refactoring: replacing singularity with apptainer in variable names #1366
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MontrealSergiy
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prioux
requested changes
Mar 11, 2024
BrainPortal/db/migrate/20231214214407_rename_singularity_to_apptainer_overlays_specs.rb
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prioux
requested changes
Mar 13, 2025
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This first thing to do is to rebase and make sure the database changes are applied on top of the schema that the current head of master implements.
After that, some minor renaming comments.
I would remove all the "Apptainer/Singularity" comments and just say "Apptainer".
| @@ -206,7 +206,7 @@ def update #:nodoc: | |||
| @tool_config.container_image_userfile_id = other_tc.container_image_userfile_id | |||
| @tool_config.container_exec_args = other_tc.container_exec_args.presence | |||
| @tool_config.container_index_location = other_tc.container_index_location | |||
| @tool_config.singularity_overlays_specs = other_tc.singularity_overlays_specs | |||
| @tool_config.apptainer_overlays_specs = other_tc.apptainer_overlays_specs | |||
| @@ -424,15 +424,15 @@ def make_available(userfile, file_path, userfile_sub_path = nil, start_dir = nil | |||
| userfile = Userfile.find(userfile) unless userfile.is_a?(Userfile) | |||
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| # Detect if we're trying to access a userfile content that is | |||
| # containerized in a singularity overlay. | |||
| # containerized in a apptainer overlay. | |||
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"an Apptainer" ; use uppercase when talking about the program itself.
| is_local = nil | ||
| if self.tool_config | ||
| .data_providers_with_overlays | ||
| .map(&:id) | ||
| .include? userfile.data_provider_id | ||
| userfile_path = Pathname.new(userfile.provider_full_path) # path inside container | ||
| is_local = true | ||
| self.addlog("Input file '#{userfile.name}' is on a local Singularity overlay") | ||
| self.addlog("Input file '#{userfile.name}' is on a local apptainer overlay") |
| @@ -618,10 +618,10 @@ def tool_config_system(command) | |||
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| # Build script | |||
| script = "" | |||
| # flag to guaranty propagation of env variables to the singularity/apptainer | |||
| # flag to guaranty propagation of env variables to the singularity/Apptainer | |||
| @@ -2406,26 +2406,26 @@ def singularity_commands(command_script) | |||
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| # These two variables control the mode switching at the end of the script. | |||
| mode="exec" | |||
| sing_basename=./#{singularity_wrapper_basename.bash_escape} # note: the ./ is necessary | |||
| sing_basename=./#{apptainer_wrapper_basename.bash_escape} # note: the ./ is necessary | |||
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Also rename the shell variable "sing_basename" ? Maybe 'apptainer_basename' ?
| @@ -22,22 +22,22 @@ | |||
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| # This class implements a Data Provider which fetches | |||
| # files out of a single filesystem file. The | |||
| # implementation requires Singularity 3.2 or better to | |||
| # be installed on the host, as well as a singularity | |||
| # implementation requires Apptainer 1.1 or Singularity 3.7 and better | |||
BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
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BrainPortal/db/schema.rb
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| @@ -10,7 +10,7 @@ | |||
| # | |||
| # It's strongly recommended that you check this file into your version control system. | |||
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| ActiveRecord::Schema.define(version: 20230418205141) do | |||
| ActiveRecord::Schema.define(version: 20240408164549) do | |||
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THis PR will ahev to be rebased and the version numbers edited to match the current version
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Please rebase and address the comments. |
MontrealSergiy
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resolves #1362