rbbt-util 5.32.13 → 5.32.18
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- checksums.yaml +4 -4
- data/lib/rbbt/annotations/util.rb +1 -0
- data/lib/rbbt/entity.rb +6 -1
- data/lib/rbbt/hpc/batch.rb +3 -2
- data/lib/rbbt/hpc/orchestrate.rb +1 -0
- data/lib/rbbt/hpc/slurm.rb +2 -0
- data/lib/rbbt/resource/path.rb +6 -6
- data/lib/rbbt/tsv.rb +5 -0
- data/lib/rbbt/tsv/parallel/traverse.rb +9 -12
- data/lib/rbbt/util/log.rb +15 -4
- data/lib/rbbt/util/log/progress/util.rb +2 -1
- data/lib/rbbt/util/misc/inspect.rb +3 -1
- data/lib/rbbt/util/misc/omics.rb +2 -2
- data/lib/rbbt/util/misc/system.rb +2 -2
- data/lib/rbbt/util/open.rb +1 -0
- data/lib/rbbt/util/python.rb +39 -0
- data/lib/rbbt/workflow.rb +54 -2
- data/lib/rbbt/workflow/accessor.rb +15 -242
- data/lib/rbbt/workflow/definition.rb +2 -1
- data/lib/rbbt/workflow/dependencies.rb +195 -0
- data/lib/rbbt/workflow/step.rb +10 -158
- data/lib/rbbt/workflow/step/accessor.rb +1 -311
- data/lib/rbbt/workflow/step/dependencies.rb +43 -3
- data/lib/rbbt/workflow/step/info.rb +294 -0
- data/lib/rbbt/workflow/step/status.rb +146 -0
- data/lib/rbbt/workflow/usage.rb +4 -2
- data/lib/rbbt/workflow/util/data.rb +5 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +1 -1
- data/lib/rbbt/workflow/util/provenance.rb +40 -9
- data/python/rbbt.py +5 -1
- data/share/rbbt_commands/hpc/orchestrate +4 -1
- data/share/rbbt_commands/hpc/task +2 -0
- data/share/rbbt_commands/lsf/orchestrate +4 -1
- data/share/rbbt_commands/lsf/task +2 -0
- data/share/rbbt_commands/slurm/orchestrate +4 -1
- data/share/rbbt_commands/slurm/task +2 -0
- data/share/rbbt_commands/system/clean +1 -0
- data/share/rbbt_commands/workflow/prov +1 -1
- data/test/rbbt/workflow/util/test_data.rb +15 -2
- metadata +5 -2
data/lib/rbbt/workflow/usage.rb
CHANGED
@@ -67,11 +67,13 @@ end
|
|
67
67
|
|
68
68
|
module Workflow
|
69
69
|
|
70
|
-
def dep_tree(name)
|
70
|
+
def dep_tree(name, seen = [])
|
71
71
|
@dep_tree ||= {}
|
72
72
|
@dep_tree[name] ||= begin
|
73
73
|
dep_tree = {}
|
74
74
|
self.task_dependencies[name.to_sym].reverse.each do |dep|
|
75
|
+
next if seen.include? dep
|
76
|
+
seen << dep
|
75
77
|
dep = dep.first if Array === dep && dep.length == 1
|
76
78
|
dep = dep.dependency if DependencyBlock === dep
|
77
79
|
|
@@ -87,7 +89,7 @@ module Workflow
|
|
87
89
|
|
88
90
|
key = [workflow, task]
|
89
91
|
|
90
|
-
dep_tree[key] = workflow.dep_tree(task)
|
92
|
+
dep_tree[key] = workflow.dep_tree(task, seen)
|
91
93
|
end if name && self.task_dependencies[name.to_sym]
|
92
94
|
dep_tree
|
93
95
|
end
|
@@ -23,7 +23,11 @@ module Workflow
|
|
23
23
|
task_info = workflow.task_info(oname)
|
24
24
|
dir_options = Workflow.load_inputs(data_dir.options, task_info[:inputs], task_info[:input_types])
|
25
25
|
data_options = block.call data_dir, dir_options, task_info
|
26
|
-
|
26
|
+
if data_options.include?(:inputs)
|
27
|
+
data_options
|
28
|
+
else
|
29
|
+
{:inputs => data_options.merge(options)}
|
30
|
+
end
|
27
31
|
end
|
28
32
|
end
|
29
33
|
end
|
@@ -81,7 +81,7 @@ module Workflow
|
|
81
81
|
def self.candidates(workload, rules)
|
82
82
|
if rules.empty?
