rbbt-util 5.34.20 → 5.34.22
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- checksums.yaml +4 -4
- data/lib/rbbt/resource/path.rb +1 -1
- data/lib/rbbt/tsv/accessor.rb +1 -1
- data/lib/rbbt/tsv/parser.rb +1 -1
- data/lib/rbbt/util/migrate.rb +2 -2
- data/lib/rbbt/util/misc/development.rb +31 -1
- data/lib/rbbt/workflow/dependencies.rb +5 -2
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +52 -15
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +5 -2
- data/lib/rbbt/workflow/step/run.rb +6 -0
- data/lib/rbbt/workflow/step/save_load_inputs.rb +1 -0
- data/lib/rbbt/workflow/util/archive.rb +7 -0
- data/lib/rbbt/workflow.rb +40 -3
- data/share/rbbt_commands/study/task +2 -2
- data/share/rbbt_commands/workflow/task +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 40183cfe120bb6545a1bb59f150bb3cac9426ce018d18485afdbf0c8f1de92b2
|
4
|
+
data.tar.gz: fd625b45572be4a158bc9f08007225e284659ec9ef26fbe66a2e9ae7fb84ce9f
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: f9f2a5ee2e22b84c8bce0f0da023a39cb917a8210ab1c9a4daca7d67902134221fd671da62ca19a2ce02fb06049ea00f4a8a282a1906235f91380d936240b987
|
7
|
+
data.tar.gz: 5124409cb58db3eea7029042ec8671e13075bd814b40a25a905a56ccc52ae660e9981f3146f8a2ecaad2c122ea6edea1ea8b4c7d1a1191a58621c797f317577c
|
data/lib/rbbt/resource/path.rb
CHANGED
data/lib/rbbt/tsv/accessor.rb
CHANGED
@@ -11,7 +11,7 @@ module TSV
|
|
11
11
|
attr_accessor :unnamed, :serializer_module, :entity_options, :entity_templates
|
12
12
|
|
13
13
|
def info
|
14
|
-
{:key_field => key_field, :fields => fields, :namespace => namespace, :entity_options => entity_options, :type => type, :filename => filename, :identifiers => identifiers, :unnamed => unnamed, :cast => cast}.delete_if{|k,v| v.nil? }
|
14
|
+
{:key_field => key_field, :fields => fields.dup, :namespace => namespace, :entity_options => entity_options, :type => type, :filename => filename, :identifiers => identifiers, :unnamed => unnamed, :cast => cast}.delete_if{|k,v| v.nil? }
|
15
15
|
end
|
16
16
|
|
17
17
|
def annotate(tsv)
|
data/lib/rbbt/tsv/parser.rb
CHANGED
@@ -516,7 +516,7 @@ module TSV
|
|
516
516
|
data.extend TSV unless TSV === data
|
517
517
|
data.type = @type
|
518
518
|
data.key_field = @key_field
|
519
|
-
data.fields = @fields
|
519
|
+
data.fields = @fields.nil? ? nil : @fields.dup
|
520
520
|
data.namespace = @namespace
|
521
521
|
data.filename = @filename
|
522
522
|
data.identifiers = @identifiers
|
data/lib/rbbt/util/migrate.rb
CHANGED
@@ -84,7 +84,7 @@ puts resource[path].find(search_path)
|
|
84
84
|
#cmd = "rsync -avztAXHP --copy-unsafe-links #{test_str} #{files_from_str} #{excludes_str} '#{source_path}' #{target_path} #{other * " "}"
|
85
85
|
|
86
86
|
# rsync_args = "-avztAXHP --copy-unsafe-links"
|
87
|
-
rsync_args = "-
|
87
|
+
rsync_args = "-avztHP --copy-unsafe-links"
|
88
88
|
|
89
89
|
rsync_args << " --link-dest '#{source_path}'" if hard_link && ! options[:source]
