rbbt-util 5.28.6 → 5.28.11
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- checksums.yaml +4 -4
- data/lib/rbbt/entity.rb +1 -1
- data/lib/rbbt/fix_width_table.rb +5 -4
- data/lib/rbbt/persist.rb +9 -3
- data/lib/rbbt/persist/tsv/adapter.rb +0 -1
- data/lib/rbbt/persist/tsv/fix_width_table.rb +5 -3
- data/lib/rbbt/resource.rb +12 -6
- data/lib/rbbt/tsv/accessor.rb +10 -2
- data/lib/rbbt/tsv/dumper.rb +14 -2
- data/lib/rbbt/tsv/parallel/traverse.rb +2 -0
- data/lib/rbbt/tsv/util.rb +5 -1
- data/lib/rbbt/util/R.rb +2 -2
- data/lib/rbbt/util/cmd.rb +10 -0
- data/lib/rbbt/util/config.rb +2 -1
- data/lib/rbbt/util/misc/bgzf.rb +1 -1
- data/lib/rbbt/util/misc/inspect.rb +11 -7
- data/lib/rbbt/util/misc/system.rb +1 -1
- data/lib/rbbt/util/named_array.rb +1 -1
- data/lib/rbbt/util/open.rb +18 -17
- data/lib/rbbt/workflow/accessor.rb +1 -1
- data/lib/rbbt/workflow/definition.rb +8 -4
- data/lib/rbbt/workflow/integration/ansible.rb +53 -0
- data/lib/rbbt/workflow/integration/ansible/workflow.rb +60 -0
- data/lib/rbbt/workflow/step.rb +22 -5
- data/lib/rbbt/workflow/step/accessor.rb +6 -6
- data/lib/rbbt/workflow/util/archive.rb +3 -0
- data/lib/rbbt/workflow/util/orchestrator.rb +228 -0
- data/lib/rbbt/workflow/util/provenance.rb +7 -3
- data/lib/rbbt/workflow/util/trace.rb +182 -0
- data/share/rbbt_commands/ansible +55 -0
- data/share/rbbt_commands/purge_job +2 -5
- data/share/rbbt_commands/system/status +23 -23
- data/share/rbbt_commands/workflow/forget_deps +10 -3
- data/share/rbbt_commands/workflow/prov +2 -1
- data/test/rbbt/association/test_index.rb +6 -6
- data/test/rbbt/knowledge_base/test_query.rb +3 -3
- data/test/rbbt/knowledge_base/test_registry.rb +1 -1
- data/test/rbbt/persist/tsv/test_cdb.rb +0 -7
- data/test/rbbt/persist/tsv/test_kyotocabinet.rb +2 -8
- data/test/rbbt/persist/tsv/test_leveldb.rb +0 -6
- data/test/rbbt/persist/tsv/test_lmdb.rb +0 -6
- data/test/rbbt/persist/tsv/test_tokyocabinet.rb +15 -14
- data/test/rbbt/test_entity.rb +0 -1
- data/test/rbbt/test_knowledge_base.rb +3 -4
- data/test/rbbt/test_persist.rb +10 -6
- data/test/rbbt/test_workflow.rb +17 -16
- data/test/rbbt/tsv/parallel/test_traverse.rb +14 -0
- data/test/rbbt/tsv/test_accessor.rb +11 -0
- data/test/rbbt/tsv/test_attach.rb +0 -2
- data/test/rbbt/tsv/test_index.rb +6 -7
- data/test/rbbt/tsv/test_manipulate.rb +22 -3
- data/test/rbbt/util/R/test_model.rb +2 -1
- data/test/rbbt/util/R/test_plot.rb +0 -2
- data/test/rbbt/util/concurrency/test_processes.rb +1 -1
- data/test/rbbt/util/misc/test_bgzf.rb +11 -7
- data/test/rbbt/util/misc/test_lock.rb +0 -1
- data/test/rbbt/util/misc/test_multipart_payload.rb +1 -1
- data/test/rbbt/util/misc/test_pipes.rb +0 -5
- data/test/rbbt/util/test_R.rb +1 -0
- data/test/rbbt/util/test_log.rb +4 -6
- data/test/rbbt/util/test_misc.rb +0 -2
- data/test/rbbt/util/test_open.rb +0 -1
- data/test/rbbt/util/test_python.rb +17 -1
- data/test/rbbt/workflow/test_remote_workflow.rb +1 -1
- data/test/rbbt/workflow/test_schedule.rb +0 -0
- data/test/rbbt/workflow/test_step.rb +8 -3
- data/test/rbbt/workflow/util/test_orchestrator.rb +273 -0
- metadata +11 -5
- data/lib/rbbt/workflow/schedule.rb +0 -238
- data/test/rbbt/workflow/remote/test_client.rb +0 -56
@@ -66,7 +66,7 @@ class Step
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str << "\n"
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end
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-
def self.prov_report(step, offset = 0, task = nil, seen = [])
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def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false)
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info = step.info || {}
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info[:task_name] = task
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path = step.path
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@@ -82,9 +82,13 @@ class Step
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new = ! seen.include?(path)
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if new
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seen << path
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str << prov_report(dep, offset + 1, task, seen)
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str << prov_report(dep, offset + 1, task, seen, expand_repeats)
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else
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-
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if expand_repeats
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str << Log.color(:green, Log.uncolor(prov_report(dep, offset+1, task)))
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else
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str << Log.color(:green, " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
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end
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end
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end if step.dependencies
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str
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@@ -0,0 +1,182 @@
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require 'rbbt/util/R'
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module Workflow
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def self.trace(seed_jobs, options = {})
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jobs = []
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seed_jobs.each{|j| jobs << j; jobs += j.rec_dependencies}
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data = TSV.setup({}, "Job~Workflow,Task,Start,End#:type=:list")
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min_start = nil
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max_done = nil
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jobs.each do |job|
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next unless job.info[:done]
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started = job.info[:started]
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ddone = job.info[:done]
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code = [job.workflow, job.task_name].compact.collect{|s| s.to_s} * "."
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code = code + '.' + job.name
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data[code] = [job.workflow.to_s, job.task_name, started, ddone]
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if min_start.nil?