|
83
83
|
candidates = workload.select{|k,v| v.empty? }.
|
84
|
-
collect{|k,v| k}.
|
84
|
+
collect{|k,v| k }.
|
85
85
|
reject{|k| k.done? }
|
86
86
|
else
|
87
87
|
candidates = workload. #select{|k,v| Orchestrator.job_rules(rules, k) }.
|
@@ -26,7 +26,7 @@ class Step
|
|
26
26
|
Log.color(color, status.to_s)
|
27
27
|
end
|
28
28
|
|
29
|
-
def self.prov_report_msg(status, name, path, info = nil)
|
29
|
+
def self.prov_report_msg(status, name, path, info, input = nil)
|
30
30
|
parts = path.sub(/\{.*/,'').split "/"
|
31
31
|
|
32
32
|
parts.pop
|
@@ -43,10 +43,19 @@ class Step
|
|
43
43
|
rescue Exception
|
44
44
|
nil
|
45
45
|
end
|
46
|
+
|
47
|
+
if input.nil? || input.empty?
|
48
|
+
input_str = nil
|
49
|
+
else
|
50
|
+
input = input.reject{|dep,name| (input & dep.dependencies.collect{|d| [d,name]}).any? }
|
51
|
+
input = input.reject{|dep,name| (input & dep.input_dependencies.collect{|d| [d,name]}).any? }
|
52
|
+
input_str = Log.color(:magenta, "-> ") + input.collect{|dep,name| Log.color(:yellow, dep.task_name.to_s) + ":" + Log.color(:yellow, name) }.uniq * " "
|
53
|
+
end
|
54
|
+
|
46
55
|
str = if ! (Open.remote?(path) || Open.ssh?(path)) && (Open.exists?(path) && $main_mtime && path_mtime && ($main_mtime - path_mtime) < -2)
|
47
|
-
prov_status_msg(status.to_s) << " " << [workflow, task, path].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
|
56
|
+
prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
|
48
57
|
else
|
49
|
-
prov_status_msg(status.to_s) << " " << [workflow, task, path].compact * " "
|
58
|
+
prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " "
|
50
59
|
end
|
51
60
|
|
52
61
|
if $inputs and $inputs.any?
|
@@ -74,7 +83,7 @@ class Step
|
|
74
83
|
str << "\n"
|
75
84
|
end
|
76
85
|
|
77
|
-
def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false)
|
86
|
+
def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false, input = nil)
|
78
87
|
info = step.info || {}
|
79
88
|
info[:task_name] = task
|
80
89
|
path = step.path
|
@@ -84,14 +93,33 @@ class Step
|
|
84
93
|
status = :unsync if status == :done and not Open.exist?(path)
|
85
94
|
status = :notfound if status == :noinfo and not Open.exist?(path)
|
86
95
|
|
87
|
-
|
88
|
-
|
89
|
-
|
96
|
+
|
97
|
+
this_step_msg = prov_report_msg(status, name, path, info, input)
|
98
|
+
|
99
|
+
input_dependencies = {}
|
100
|
+
step.dependencies.each do |dep|
|
101
|
+
if dep.input_dependencies.any?
