refactoring: replacing singularity with apptainer in variable names

BrainPortal/app/controllers/bourreaux_controller.rb

@@ -623,7 +623,7 @@ def bourreau_params #:nodoc:
  :cms_default_queue, :cms_extra_qsub_args, :cms_shared_dir, :workers_instances,
  :workers_chk_time, :workers_log_to, :workers_verbose, :help_url, :rr_timeout, :proxied_host,
  :spaced_dp_ignore_patterns, :support_email, :system_from_email, :external_status_page_url,
- :docker_executable_name, :docker_present, :singularity_executable_name, :singularity_present,
+ :docker_executable_name, :docker_present, :apptainer_executable_name, :apptainer_present,
  :small_logo, :large_logo, :license_agreements
  )
  end

BrainPortal/app/controllers/tool_configs_controller.rb

@@ -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
  @tool_config.extra_qsub_args = other_tc.extra_qsub_args
  @tool_config.cloud_disk_image = other_tc.cloud_disk_image
  @tool_config.cloud_vm_user = other_tc.cloud_vm_user
@@ -243,7 +243,7 @@ def update #:nodoc:
  container_image_userfile_id containerhub_image_name
  container_engine container_index_location container_exec_args
  inputs_readonly
- singularity_overlays_specs singularity_use_short_workdir
+ apptainer_overlays_specs apptainer_use_short_workdir
  boutiques_descriptor_path
  )
  )
@@ -304,8 +304,8 @@ def tool_config_params #:nodoc:
  :version_name, :description, :tool_id, :bourreau_id, :env_array, :script_prologue, :script_epilogue,
  :group_id, :ncpus, :container_image_userfile_id, :containerhub_image_name, :container_index_location,
  :inputs_readonly,
- :container_engine, :extra_qsub_args, :singularity_overlays_specs, :container_exec_args,
- :singularity_use_short_workdir,
+ :container_engine, :extra_qsub_args, :apptainer_overlays_specs, :container_exec_args,
+ :apptainer_use_short_workdir,
  :boutiques_descriptor_path,
  # The configuration of a tool in a VM managed by a
  # ScirCloud Bourreau is defined by the following

BrainPortal/app/models/bourreau.rb

@@ -80,11 +80,11 @@ def docker_present? #:nodoc:
  alias docker_present docker_present? #:nodoc:
 
 
- def singularity_present? #:nodoc:
- singularity_executable_name.present?
+ def apptainer_present? #:nodoc:
+ apptainer_executable_name.present?
  end
 
- alias singularity_present singularity_present? #:nodoc:
+ alias apptainer_present apptainer_present? #:nodoc:
 
 
 

BrainPortal/app/models/sing_bindmount_data_provider.rb

@@ -22,22 +22,22 @@
 
 # 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
+# be installed on the host, as well as an Apptainer
 # container image that contains the basic Linux
 # commands and the 'rsync' command too.
 #
 # For the moment the DP is read-only. Allowing
 # write access would require a mechanism in CBRAIN
-# to prevent more than one singularity process to
+# to prevent more than one Apptainer process to
 # be accessing the mounted file at any one time.
 #
 # Bind mounts are performed using a command such as:
 #
-# singularity shell -B filesystem.img:/my/mount/point:image-src=/inside/dir,ro sing_squashfs.simg
+# apptainer shell -B filesystem.img:/my/mount/point:image-src=/inside/dir,ro sing_squashfs.simg
 #
 # where:
-# 1- sing_squashfs.simg is a singularity image file,
+# 1- sing_squashfs.simg is an Apptainer image file,
 # 2- filesystem.img is either a ext3 or squashfs filesystem,
 # 3- /inside/dir is a path inside that filesystem,
 # 4- /my/mount/point is a path where the data will be mounted under
@@ -51,7 +51,7 @@
 #
 # The attribute 'remote_dir' must be a full path to the location of
 # the filesystem image 'filesystem.img' (even though it is not a 'dir').
-# The singularity image file will be expected to be called 'sing_squashfs.simg'
+# The apptainer image file will be expected to be called 'sing_squashfs.simg'
 # and be located in the same subdirectory as 'filesystem.img'.
 class SingBindmountDataProvider < SshDataProvider
 
@@ -64,14 +64,14 @@ class SingBindmountDataProvider < SshDataProvider
  # TODO: Change this is the DP is ever made writable!
  BROWSE_CACHE_EXPIRATION = 2.months #:nodoc:
 
