rbbt-util 5.44.1 → 6.0.3
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- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +2 -2
- data/etc/app.d/semaphores.rb +3 -3
- data/lib/rbbt/annotations/annotated_array.rb +207 -207
- data/lib/rbbt/annotations/refactor.rb +27 -0
- data/lib/rbbt/annotations/util.rb +282 -282
- data/lib/rbbt/annotations.rb +343 -320
- data/lib/rbbt/association/database.rb +200 -225
- data/lib/rbbt/association/index.rb +294 -291
- data/lib/rbbt/association/item.rb +227 -227
- data/lib/rbbt/association/open.rb +35 -34
- data/lib/rbbt/association/util.rb +0 -169
- data/lib/rbbt/association.rb +2 -4
- data/lib/rbbt/entity/identifiers.rb +119 -118
- data/lib/rbbt/entity/refactor.rb +12 -0
- data/lib/rbbt/entity.rb +319 -315
- data/lib/rbbt/hpc/batch.rb +72 -53
- data/lib/rbbt/hpc/lsf.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
- data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
- data/lib/rbbt/hpc/orchestrate.rb +19 -13
- data/lib/rbbt/hpc/slurm.rb +18 -18
- data/lib/rbbt/knowledge_base/entity.rb +13 -5
- data/lib/rbbt/knowledge_base/query.rb +2 -2
- data/lib/rbbt/knowledge_base/registry.rb +32 -31
- data/lib/rbbt/knowledge_base/traverse.rb +1 -1
- data/lib/rbbt/knowledge_base.rb +1 -1
- data/lib/rbbt/monitor.rb +36 -25
- data/lib/rbbt/persist/refactor.rb +166 -0
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
- data/lib/rbbt/persist/tsv.rb +187 -185
- data/lib/rbbt/persist.rb +556 -551
- data/lib/rbbt/refactor.rb +20 -0
- data/lib/rbbt/resource/path/refactor.rb +178 -0
- data/lib/rbbt/resource/path.rb +317 -497
- data/lib/rbbt/resource/util.rb +0 -48
- data/lib/rbbt/resource.rb +3 -390
- data/lib/rbbt/tsv/accessor.rb +2 -838
- data/lib/rbbt/tsv/attach.rb +303 -299
- data/lib/rbbt/tsv/change_id.rb +244 -245
- data/lib/rbbt/tsv/csv.rb +87 -85
- data/lib/rbbt/tsv/dumper.rb +2 -100
- data/lib/rbbt/tsv/excel.rb +26 -24
- data/lib/rbbt/tsv/field_index.rb +4 -1
- data/lib/rbbt/tsv/filter.rb +3 -2
- data/lib/rbbt/tsv/index.rb +2 -284
- data/lib/rbbt/tsv/manipulate.rb +750 -747
- data/lib/rbbt/tsv/marshal.rb +3 -3
- data/lib/rbbt/tsv/matrix.rb +2 -2
- data/lib/rbbt/tsv/parallel/through.rb +2 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
- data/lib/rbbt/tsv/parser.rb +678 -678
- data/lib/rbbt/tsv/refactor.rb +195 -0
- data/lib/rbbt/tsv/stream.rb +253 -251
- data/lib/rbbt/tsv/util.rb +420 -420
- data/lib/rbbt/tsv.rb +210 -208
- data/lib/rbbt/util/R/eval.rb +4 -4
- data/lib/rbbt/util/R/plot.rb +62 -166
- data/lib/rbbt/util/R.rb +21 -18
- data/lib/rbbt/util/cmd.rb +2 -318
- data/lib/rbbt/util/color.rb +269 -269
- data/lib/rbbt/util/colorize.rb +89 -89
- data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
- data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
- data/lib/rbbt/util/concurrency/processes.rb +389 -386
- data/lib/rbbt/util/config.rb +169 -167
- data/lib/rbbt/util/iruby.rb +20 -0
- data/lib/rbbt/util/log/progress/report.rb +241 -241
- data/lib/rbbt/util/log/progress/util.rb +99 -99
- data/lib/rbbt/util/log/progress.rb +102 -102
- data/lib/rbbt/util/log/refactor.rb +49 -0
- data/lib/rbbt/util/log.rb +486 -532
- data/lib/rbbt/util/migrate.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
- data/lib/rbbt/util/misc/development.rb +12 -11
- data/lib/rbbt/util/misc/exceptions.rb +117 -112
- data/lib/rbbt/util/misc/format.rb +2 -230
- data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
- data/lib/rbbt/util/misc/inspect.rb +2 -476
- data/lib/rbbt/util/misc/lock.rb +109 -106
- data/lib/rbbt/util/misc/omics.rb +9 -1
- data/lib/rbbt/util/misc/pipes.rb +765 -793
- data/lib/rbbt/util/misc/refactor.rb +20 -0
- data/lib/rbbt/util/misc/ssw.rb +27 -17
- data/lib/rbbt/util/misc/system.rb +0 -15
- data/lib/rbbt/util/misc.rb +39 -20