|
90
90
|
|
@@ -96,7 +96,7 @@ puts resource[path].find(search_path)
|
|
96
96
|
puts cmd
|
97
97
|
exit 0
|
98
98
|
else
|
99
|
-
CMD.cmd_log(cmd, :log => Log::
|
99
|
+
CMD.cmd_log(cmd, :log => Log::HIGH)
|
100
100
|
|
101
101
|
if options[:delete] && options[:files]
|
102
102
|
remove_files = options[:files].collect{|f| File.join(source_path, f) }
|
@@ -417,12 +417,42 @@ def self.add_libdir(dir=nil)
|
|
417
417
|
end
|
418
418
|
end
|
419
419
|
|
420
|
-
def self.ssh_run(server, script = nil
|
420
|
+
def self.ssh_run(server, script = nil)
|
421
421
|
Log.debug "Run ssh script in #{server}:\n#{script}"
|
422
422
|
|
423
423
|
CMD.cmd("ssh '#{server}' 'shopt -s expand_aliases; bash -l -c \"ruby\"' ", :in => script, :log => true).read
|
424
424
|
end
|
425
425
|
|
426
|
+
def self.ssh_connection(server, reset = false)
|
427
|
+
@@ssh_connections ||= {}
|
428
|
+
@@ssh_connections.delete server if reset
|
429
|
+
@@ssh_connections[server] ||= begin
|
430
|
+
require 'pty'
|
431
|
+
master, slave = PTY.open
|
432
|
+
read, write = Misc.pipe
|
433
|
+
pid = spawn("ssh '#{server}' 'shopt -s expand_aliases; bash -l' ", :in => read, :out => slave, :err => STDERR.fileno)
|
434
|
+
read.close
|
435
|
+
slave.close
|
436
|
+
[write, master, pid]
|
437
|
+
end
|
438
|
+
end
|
439
|
+
|
440
|
+
def self.ssh_run(server, script = nil)
|
441
|
+
Log.debug "Run ssh script in #{server}:\n#{script}"
|
442
|
+
|
443
|
+
write, master, pid = ssh_connection(server)
|
444
|
+
write, master = ssh_connection(server, true) if PTY.check pid
|
445
|
+
write.puts "echo '#{script.gsub("'", '"') + "\n" + 'puts "\nCMD_OUT_END"'}' | ruby "
|
446
|
+
lines = []
|
447
|
+
while true
|
448
|
+
line = master.gets
|
449
|
+
break if line.strip == "CMD_OUT_END"
|
450
|
+
lines << line.strip unless line.strip.empty?
|
451
|
+
end
|
452
|
+
lines * "\n"
|
453
|
+
|
454
|
+
end
|
455
|
+
|
426
456
|
def self.timeout_insist(time, msg = nil, &block)
|
427
457
|
Misc.insist do
|
428
458
|
begin
|
@@ -72,7 +72,10 @@ module Workflow
|
|
72
72
|
def setup_override_dependency(dep, workflow, task_name)
|
73
73
|
return [] if dep == :skip || dep == 'skip'
|
74
74
|
|
75
|
-
|
75
|
+
if ! Step === dep
|
76
|
+
located = Open.exists?(dep)
|
77
|
+
dep = Workflow.load_step(dep)
|
78
|
+
end
|
76
79
|
|
77
80
|
dep.original_workflow ||= dep.workflow if dep.workflow
|
78
81
|
dep.original_task_name ||= dep.task_name if dep.task_name
|
@@ -92,7 +95,7 @@ module Workflow
|
|
92
95
|
end
|
93
96
|
|
94
97
|
dep.task_name = task_name
|
95
|
-
dep.overriden = dep.original_task_name.to_sym if dep.original_task_name
|
98
|
+
dep.overriden = dep.original_task_name.to_sym if dep.original_task_name && located
|
96
99
|
|
97
100
|
dep.extend step_module
|
98
101
|
|
@@ -106,9 +106,9 @@ STDOUT.write res
|
|
106
106
|
script += job_script(inputs_id, jobname)
|
107
107
|
script +=<<-EOF
|
108
108
|
job.init_info
|
109
|
-
STDOUT.write job.