|
102
|
+
dep.input_dependencies.each do |id|
|
103
|
+
input_name = dep.recursive_inputs.fields.zip(dep.recursive_inputs).select{|f,d|
|
104
|
+
d == id || (String === d && d.start_with?(id.files_dir)) || (Array === d && d.include?(id))
|
105
|
+
}.last.first
|
106
|
+
input_dependencies[id] ||= []
|
107
|
+
input_dependencies[id] << [dep, input_name]
|
108
|
+
end
|
109
|
+
end
|
110
|
+
end
|
111
|
+
|
112
|
+
str = ""
|
113
|
+
str = " " * offset + this_step_msg if ENV["RBBT_ORIGINAL_STACK"] == 'true'
|
114
|
+
|
115
|
+
step.dependencies.dup.tap{|l|
|
116
|
+
l.reverse! if ENV["RBBT_ORIGINAL_STACK"] == 'true'
|
117
|
+
}.each do |dep|
|
90
118
|
path = dep.path
|
91
119
|
new = ! seen.include?(path)
|
92
120
|
if new
|
93
121
|
seen << path
|
94
|
-
str << prov_report(dep, offset + 1, task, seen, expand_repeats)
|
122
|
+
str << prov_report(dep, offset + 1, task, seen, expand_repeats, input_dependencies[dep])
|
95
123
|
else
|
96
124
|
if expand_repeats
|
97
125
|
str << Log.color(Step.status_color(dep.status), Log.uncolor(prov_report(dep, offset+1, task)))
|
@@ -103,10 +131,13 @@ class Step
|
|
103
131
|
status = :unsync if status == :done and not Open.exist?(path)
|
104
132
|
status = :notfound if status == :noinfo and not Open.exist?(path)
|
105
133
|
|
106
|
-
str << Log.color(Step.status_color(status), " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
|
134
|
+
str << Log.color(Step.status_color(status), " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info, input_dependencies[dep])))
|
107
135
|
end
|
108
136
|
end
|
109
137
|
end if step.dependencies
|
138
|
+
|
139
|
+
str += (" " * offset) + this_step_msg unless ENV["RBBT_ORIGINAL_STACK"] == 'true'
|
140
|
+
|
110
141
|
str
|
111
142
|
end
|
112
143
|
end
|
data/python/rbbt.py
CHANGED
@@ -28,12 +28,15 @@ $slurm_options = SOPT.get <<EOF
|
|
28
28
|
-t--task_cpus* Tasks
|
29
29
|
-tm--time* Time
|
30
30
|
-m--mem* SLURM minimum memory
|
31
|
+
--gres* SLURM Generic resources
|
31
32
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
32
33
|
-lin--licenses* SLURM licenses
|
33
34
|
-cons--constraint* SLURM constraint
|
34
35
|
-W--workflows* Additional workflows
|
35
|
-
-OR--orchestration_rules* Orchestration rules
|
36
36
|
-rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
|
37
|
+
-lmod--lua_modules* Lua Modules to load
|
38
|
+
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
39
|
+
-OR--orchestration_rules* Orchestration rules
|
37
40
|
EOF
|
38
41
|
|
39
42
|
batch_system = $slurm_options.delete :batch_system
|
@@ -27,11 +27,13 @@ $slurm_options = SOPT.get <<EOF
|
|
27
27
|
-t--task_cpus* Tasks
|
28
28
|
-tm--time* Time
|
29
29
|
-m--mem* SLURM minimum memory
|
30
|
+
--gres* SLURM Generic resources
|
30
31
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
31
32
|
-lin--licenses* SLURM licenses
|
32
33
|
-cons--constraint* SLURM constraint
|
33
34
|
-W--workflows* Additional workflows
|
34
35
|
-rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
|
36
|
+
-lmod--lua_modules* Lua Modules to load
|
35
37
|
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
36
38
|
EOF
|
37
39
|
|
@@ -28,12 +28,15 @@ $slurm_options = SOPT.get <<EOF
|
|
28
28
|
-t--task_cpus* Tasks
|
29
29
|
-tm--time* Time
|
30
30
|
-m--mem* SLURM minimum memory
|
31
|
+
--gres* SLURM Generic resources
|
31
32
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
32
33
|
-lin--licenses* SLURM licenses
|
33
34
|
-cons--constraint* SLURM constraint
|
34
35
|
-W--workflows* Additional workflows
|
35
|
-
-OR--orchestration_rules* Orchestration rules
|
36
36
|
-rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
|
37
|
+
-lmod--lua_modules* Lua Modules to load
|
38
|
+
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
39
|
+
-OR--orchestration_rules* Orchestration rules
|
37
40
|
EOF
|
38
41
|
|
39
42
|
batch_system = $slurm_options.delete :batch_system
|
@@ -27,11 +27,13 @@ $slurm_options = SOPT.get <<EOF
|
|
27
27
|
-t--task_cpus* Tasks
|
28
28
|
-tm--time* Time
|
29
29
|
-m--mem* SLURM minimum memory
|
30
|
+
--gres* SLURM Generic resources
|
30
31
