rbbt-util 5.31.0 → 5.31.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/hpc/batch.rb +0 -2
- data/lib/rbbt/workflow/step/accessor.rb +11 -7
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 61b346a2806a9f5c6f32dd2e972386ad2ebd5d748b4d71ac89fdeabc0250567b
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4
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data.tar.gz: faa0e2b8eee1eb1271406f16bf8b030ee4ecd3d83e6dfce205a5129e6676e2c9
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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data.tar.gz:
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6
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+
metadata.gz: 57f76043890f5ad9ecdf7b397f7803d59556bc39fe8110fd719db68192cda82542ccf072899f37f23fd497a03fe79b9d1119146c268e7571843dee9a35eeb506
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7
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data.tar.gz: 8b4b959e19804a206abb1a080d81866aa73388eee85d1c031021ed79e239df570b055a3f9d007fbe406eb372edd76ade85a556bf9d38dca16011b326efbf8117
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data/lib/rbbt/hpc/batch.rb
CHANGED
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@@ -11,8 +11,6 @@ module HPC
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11
11
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env_cmd = Misc.process_options options, :env_cmd
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development = Misc.process_options options, :development
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14
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-
job_cmd = self.rbbt_job_exec_cmd(job, options)
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15
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-
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if options[:singularity]
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group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir
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@@ -99,7 +99,8 @@ class Step
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if String === value && File.exists?(value)
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Open.ln_s(value, path)
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else
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-
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value = "#{value}" if Path === value
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Open.write(path + '.yaml', value.to_yaml)
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end
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when Array === value
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Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
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@@ -122,15 +123,18 @@ class Step
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workflow = job.workflow
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workflow = Kernel.const_get workflow if String === workflow
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if workflow
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-
task_info = workflow.task_info(task_name)
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-
input_types = task_info[:input_types]
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-
task_inputs = task_info[:inputs]
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-
input_defaults = task_info[:input_defaults]
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task_info = IndiferentHash.setup(workflow.task_info(task_name))
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input_types = IndiferentHash.setup(task_info[:input_types])
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task_inputs = IndiferentHash.setup(task_info[:inputs])
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input_defaults = IndiferentHash.setup(task_info[:input_defaults])
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else
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task_info =
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task_info = IndiferentHash.setup({})
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input_types = IndiferentHash.setup({})
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task_inputs = IndiferentHash.setup({})
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input_defaults = IndiferentHash.setup({})
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end
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-
inputs = {}
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inputs = IndiferentHash.setup({})
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real_inputs = job.real_inputs || job.info[:real_inputs]
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job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
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next unless task_inputs.include? name.to_sym
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