|
109
|
+
STDOUT.write job.path
|
110
110
|
EOF
|
111
|
-
|
111
|
+
Misc.ssh_run(server, script)
|
112
112
|
end
|
113
113
|
|
114
114
|
def self.run_job(url, input_id, jobname = nil)
|
@@ -117,6 +117,7 @@ STDOUT.write job.name
|
|
117
117
|
script = path_script(path)
|
118
118
|
script += job_script(input_id, jobname)
|
119
119
|
script +=<<-EOF
|
120
|
+
ENV["RBBT_UPDATE"]="#{(ENV["RBBT_UPDATE"] || false).to_s}"
|
120
121
|
job.produce
|
121
122
|
STDOUT.write job.path
|
122
123
|
EOF
|
@@ -153,31 +154,67 @@ job.clean
|
|
153
154
|
new = Step.migrate(path, :user, :target => server)
|
154
155
|
Open.write(file, new)
|
155
156
|
end
|
156
|
-
CMD.
|
157
|
+
CMD.cmd_log("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/; scp -r '#{dir}' #{server}:.rbbt/tmp/tmp-ssh_job_inputs/#{input_id}")
|
157
158
|
end
|
158
159
|
end
|
159
160
|
end
|
160
161
|
|
161
|
-
def self.
|
162
|
-
|
163
|
-
|
162
|
+
#def self.relay_old(workflow, task, jobname, inputs, server, options = {})
|
163
|
+
# options = Misc.add_defaults options, :search_path => 'user'
|
164
|
+
# search_path = options[:search_path]
|
164
165
|
|
165
|
-
|
166
|
+
# job = workflow.job(task, jobname, inputs)
|
166
167
|
|
167
|
-
|
168
|
-
|
169
|
-
|
168
|
+
# job.dependencies.each do |dep|
|
169
|
+
# dep.produce
|
170
|
+
# end
|
170
171
|
|
171
|
-
|
172
|
+
# override_dependencies = job.dependencies.collect{|dep| [dep.workflow.to_s, dep.task_name.to_s] * "#" << "=" << Rbbt.identify(dep.path)}
|
173
|
+
|
174
|
+
# job.dependencies.each do |dep|
|
175
|
+
# Step.migrate(dep.path, search_path, :target => server)
|
176
|
+
# end
|
177
|
+
|
178
|
+
# remote = RemoteWorkflow.new("ssh://#{server}:#{workflow.to_s}", "#{workflow.to_s}")
|
179
|
+
# rjob = remote.job(task, jobname, {})
|
180
|
+
# rjob.override_dependencies = override_dependencies
|
181
|
+
# rjob.run
|
182
|
+
#end
|
183
|
+
|
184
|
+
def self.relay_job(job, server, options = {})
|
185
|
+
migrate, produce, produce_dependencies, search_path = Misc.process_options options.dup,
|
186
|
+
:migrate, :produce, :produce_dependencies, :search_path
|
187
|
+
|
188
|
+
search_path ||= 'user'
|
189
|
+
|
190
|
+
produce = true if migrate
|
191
|
+
|
192
|
+
workflow_name = job.workflow.to_s
|
193
|
+
inputs = job.inputs.to_hash
|
194
|
+
job.dependencies.each do |dep|
|
195
|
+
dep.produce if options[:produce_dependencies]
|
196
|
+
next unless dep.done?