- data/lib/rbbt/util/named_array/refactor.rb +4 -0
- data/lib/rbbt/util/named_array.rb +3 -220
- data/lib/rbbt/util/open/refactor.rb +7 -0
- data/lib/rbbt/util/open.rb +3 -857
- data/lib/rbbt/util/procpath.rb +6 -6
- data/lib/rbbt/util/python/paths.rb +27 -0
- data/lib/rbbt/util/python/run.rb +115 -0
- data/lib/rbbt/util/python/script.rb +110 -0
- data/lib/rbbt/util/python/util.rb +3 -3
- data/lib/rbbt/util/python.rb +22 -81
- data/lib/rbbt/util/semaphore.rb +152 -148
- data/lib/rbbt/util/simpleopt.rb +9 -8
- data/lib/rbbt/util/ssh/refactor.rb +19 -0
- data/lib/rbbt/util/ssh.rb +122 -118
- data/lib/rbbt/util/tar.rb +117 -115
- data/lib/rbbt/util/tmpfile.rb +69 -67
- data/lib/rbbt/util/version.rb +2 -0
- data/lib/rbbt/workflow/refactor/entity.rb +11 -0
- data/lib/rbbt/workflow/refactor/export.rb +66 -0
- data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
- data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
- data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
- data/lib/rbbt/workflow/refactor.rb +153 -0
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
- data/lib/rbbt/workflow/remote_workflow.rb +6 -1
- data/lib/rbbt/workflow/step/run.rb +766 -766
- data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
- data/lib/rbbt/workflow/step.rb +2 -362
- data/lib/rbbt/workflow/task.rb +118 -118
- data/lib/rbbt/workflow/usage.rb +289 -287
- data/lib/rbbt/workflow/util/archive.rb +6 -5
- data/lib/rbbt/workflow/util/data.rb +1 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
- data/lib/rbbt/workflow/util/trace.rb +79 -44
- data/lib/rbbt/workflow.rb +4 -882
- data/lib/rbbt-util.rb +21 -13
- data/lib/rbbt.rb +16 -3
- data/python/rbbt/__init__.py +19 -1
- data/share/Rlib/plot.R +37 -37
- data/share/Rlib/svg.R +22 -5
- data/share/install/software/lib/install_helpers +1 -1
- data/share/rbbt_commands/hpc/list +2 -3
- data/share/rbbt_commands/hpc/orchestrate +4 -4
- data/share/rbbt_commands/hpc/tail +2 -0
- data/share/rbbt_commands/hpc/task +10 -7
- data/share/rbbt_commands/lsf/list +2 -3
- data/share/rbbt_commands/lsf/orchestrate +4 -4
- data/share/rbbt_commands/lsf/tail +2 -0
- data/share/rbbt_commands/lsf/task +10 -7
- data/share/rbbt_commands/migrate +1 -1
- data/share/rbbt_commands/pbs/list +2 -3
- data/share/rbbt_commands/pbs/orchestrate +4 -4
- data/share/rbbt_commands/pbs/tail +2 -0
- data/share/rbbt_commands/pbs/task +10 -7
- data/share/rbbt_commands/resource/produce +8 -1
- data/share/rbbt_commands/slurm/list +2 -3
- data/share/rbbt_commands/slurm/orchestrate +4 -4
- data/share/rbbt_commands/slurm/tail +2 -0
- data/share/rbbt_commands/slurm/task +10 -7
- data/share/rbbt_commands/system/clean +5 -5
- data/share/rbbt_commands/system/status +5 -5
- data/share/rbbt_commands/tsv/get +2 -3
- data/share/rbbt_commands/tsv/info +10 -13
- data/share/rbbt_commands/tsv/keys +18 -14
- data/share/rbbt_commands/tsv/slice +2 -2
- data/share/rbbt_commands/tsv/transpose +6 -2
- data/share/rbbt_commands/workflow/info +20 -24
- data/share/rbbt_commands/workflow/list +1 -1
- data/share/rbbt_commands/workflow/prov +20 -13
- data/share/rbbt_commands/workflow/server +11 -1
- data/share/rbbt_commands/workflow/task +76 -71
- data/share/rbbt_commands/workflow/write_info +26 -9
- data/share/software/opt/ssw/ssw.c +861 -0
- data/share/software/opt/ssw/ssw.h +130 -0
- data/share/workflow_config.ru +3 -3
- metadata +40 -2
data/lib/rbbt/persist/tsv.rb
CHANGED
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require 'rbbt/persist/tsv/
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when
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when
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when "
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when "
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Persist.