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min_start = started
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else
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min_start = started if started < min_start
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end
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if max_done.nil?
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max_done = ddone
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else
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max_done = ddone if ddone > max_done
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end
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end
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data.add_field "Start.second" do |k,value|
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value["Start"] - min_start
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end
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data.add_field "End.second" do |k,value|
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value["End"] - min_start
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end
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if options[:fix_gap]
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ranges = []
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data.through do |k,values|
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start, eend = values.values_at "Start.second", "End.second"
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ranges << (start..eend)
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end
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gaps = {}
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last = nil
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Misc.collapse_ranges(ranges).each do |range|
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start = range.begin
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eend = range.end
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if last
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gaps[last] = start - last
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end
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last = eend
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end
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data.process "End.second" do |value,k,values|
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gap = Misc.sum(gaps.select{|pos,size| pos < values["Start.second"]}.collect{|pos,size| size})
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value - gap
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end
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data.process "Start.second" do |value,k,values|
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gap = Misc.sum(gaps.select{|pos,size| pos < values["Start.second"]}.collect{|pos,size| size})
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value - gap
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end
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end
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tasks_info = {}
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jobs.each do |dep|
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next unless dep.info[:done]
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task = [dep.workflow, dep.task_name].compact.collect{|s| s.to_s} * "#"
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info = tasks_info[task] ||= {}
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time = dep.info[:done] - dep.info[:started]
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info[:time] ||= []
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info[:time] << time
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cpus = nil
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spark = false
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shard = false
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dep.info[:config_keys].select do |kinfo|
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key, value, tokens = kinfo
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key = key.to_s
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cpus = value if key.include? 'cpu'
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spark = value if key == 'spark'
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shard = value if key == 'shard'
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end
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info[:cpus] = cpus || 1
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info[:spark] = spark
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info[:shard] = shard
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end
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stats = TSV.setup({}, "Task~Calls,Avg. Time,Total Time,Cpus,Spark,Shard#:type=:list")
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tasks_info.each do |task, info|
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time_lists, cpus, spark, shard = info.values_at :time, :cpus, :spark, :shard
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avg_time = Misc.mean(time_lists)
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total_time = Misc.sum(time_lists)
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calls = time_lists.length
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stats[task] = [calls, avg_time, total_time, cpus, spark, shard]
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end
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raise "No jobs to process" if data.size == 0
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start = data.column("Start.second").values.flatten.collect{|v| v.to_f}.min
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eend = data.column("End.second").values.flatten.collect{|v| v.to_f}.max
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total = eend - start
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Log.info "Total time elapsed: #{total} seconds"
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if options[:fix_gap]
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total_gaps = Misc.sum(gaps.collect{|k,v| v})
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Log.info "Total gaps: #{total_gaps} seconds"
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end