|
172
197
|
|
173
|
-
job.dependencies.each do |dep|
|
174
198
|
Step.migrate(dep.path, search_path, :target => server)
|
175
199
|
end
|
176
200
|
|
177
|
-
|
178
|
-
rjob =
|
201
|
+
remote_workflow = RemoteWorkflow.new("ssh://#{server}:#{job.workflow.to_s}", "#{job.workflow.to_s}")
|
202
|
+
rjob = remote_workflow.job(job.task_name.to_s, job.clean_name, inputs)
|
203
|
+
|
204
|
+
override_dependencies = job.dependencies.collect{|dep| [dep.workflow.to_s, dep.task_name.to_s] * "#" << "=" << Rbbt.identify(dep.path)}
|
179
205
|
rjob.override_dependencies = override_dependencies
|
180
|
-
|
206
|
+
|
207
|
+
if options[:migrate]
|
208
|
+
rjob.produce
|
209
|
+
Step.migrate(Rbbt.identify(job.path), 'user', :source => server)
|
210
|
+
end
|
211
|
+
|
212
|
+
rjob
|
213
|
+
end
|
214
|
+
|
215
|
+
def self.relay(workflow, task, jobname, inputs, server, options = {})
|
216
|
+
job = workflow.job(task, jobname, inputs)
|
217
|
+
relay_job(job, server, options)
|
181
218
|
end
|
182
219
|
|
183
220
|
def workflow_description
|
@@ -22,12 +22,13 @@ class RemoteStep
|
|
22
22
|
|
23
23
|
RemoteWorkflow::SSH.upload_inputs(@server, inputs, @input_types, @input_id)
|
24
24
|
|
25
|
-
@
|
25
|
+
@remote_path ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
|
26
26
|
Misc.insist do
|
27
27
|
input_types = {}
|
28
28
|
RemoteWorkflow::SSH.post_job(File.join(base_url, task.to_s), @input_id, @base_name)
|
29
29
|
end
|
30
30
|
end
|
31
|
+
@name = @remote_path.split("/").last
|
31
32
|
|
32
33
|
if Open.remote?(@name)
|
33
34
|
@url = @name
|
@@ -41,9 +42,10 @@ class RemoteStep
|
|
41
42
|
|
42
43
|
def path
|
43
44
|
@server, @server_path = RemoteWorkflow::SSH.parse_url @base_url
|
44
|
-
init_job unless @name
|
45
45
|
if info[:path]
|
46
46
|
"ssh://" + @server + ":" + info[:path]
|
47
|
+
elsif @remote_path
|
48
|
+
"ssh://" + @server + ":" + @remote_path
|
47
49
|
else
|
48
50
|
"ssh://" + @server + ":" + ["var/jobs", self.workflow.to_s, task_name.to_s, @name] * "/"
|
49
51
|
end
|
@@ -57,6 +59,7 @@ class RemoteStep
|
|
57
59
|
while ! done?
|
58
60
|
sleep 1
|
59
61
|
end
|
62
|
+
self
|
60
63
|
end
|
61
64
|
|
62
65
|
def load
|
@@ -216,6 +216,12 @@ class Step
|
|
216
216
|
def run(no_load = false)
|
217
217
|
result = nil
|
218
218
|
|
219
|
+
if Workflow === workflow && workflow.relay_tasks && workflow.relay_tasks.include?(task_name)
|
220
|
+
server, options = workflow.relay_tasks[task_name]
|
221
|
+
options[:migrate] = true
|
222
|
+
return RemoteWorkflow::SSH.relay_job(self, server, options)
|
223
|
+
end
|
224
|
+
|
219
225
|
begin
|
220
226
|
time_elapsed = total_time_elapsed = nil
|
221
227
|
res = @mutex.synchronize do
|
@@ -161,6 +161,13 @@ puts files * "\n"
|
|
161
161
|
end
|
162
162
|
|
163
163
|
def self.migrate(path, search_path, options = {})
|
164
|
+
if Step === path
|
165
|
+
if options[:source]
|
166
|
+
path = Rbbt.identify(path.path)
|
167
|
+
else
|
168
|
+
path = path.path
|
169
|
+
end
|
170
|
+
end
|
164
171
|
search_path = 'user' if search_path.nil?