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when
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Persist.
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when '
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Persist.open_fwt(path, value_size, range, serializer, update, in_memory)
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tsv.
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end
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require_relative '../refactor'
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Rbbt.require_instead 'scout/persist/tsv'
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#require 'rbbt/persist/tsv/adapter'
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#
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#require 'rbbt/persist/tsv/fix_width_table'
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#require 'rbbt/persist/tsv/packed_index'
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#
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#begin
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# require 'rbbt/persist/tsv/tokyocabinet'
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#rescue Exception
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# Log.warn "The tokyocabinet gem could not be loaded. Persistence using this engine will fail."
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#end
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#
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#begin
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# require 'rbbt/persist/tsv/lmdb'
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#rescue Exception
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# Log.debug "The lmdb gem could not be loaded. Persistence using this engine will fail."
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#end
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#
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#begin
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# require 'rbbt/persist/tsv/leveldb'
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#rescue Exception
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# Log.debug "The LevelDB gem could not be loaded. Persistence using this engine will fail."
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#end
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#
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#begin
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# require 'rbbt/persist/tsv/cdb'
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#rescue Exception
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# Log.debug "The CDB gem could not be loaded. Persistence using this engine will fail."
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#end
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#
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#begin
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# require 'rbbt/persist/tsv/kyotocabinet'
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#rescue Exception
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# Log.debug "The kyotocabinet gem could not be loaded. Persistence using this engine will fail."
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#end
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#
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#module Persist
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# CONNECTIONS = {}
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#
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# def self.get_filename(source)
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# case
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# when Path === source
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# source
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# when (source.respond_to?(:filename) and source.filename)
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# source.filename
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# when source.respond_to?(:cmd)
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# "CMD-#{Misc.digest(source.cmd)}"
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# when TSV === source
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# "TSV[#{Misc.digest Misc.fingerprint(source)}]"
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# end || source.object_id.to_s
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# end
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#
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# def self.open_database(path, write, serializer = nil, type = "HDB", options = {})
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# case type
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# when "LevelDB"
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# Persist.open_leveldb(path, write, serializer)
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# when "CDB"
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# Persist.open_cdb(path, write, serializer)
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# when "LMDB"
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# Persist.open_lmdb(path, write, serializer)
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# when 'kch', 'kct'
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# Persist.open_kyotocabinet(path, write, serializer, type)
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# when 'fwt'
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# value_size, range, update, in_memory, pos_function = Misc.process_options options.dup, :value_size, :range, :update, :in_memory, :pos_function
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# if pos_function