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
31
32
|
-lin--licenses* SLURM licenses
|
32
33
|
-cons--constraint* SLURM constraint
|
33
34
|
-W--workflows* Additional workflows
|
34
35
|
-rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
|
36
|
+
-lmod--lua_modules* Lua Modules to load
|
35
37
|
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
36
38
|
EOF
|
37
39
|
|
@@ -28,12 +28,15 @@ $slurm_options = SOPT.get <<EOF
|
|
28
28
|
-t--task_cpus* Tasks
|
29
29
|
-tm--time* Time
|
30
30
|
-m--mem* SLURM minimum memory
|
31
|
+
--gres* SLURM Generic resources
|
31
32
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
32
33
|
-lin--licenses* SLURM licenses
|
33
34
|
-cons--constraint* SLURM constraint
|
34
35
|
-W--workflows* Additional workflows
|
35
|
-
-OR--orchestration_rules* Orchestration rules
|
36
36
|
-rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
|
37
|
+
-lmod--lua_modules* Lua Modules to load
|
38
|
+
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
39
|
+
-OR--orchestration_rules* Orchestration rules
|
37
40
|
EOF
|
38
41
|
|
39
42
|
batch_system = $slurm_options.delete :batch_system
|
@@ -27,11 +27,13 @@ $slurm_options = SOPT.get <<EOF
|
|
27
27
|
-t--task_cpus* Tasks
|
28
28
|
-tm--time* Time
|
29
29
|
-m--mem* SLURM minimum memory
|
30
|
+
--gres* SLURM Generic resources
|
30
31
|
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
31
32
|
-lin--licenses* SLURM licenses
|
32
33
|
-cons--constraint* SLURM constraint
|
33
34
|
-W--workflows* Additional workflows
|
34
35
|
-rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
|
36
|
+
-lmod--lua_modules* Lua Modules to load
|
35
37
|
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
36
38
|
EOF
|
37
39
|
|
@@ -5,15 +5,24 @@ module TestDataWF
|
|
5
5
|
extend Workflow
|
6
6
|
extend Workflow::Data
|
7
7
|
|
8
|
+
input :salutation, :string
|
9
|
+
task :salute_luis => :string do |name,salutation|
|
10
|
+
"Hi Luis: #{salutation}"
|
11
|
+
end
|
12
|
+
|
8
13
|
input :name, :string
|
9
14
|
input :salutation, :string
|
10
15
|
task :salute => :string do |name,salutation|
|
11
16
|
"Hi #{name}: #{salutation}"
|
12
17
|
end
|
13
18
|
|
14
|
-
data_task :salute_data, TestDataWF, :salute do |directory,options|
|
19
|
+
data_task :salute_data, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
|
15
20
|
options.merge({:salutation => directory.salutation.read})
|
16
21
|
end
|
22
|
+
|
23
|
+
data_task :salute_data2, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
|
24
|
+
{:task => :salute_luis, :inputs => options.merge({:salutation => directory.salutation.read})}
|
25
|
+
end
|
17
26
|
end
|
18
27
|
|
19
28
|
class TestWorkflowData < Test::Unit::TestCase
|
@@ -28,7 +37,11 @@ class TestWorkflowData < Test::Unit::TestCase
|
|
28
37
|
|
29
38
|
job = TestDataWF.job(:salute_data, "TestDir")
|
30
39
|
job.recursive_clean.run
|
31
|
-
|
40
|
+
assert job.run.include? "Miguel"
|
41
|
+
|
42
|
+
job = TestDataWF.job(:salute_data2, "TestDir")
|
43
|
+
job.recursive_clean.run
|
44
|
+
assert job.run.include? "Luis"
|
32
45
|
end
|
33
46
|
end
|
34
47
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.32.
|
4
|
+
version: 5.32.18
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-
|
11
|
+
date: 2021-07-14 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -322,6 +322,7 @@ files:
|
|
322
322
|
- lib/rbbt/workflow/accessor.rb
|
323
323
|
- lib/rbbt/workflow/annotate.rb
|
324
324
|
- lib/rbbt/workflow/definition.rb
|
325
|
+
- lib/rbbt/workflow/dependencies.rb
|
325
326
|
- lib/rbbt/workflow/doc.rb
|
326
327
|
- lib/rbbt/workflow/examples.rb
|
327
328
|
- lib/rbbt/workflow/integration/ansible.rb
|
@@ -339,8 +340,10 @@ files:
|
|
339
340
|
- lib/rbbt/workflow/step.rb
|
340
341
|
- lib/rbbt/workflow/step/accessor.rb
|
341
342
|
- lib/rbbt/workflow/step/dependencies.rb
|
343
|
+
- lib/rbbt/workflow/step/info.rb
|
342
344
|
- lib/rbbt/workflow/step/prepare.rb
|
343
345
|
- lib/rbbt/workflow/step/run.rb
|
346
|
+
- lib/rbbt/workflow/step/status.rb
|
344
347
|
- lib/rbbt/workflow/task.rb
|
345
348
|
- lib/rbbt/workflow/usage.rb
|
346
349
|
- lib/rbbt/workflow/util/archive.rb
|