|
165
172
|
|
166
173
|
resource = Rbbt
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -45,6 +45,13 @@ module Workflow
|
|
45
45
|
load_remote_tasks(Rbbt.root.etc.remote_tasks.find) if Rbbt.root.etc.remote_tasks.exists?
|
46
46
|
end
|
47
47
|
|
48
|
+
def self.init_relay_tasks
|
49
|
+
return if defined? @@init_relay_tasks and @@init_relay_tasks
|
50
|
+
@@init_relay_tasks = true
|
51
|
+
load_relay_tasks(Rbbt.root.etc.relay_tasks.find) if Rbbt.root.etc.relay_tasks.exists?
|
52
|
+
end
|
53
|
+
|
54
|
+
|
48
55
|
|
49
56
|
def self.require_remote_workflow(wf_name, url)
|
50
57
|
require 'rbbt/workflow/remote_workflow'
|
@@ -142,6 +149,7 @@ module Workflow
|
|
142
149
|
|
143
150
|
def self.require_workflow(wf_name, force_local=false)
|
144
151
|
Workflow.init_remote_tasks
|
152
|
+
Workflow.init_relay_tasks
|
145
153
|
# Already loaded
|
146
154
|
begin
|
147
155
|
workflow = Misc.string2const wf_name
|
@@ -219,6 +227,7 @@ module Workflow
|
|
219
227
|
attr_accessor :step_cache
|
220
228
|
attr_accessor :load_step_cache
|
221
229
|
attr_accessor :remote_tasks
|
230
|
+
attr_accessor :relay_tasks
|
222
231
|
|
223
232
|
#{{{ ATTR DEFAULTS
|
224
233
|
|
@@ -244,7 +253,7 @@ module Workflow
|
|
244
253
|
when :hash
|
245
254
|
clean_inputs = Annotated.purge(inputs)
|
246
255
|
clean_inputs = clean_inputs.collect{|i| Symbol === i ? i.to_s : i }
|
247
|
-
deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep ===
|
256
|
+
deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep === d)) ? "Step: " << (Symbol === d.overriden ? d.path : d.short_path) : d }
|
248
257
|
key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
|
249
258
|
key_str = Misc.obj2str(key_obj)
|
250
259
|
hash_str = Misc.digest(key_str)
|
@@ -543,7 +552,10 @@ module Workflow
|
|
543
552
|
persist = input_values.nil? ? false : true
|
544
553
|
persist = false
|
545
554
|
|
546
|
-
if ! (Path === step_path ? step_path.find : File.exist?(step_path)) &&
|
555
|
+
if ! (Path === step_path ? step_path.find : File.exist?(step_path)) &&
|
556
|
+
step_path.split("/").length == 3 &&
|
557
|
+
File.exist?(new_path = Rbbt.var.jobs[step_path].find)
|
558
|
+
|
547
559
|
step_path = new_path
|
548
560
|
end
|
549
561
|
|
@@ -638,7 +650,7 @@ module Workflow
|
|
638
650
|
end
|
639
651
|
step = Step.new path
|
640
652
|
relocated = false
|
641
|
-
|
653
|
+
dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
|
642
654
|
if Open.exists?(dep_path) || Open.exists?(dep_path + '.info') || Open.remote?(dep_path) || Open.ssh?(dep_path)
|
643
655
|
Workflow._load_step dep_path
|
644
656
|
else
|
@@ -647,6 +659,7 @@ module Workflow
|
|
647
659
|
Workflow._load_step new_path
|
648
660
|
end
|
649
661
|
end
|
662
|
+
step.instance_variable_set("@dependencies", dependencies)
|
650
663
|
step.relocated = relocated
|
651
664
|
step.load_inputs_from_info
|
652
665
|
step
|
@@ -828,4 +841,28 @@ module Workflow
|
|
828
841
|
Workflow.process_remote_tasks(remote_workflow_tasks)
|
829
842
|
end
|
830
843
|
|
844
|
+
def self.process_relay_tasks(relay_tasks)
|
845
|
+
require 'rbbt/workflow/remote_workflow'
|
846
|
+
relay_tasks.each do |workflow, servers|
|
847
|
+
wf = Workflow.require_workflow workflow
|
848
|
+