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plot, width, height = options.values_at :plot, :width, :height
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if plot
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data.R <<-EOF, [:svg]
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rbbt.require('tidyverse')
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rbbt.require('ggplot2')
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names(data) <- make.names(names(data))
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data$id = rownames(data)
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data$content = data$Task
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data$start = data$Start
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data$end = data$End
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data$Project = data$Workflow
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tasks = data
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#theme_gantt <- function(base_size=11, base_family="Source Sans Pro Light") {
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theme_gantt <- function(base_size=11, base_family="Sans Serif") {
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ret <- theme_bw(base_size, base_family) %+replace%
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theme(panel.background = element_rect(fill="#ffffff", colour=NA),
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axis.title.x=element_text(vjust=-0.2), axis.title.y=element_text(vjust=1.5),
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title=element_text(vjust=1.2, family="Source Sans Pro Semibold"),
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panel.border = element_blank(), axis.line=element_blank(),
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panel.grid.minor=element_blank(),
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panel.grid.major.y = element_blank(),
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panel.grid.major.x = element_line(size=0.5, colour="grey80"),
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axis.ticks=element_blank(),
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legend.position="bottom",
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axis.title=element_text(size=rel(1.2), family="Source Sans Pro Semibold"),
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strip.text=element_text(size=rel(1.5), family="Source Sans Pro Semibold"),
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strip.background=element_rect(fill="#ffffff", colour=NA),
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panel.spacing.y=unit(1.5, "lines"),
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legend.key = element_blank())
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ret
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}
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tasks.long <- tasks %>%
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gather(date.type, task.date, -c(Project, Task, id, Start.second, End.second)) %>%
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arrange(date.type, task.date) %>%
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mutate(id = factor(id, levels=rev(unique(id)), ordered=TRUE))
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x.breaks <- seq(length(tasks$Task) + 0.5 - 3, 0, by=-3)
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timeline <- ggplot(tasks.long, aes(y=id, yend=id, x=Start.second, xend=End.second, colour=Task)) +
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geom_segment() +
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geom_vline(xintercept=x.breaks, colour="grey80", linetype="dotted") +
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guides(colour=guide_legend(title=NULL)) +
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labs(x=NULL, y=NULL) +
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theme_gantt() + theme(axis.text.x=element_text(angle=45, hjust=1))
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rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, pointsize=6)
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EOF
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end
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if options[:plot_data]
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data
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else
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stats
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end
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end
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end
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@@ -0,0 +1,55 @@
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#!/usr/bin/env ruby
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require 'rbbt-util'
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require 'rbbt/util/simpleopt'
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$0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_commands
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options = SOPT.setup <<EOF
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Run ansible
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$ #{$0} [options] <rules.yml|->
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Use - to read from STDIN
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-h--help Print this help
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-dr--dry_run Only print the playbook
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-H--hosts* hosts to run it on
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EOF
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if options[:help]
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if defined? rbbt_usage
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rbbt_usage
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else
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puts SOPT.doc
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end
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exit 0
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end
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require 'rbbt/workflow/integration/ansible'
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playbook, task = ARGV
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playbook_file = Rbbt.share.ansible["test.yaml"].find if playbook.nil?
