method Details
#error_received(worker_error, obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 142 def error_received(worker_error, obj) @@errors_file.puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception. + ":\n" +worker_error.original_exception.backtrace.join("\n") @@errors_file.puts "="*60 @@exit_status=-1 SeqtrimWorkManager.controlled_exit end |
#get_file(file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 345 def get_file(file_name) res_file = @@files[file_name] # if file is not already open, create it if res_file.nil? # create dir if necessary dir = File.dirname(file_name) if !File.exists?(dir) FileUtils.mkdir_p(dir) end # open file if @@write_in_gzip && file_name.upcase.index('.FASTQ') file=File.open(file_name+'.gz',@@open_mode) res_file=Zlib::GzipWriter.new(file) else res_file=File.open(file_name,@@open_mode) end # save it in hash for next use @@files[file_name]=res_file end return res_file end |
#get_next_seq_from_file(file) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 243 def get_next_seq_from_file(file) # find a valid and no repeated sequence in file begin n,f,q,c = file.next_seq if !n.nil? && @@params.repeated_seq?(n) @@full_stats.add_stats({'sequences' => {'count' => {'rejected' => 1}}}) @@full_stats.add_stats({'sequences' => {'rejected' => {'repeated' => 1}}}) get_file(File.join(OUTPUT_PATH,'rejected.txt')).puts('>'+n+ ' repeated') end if !n.nil? @@ongoing_stats[:sequence_count] += 1 @@ongoing_stats[:smallest_sequence_size] = [f.size, @@ongoing_stats[:smallest_sequence_size]].min @@ongoing_stats[:biggest_sequence_size] = [f.size, @@ongoing_stats[:smallest_sequence_size]].max @@full_stats.add_stats({'sequences' => {'count' => {'input_count' => 1}}}) end end while (!n.nil? && @@params.repeated_seq?(n)) return n,f,q,c end |
#load_user_checkpoint(checkpoint) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 159 def load_user_checkpoint(checkpoint) # load full_stats from file !!!!!!!!!!!!! if File.exists?(STATS_PATH) # load stats text = File.read(STATS_PATH) # wipe text # text=text.grep(/^\s*[^#]/).to_s # decode json @@full_stats = JSON.parse(text) end # reset count stats since they are repeated by checkpointing # { # "sequences": { # "count": { # "input_count": 1600, # "output_seqs": 933, # "rejected": 67 # }, # "rejected": { # "short insert": 39, # "contaminated": 26, # "unexpected vector": 2 # } # } # } if @@full_stats['sequences'] if @@full_stats['sequences']['count'] # set input count to 0 @@full_stats['sequences']['count']['input_count']=0 # do not remove outputseqs # @@full_stats['sequences']['count']['output_seqs']=0 end # remove rejected due to repetitions from rejected count if @@full_stats['sequences']['rejected'] # it there are repeated if (@@full_stats['sequences']['rejected']['repeated']) # if repeated count > 0 and there count exists if (@@full_stats['sequences']['rejected']['repeated'] > 0) and @@full_stats['sequences']['count'] # discount repeated from rejected, since they are going to be added again by checkout process @@full_stats['sequences']['count']['rejected'] -= @@full_stats['sequences']['rejected']['repeated'] end # set repeated to 0 @@full_stats['sequences']['rejected']['repeated']=0 end end end # puts "Loaded Stats" # puts "FULL STATS:\n" +JSON.pretty_generate(@@full_stats) # TODO - remove sequences from rejected file that were added by cloned super # return checkpoint end |
#next_work ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 271 def next_work if @@exit return nil end tuple=[] order_in_tuple=0 @@tuple_id += 1 tuple_size=@@sequence_readers.count @@sequence_readers.each do |sequence_reader| n,f,q,c = get_next_seq_from_file(sequence_reader) if !n.nil? seq=SequenceWithAction.new(n,f.upcase,q,c) seq.tuple_id=@@tuple_id seq.order_in_tuple=order_in_tuple seq.tuple_size=tuple_size tuple << seq order_in_tuple+=1 end end if tuple_size>1 # check duplicated names names = tuple.map{|s| s.seq_name} if names.uniq.count!=tuple_size # puts "NAMES EQUAL IN TUPLE" tuple.each_with_index do |seq,i| # puts seq.class # seq_name seq.seq_name = "#{seq.seq_name}/#{i+1}" end end end # tuple is complete if tuple.count==tuple_size return tuple else return nil end end |
#save_files(obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 337 def save_files(obj) files=obj.output_files files.each do |file_name,content| f=get_file(file_name) f.puts content end end |
#save_user_checkpoint ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 229 def save_user_checkpoint f = File.open(STATS_PATH,'w') f.puts JSON.pretty_generate(@@full_stats) f.close end |
#too_many_errors_received ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 150 def too_many_errors_received $LOG.error "Too many errors: #{@@error_count} errors on #{@@count} executed sequences, exiting before finishing" @@exit_status=-1 end |
#trash_checkpointed_work ⇒ Object
read a work that will not be processed, only to skip until checkpoint
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 239 def trash_checkpointed_work warn "Deprecated: trash_checkpointed_work was deprecated, it is automatic now" end |
#work_received(obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 320 def work_received(obj) res = obj # collect stats @@full_stats.add_stats(obj.stats) # print output in screen if !@@skip_output puts obj.output_text end # save results to files save_files(obj) end |
#worker_initial_config ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb', line 155 def worker_initial_config return @@params end |