wf.relay_tasks ||= {}
|
849
|
+
IndiferentHash.setup wf.relay_tasks
|
850
|
+
servers.each do |server, tasks|
|
851
|
+
case tasks
|
852
|
+
when Array
|
853
|
+
tasks.each do |task|
|
854
|
+
wf.relay_tasks[task.to_sym] = [server, {:migrate => :true}]
|
855
|
+
end
|
856
|
+
else
|
857
|
+
wf.relay_tasks[tasks.to_sym] = [server, {:migrate => :true}]
|
858
|
+
end
|
859
|
+
end
|
860
|
+
end
|
861
|
+
end
|
862
|
+
|
863
|
+
def self.load_relay_tasks(filename)
|
864
|
+
yaml_text = Open.read(filename)
|
865
|
+
relay_workflow_tasks = YAML.load(yaml_text)
|
866
|
+
Workflow.process_relay_tasks(relay_workflow_tasks)
|
867
|
+
end
|
831
868
|
end
|
@@ -106,7 +106,7 @@ options = SOPT.get <<EOF
|
|
106
106
|
-as--array_separator* Change the character that separates elements of Arrays, ',', '|', or '\\n' by default:
|
107
107
|
-cl--clean Clean the last step of the job so that it gets recomputed:
|
108
108
|
-rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
|
109
|
-
-n--name* Job name to use. The name '
|
109
|
+
-n--name* Job name to use. The name '#{Workflow::DEFAULT_NAME}' is used by default:
|
110
110
|
-pn--printname Print the name of the job and exit without starting it:
|
111
111
|
-rw--require_workflow* Workflows to require, separated by commas
|
112
112
|
EOF
|
@@ -155,7 +155,7 @@ end
|
|
155
155
|
|
156
156
|
usage workflow, task if help
|
157
157
|
|
158
|
-
name = options.delete(:name) ||
|
158
|
+
name = options.delete(:name) || Workflow::DEFAULT_NAME
|
159
159
|
|
160
160
|
# get job args
|
161
161
|
sopt_option_string = SOPT_options(workflow, task)
|
@@ -178,7 +178,7 @@ available. Examples can be enacted using `rbbt workflow example <workflow>
|
|
178
178
|
[<task>] [<example>]`.
|
179
179
|
|
180
180
|
When a task is enacted a job is instantiated. This job is identified by the
|
181
|
-
`jobname` (which is *
|
181
|
+
`jobname` (which is *#{Workflow::DEFAULT_NAME}* unless specified otherwise) and the values of the
|
182
182
|
parameters; these two things determine the filename under which the job result
|
183
183
|
will be saved. If the taks is enacted using the same `jobname` and parameters
|
184
184
|
it will result in the same job, pointing to the same result file.
|
@@ -194,7 +194,7 @@ The `recursive_clean` cleans all the job dependency steps recursively.
|
|
194
194
|
-wda--workdir_all* Change the working directory of ALL workflow
|
195
195
|
-as--array_separator* Change the character that separates elements of Arrays, ',', '|', or '\\n' by default
|
196
196
|
-fs--field_separator* Change the character that separates fields of TSV files '\\t' by default
|
197
|
-
-jn--jobname* Job name to use. The name '
|
197
|
+
-jn--jobname* Job name to use. The name '#{Workflow::DEFAULT_NAME}' is used by default
|
198
198
|
-pn--printname Print the name of the job and exit without starting it
|
199
199
|
-pf--printpath Print the path of the job result
|
200
200
|
-cl--clean Clean the last step of the job so that it gets recomputed
|
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: 5.34.
|
4
|
+
version: 5.34.22
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-11-
|
11
|
+
date: 2022-11-28 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|