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dry_run = options.delete :dry_run
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if ! Misc.filename?(playbook_file)
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playbook_file = Rbbt.share.ansible.glob(playbook + ".*").first
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end
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if ! Misc.filename?(playbook_file)
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recipe = Rbbt.share.recipes.glob(playbook + ".*").first
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playbook_file = Ansible.playbook recipe, task, options
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end
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if dry_run
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if Hash === playbook_file
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ppp playbook_file.to_yaml
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else
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ppp Log.color :magenta, playbook_file
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ppp Open.read(playbook_file)
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end
|
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else
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Ansible.play playbook_file
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end
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@@ -3,7 +3,6 @@
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3
3
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require 'rbbt-util'
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4
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require 'rbbt/util/simpleopt'
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require 'rbbt/workflow'
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-
require 'rbbt/workflow/remote/ssh/get'
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$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
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@@ -14,9 +13,7 @@ Remove a job and its dependencies
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$ rbbt purge [options] <job_path>
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-h--help Print this help
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-
-
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-r--relocate Include relocated dependencies
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-
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-r--recursive Remove recursively
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EOF
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if options[:help]
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if defined? rbbt_usage
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@@ -31,4 +28,4 @@ path, search_path, _sep, *other = ARGV
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raise ParameterException, "No path given" if path.nil?
|
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34
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-
Step.purge(path, options[:
|
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+
Step.purge(path, options[:recursive])
|
@@ -49,27 +49,27 @@ def pid_msg(pid)
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49
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end
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|
52
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-
def status_msg(status)
|
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-
color = case status.to_sym
|
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|
-
when :error, :aborted, :missing, :dead, :broken
|
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-
:red
|
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-
when :streaming, :started
|
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-
:cyan
|
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-
when :done
|
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-
:green
|
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-
when :noinfo
|
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-
:blue
|
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-
when :dependencies, :waiting, :setup
|
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-
:yellow
|
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-
else
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-
if status.to_s.index ">"
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-
:cyan
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-
else
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-
:cyan
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69
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-
end
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-
end
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-
Log.color(color, status.to_s)
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-
end
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52
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+
#def status_msg(status)
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53
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+
# color = case status.to_sym
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54
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+
# when :error, :aborted, :missing, :dead, :broken
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55
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+
# :red
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56
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+
# when :streaming, :started
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57
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+
# :cyan
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58
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+
# when :done
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59
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+
# :green
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60
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+
# when :noinfo, :notfound
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+
# :blue
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62
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+
# when :dependencies, :waiting, :setup
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+
# :yellow
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64
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+
# else
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65
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+
# if status.to_s.index ">"
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66
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+
# :cyan
|
67
|
+
# else
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68
|
+
# :cyan
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69
|
+
# end
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70
|
+
# end
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71
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+
# Log.color(color, status.to_s)
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72
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+
#end
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73
73
|
|
74
74
|
def input_msg(file, inputs)
|
75
75
|
|
@@ -201,7 +201,7 @@ workflows.sort.each do |workflow,tasks|
|
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201
201
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Step::INFO_SERIALIZER.load(f)
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202
202
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end
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203
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rescue
|
204
|
-
Log.exception $!
|
204
|
+
#Log.exception $!
|
205
205
|
{:status => :noinfo}
|
206
206
|
end
|
207
207
|
IndiferentHash.setup(info)
|
@@ -218,7 +218,7 @@ workflows.sort.each do |workflow,tasks|
|
|
218
218
|
status << Log.color(:red, " (dead)")
|
219
219
|
end
|
220
220
|
end
|
221
|
-
str << " #{
|
221
|
+
str << " #{ Step.prov_status_msg status }"
|
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222
|
str << " (dirty)" if status == 'done' && Workflow.load_step(file).dirty?
|
223
223
|
|
224
224
|
if inputs and inputs.any?
|
@@ -13,6 +13,8 @@ Make a job forget all its dependencies and archive their meta-data
|
|
13
13
|
$ #{$0} [options] <job_path>
|
14
14
|
|
15
15
|
-h--help Print this help
|
16
|
+
-p--purge Purge dependencies
|
17
|
+
-r--recursive_purge Purge dependencies recursively
|
16
18
|
|
17
19
|
EOF
|
18
20
|
if options[:help]
|
@@ -29,8 +31,13 @@ path = ARGV[0]
|
|
29
31
|
raise ParameterException, "No path given" if path.nil?