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# Persist.open_fwt(path, value_size, range, serializer, update, in_memory, &pos_function)
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# else
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# Persist.open_fwt(path, value_size, range, serializer, update, in_memory)
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# end
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# when 'pki'
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# pattern, pos_function = Misc.process_options options.dup, :pattern, :pos_function
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# if pos_function
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# Persist.open_pki(path, write, pattern, &pos_function)
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# else
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# Persist.open_pki(path, write, pattern)
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# end
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# else
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# Persist.open_tokyocabinet(path, write, serializer, type)
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# end
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# end
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#
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# def self.persist_tsv(source, filename = nil, options = {}, persist_options = {}, &block)
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# persist_options[:prefix] ||= "TSV"
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#
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# if data = persist_options[:data]
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# Log.debug "TSV persistence creating with data: #{ Misc.fingerprint(data) }"
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# yield data
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# return data
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# end
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#
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# filename ||= get_filename(source)
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#
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# if not persist_options[:persist]
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# data = {}
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#
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# yield(data)
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#
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# return data
|
100
|
+
# end
|
101
|
+
#
|
102
|
+
# path = persistence_path(filename, options)
|
103
|
+
#
|
104
|
+
# if ENV["RBBT_UPDATE_TSV_PERSIST"] == 'true' and filename
|
105
|
+
# check_options = {:check => [filename]}
|
106
|
+
# else
|
107
|
+
# check_options = {}
|
108
|
+
# end
|
109
|
+
#
|
110
|
+
# if is_persisted?(path, check_options) and not persist_options[:update]
|
111
|
+
# path = path.find if Path === path
|
112
|
+
# Log.debug "TSV persistence up-to-date: #{ path }"
|
113
|
+
# if persist_options[:shard_function]
|
114
|
+
# return open_sharder(path, false, nil, persist_options[:engine], persist_options, &persist_options[:shard_function])
|
115
|
+
# else
|
116
|
+
# return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB, persist_options)
|
117
|
+
# end
|
118
|
+
# end
|
119
|
+
#
|
120
|
+
# lock_filename = Persist.persistence_path(path, {:dir => TSV.lock_dir})
|
121
|
+
# Misc.lock lock_filename do
|
122
|
+
# begin
|
123
|
+
# if is_persisted?(path, check_options) and not persist_options[:update]
|
124
|
+
# path = path.find if Path === path
|
125
|
+
# Log.debug "TSV persistence (suddenly) up-to-date: #{ path }"
|
126
|
+
#
|
127
|
+
# if persist_options[:shard_function]
|
128
|
+
# return open_sharder(path, false, nil, persist_options[:engine], persist_options, &persist_options[:shard_function])
|
129
|
+
# else
|
130
|
+
# return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB, persist_options)
|
131
|
+
# end
|
132
|
+
# end
|
133
|
+
# path = path.find if Path === path
|
134
|
+
#
|
135
|
+
# FileUtils.rm_rf path if File.exist? path
|
136
|
+
#
|
137
|
+
# Log.medium "TSV persistence creating: #{ path }"
|
138
|
+
#
|
139
|
+
# tmp_path = path + '.persist'
|
140
|
+
#
|
141
|
+
# data = if persist_options[:shard_function]
|
142
|
+
# open_sharder(tmp_path, true, persist_options[:serializer], persist_options[:engine], persist_options, &persist_options[:shard_function])
|
143
|
+
# else
|
144
|
+
# open_database(tmp_path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB, persist_options)
|
145
|
+
# end
|
146
|
+
#
|
147
|
+
# if TSV === data and data.serializer.nil?
|
148
|
+
# data.serializer = :type
|
149
|
+
# end
|
150
|
+
#
|
151
|
+
# if persist_options[:persist] == :preload
|
152
|
+
# tmp_tsv = yield({})
|
153
|
+
# tmp_tsv.annotate data
|
154
|
+
# data.serializer = tmp_tsv.type
|
155
|
+
# data.write_and_read do
|
156
|
+
# tmp_tsv.each do |k,v|
|
157
|
+
# data[k] = v
|
158
|
+
# end
|
159
|
+
# end
|
160
|
+
# else
|
161
|
+
# data.write_and_read do
|
162
|
+
# yield data
|
163
|
+
# end
|
164
|
+
# end
|
165
|
+
#
|
166
|
+
# data.write_and_read do
|
167
|
+
# FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
|
168
|
+
# tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
|
169
|
+
# tsv.persistence_path = path
|
170
|
+
#
|
171
|
+
# tsv.fix_io if tsv.respond_to? :fix_io
|
172
|
+
# end
|
173
|
+
#
|
174
|
+
# data
|
175
|
+
# rescue Exception
|
176
|
+
# Log.error "Captured error during persist_tsv. Erasing: #{path}"
|
177
|
+
# FileUtils.rm_rf tmp_path if tmp_path and File.exist? tmp_path
|
178
|
+
# FileUtils.rm_rf path if path and File.exist? path
|
179
|
+
# raise $!
|
180
|
+
# end
|
181
|
+
# end
|
182
|
+
# end
|
183
|
+
#
|
184
|
+
#end
|
185
|
+
#
|
186
|
+
#require 'rbbt/persist/tsv/sharder'
|
187
|
+
#
|