|
30
32
|
step = Workflow.load_step path
|
31
33
|
|
32
|
-
|
33
|
-
iif step.rec_dependencies
|
34
|
-
|
35
34
|
step.archive_deps
|
35
|
+
step.copy_files_dir
|
36
|
+
dependencies = step.dependencies
|
36
37
|
step.set_info :dependencies, []
|
38
|
+
|
39
|
+
if options[:purge]
|
40
|
+
dependencies.each do |dependency|
|
41
|
+
Step.purge(dependency.path, options[:recursive_purge])
|
42
|
+
end
|
43
|
+
end
|
@@ -24,6 +24,7 @@ $ rbbt workflow prov <job-result>
|
|
24
24
|
-i--inputs* List of inputs to print
|
25
25
|
-if--info_fields* List of info fields to print
|
26
26
|
-t--touch Update modification times to be consistent
|
27
|
+
-e--expand_repeats Show all the dependency tree even if reapeated dependencies have already been seen before
|
27
28
|
EOF
|
28
29
|
|
29
30
|
SOPT.usage if options[:help]
|
@@ -130,6 +131,6 @@ if options[:plot]
|
|
130
131
|
end
|
131
132
|
|
132
133
|
else
|
133
|
-
puts Step.prov_report(step).strip
|
134
|
+
puts Step.prov_report(step, 0, nil, [], options[:expand_repeats]).strip
|
134
135
|
end
|
135
136
|
|
@@ -73,21 +73,21 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
73
73
|
|
74
74
|
def test_index_flat
|
75
75
|
require 'rbbt/sources/tfacts'
|
76
|
-
file =
|
76
|
+
file = TFactS.regulators
|
77
77
|
tsv = Association.index(file, :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
|
78
78
|
assert tsv.match("TP53").length > 10
|
79
79
|
end
|
80
80
|
|
81
81
|
def test_index_flat_to_matrix
|
82
82
|
require 'rbbt/sources/tfacts'
|
83
|
-
file =
|
83
|
+
file = TFactS.regulators
|
84
84
|
tsv = Association.index(file, :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
|
85
85
|
assert(tsv.to_matrix(false))
|
86
86
|
end
|
87
87
|
|
88
88
|
def test_filter_no_block
|
89
89
|
require 'rbbt/sources/tfacts'
|
90
|
-
file =
|
90
|
+
file = TFactS.regulators
|
91
91
|
tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
|
92
92
|
tsv.unnamed = false
|
93
93
|
matches = tsv.filter :directed?
|
@@ -96,7 +96,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
96
96
|
|
97
97
|
def test_filter_no_block_value
|
98
98
|
require 'rbbt/sources/tfacts'
|
99
|
-
file =
|
99
|
+
file = TFactS.regulators
|
100
100
|
tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
|
101
101
|
tsv.unnamed = false
|
102
102
|
matches = tsv.filter :Effect, "inhibition"
|
@@ -105,7 +105,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
105
105
|
|
106
106
|
def test_filter_block_value_field
|
107
107
|
require 'rbbt/sources/tfacts'
|
108
|
-
file =
|
108
|
+
file = TFactS.regulators
|
109
109
|
tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
|
110
110
|
tsv.unnamed = false
|
111
111
|
matches = tsv.filter :Effect do |value|
|
@@ -116,7 +116,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
116
116
|
|
117
117
|
def test_filter_block_no_value_field
|
118
118
|
require 'rbbt/sources/tfacts'
|
119
|
-
file =
|
119
|
+
file = TFactS.regulators
|
120
120
|
tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
|
121
121
|
tsv.unnamed = false
|
122
122
|
matches = tsv.filter do |key,values|
|
@@ -22,7 +22,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
22
22
|
:namespace => "Hsa"
|
23
23
|
}
|
24
24
|
|
25
|
-
EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
|
25
|
+
EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
|
26
26
|
|
27
27
|
KNOWLEDGE_BASE = KnowledgeBase.new Rbbt.tmp.test.kb_foo2, "Hsa"
|
28
28
|
KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
|
@@ -34,11 +34,11 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
34
34
|
assert_equal 6, KNOWLEDGE_BASE.subset(:effects, :all).length
|
35
35
|
|
36
36
|
assert_equal 4, KNOWLEDGE_BASE.subset(:effects, :all).target_entity.uniq.length
|
37
|
-
assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
|
37
|
+
assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
|
38
38
|
end
|
39
39
|
end
|
40
40
|
|
41
|
-
def
|
41
|
+
def _test_subset_all_persist_format
|
42
42
|
assert KNOWLEDGE_BASE.subset(:effects, :all).target_entity.reject{|e| e =~ /^ENS/}.empty?
|
43
43
|
end
|
44
44
|
|