- # This is the basename of the singularity image
+ # This is the basename of the Apptainer image
  # we use to access the remote filesystem; we
  # expect this image to be installed in the same
  # directory that contains it. Its minimum
  # requirements are that 1) basic UNIX commands
  # exist on it 2) the rsync command is installed
  # in it too.
- SINGULARITY_IMAGE_BASENAME = 'sing_squashfs.simg'
+ APPTAINER_IMAGE_BASENAME = 'sing_squashfs.simg'
 
  # We use this to point to the directory INSIDE the container
  # were the root of the data is stored.
@@ -91,7 +91,7 @@ def read_only=(val) #:nodoc:
 
  # This returns the category of the data provider
  def self.pretty_category_name #:nodoc:
- "Singularity Bind Mount"
+ "Apptainer Bind Mount"
  end
 
  # This uses the new CBRAIN capability of registering
@@ -109,20 +109,20 @@ def impl_is_alive? #:nodoc:
  # Raise an exception with a message indicating what is wrong with the config.
  # This method is not part of the official method API
  def check_remote_config! #:nodoc:
- # Check we have one singularity image file
- remote_cmd = "cd #{self.real_remote_dir.to_s.bash_escape} && test -f #{SINGULARITY_IMAGE_BASENAME} && echo OK-Exists"
+ # Check we have one apptainer image file
+ remote_cmd = "cd #{self.real_remote_dir.to_s.bash_escape} && test -f #{APPTAINER_IMAGE_BASENAME} && echo OK-Exists"
  text = self.remote_bash_this(remote_cmd)
  # The following check will also make sure the remote shell is clean!
- cb_error "No installed singularity image #{SINGULARITY_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
+ cb_error "No installed apptainer image #{APPTAINER_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
 
  # Check we have the remote filesystem file
  remote_cmd = "test -f #{self.remote_dir.to_s.bash_escape} && echo OK-Exists"
  cb_error "Filesystem file '#{self.remote_dir}' not found" unless text =~ /\AOK-Exists\s*\z/
 
- # Check we have singularity version 3.7 or better
+ # Check we have apptainer 1.1 or better or singularity version 3.7 or better
  remote_cmd = "(singularity --version 2>/dev/null || apptainer --version 2>/dev/null)"
  text = self.remote_bash_this(remote_cmd)
- cb_error "Can't find singularity version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
+ cb_error "Can't find apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
  _, _, tool, major, minor = Regexp.last_match.to_a
  major = major.to_i
  minor = minor.to_i
@@ -134,7 +134,7 @@ def check_remote_config! #:nodoc:
 
  # Check that inside the container, the containerized path exists
  checkdir = "test -d #{self.containerized_path.bash_escape} && echo OK-Exists"
- text = remote_in_sing_bash_this(checkdir)
+ text = remote_in_apptainer_bash_this(checkdir)
  cb_error "No path '#{self.containerized_path}' inside container" unless text =~ /\AOK-Exists\s*\z/
 
  # Well, we passed all the tests
@@ -179,7 +179,7 @@ def impl_provider_list_all(user=nil, browse_path=nil) #:nodoc:
 
  file_infos = Rails.cache.fetch(cache_key, :expires_in => BROWSE_CACHE_EXPIRATION) do
  dir = Pathname.new(self.containerized_path) + browse_path.to_s
- text = remote_in_sing_stat_all(dir,".",true)
+ text = remote_in_apptainer_stat_all(dir,".",true)
  stat_reports_to_fileinfos(text)
  end
 
@@ -211,7 +211,7 @@ def impl_provider_collection_index(userfile, directory = :all, allowed_types = :
  type_opt = allowed_types == [ :regular ] ? "f" :
  allowed_types == [ :directory ] ? "d" :
  nil # we can still filter for other combinations on Ruby side
- text = remote_in_sing_stat_all(basedir, subdir, one_level, type_opt)
+ text = remote_in_apptainer_stat_all(basedir, subdir, one_level, type_opt)
  file_infos = stat_reports_to_fileinfos(text)
 
  # Apply more complex filters if necessary
@@ -268,7 +268,7 @@ def impl_provider_rename(userfile,newname) #:nodoc:
  # Returns true if we have to use 'ssh' to
  # connect to the remote server. Returns false
  # when we can optimize requests by running
- # singularity locally. The local situation is
+ # apptainer locally. The local situation is
  # detected pretty much like in the Smart DP
  # module: if the hostname is the same as *remote_host*
  # or *alternate_host*, and if the *remote_dir* exists
@@ -294,16 +294,16 @@ def provider_is_remote #:nodoc:
  @provider_is_remote
  end
 
- def singularity_exec_prefix #:nodoc:
- "cd #{self.real_remote_dir.to_s.bash_escape} && singularity -s exec #{self.local_bind_opt} #{SINGULARITY_IMAGE_BASENAME}"
+ def apptainer_exec_prefix #:nodoc:
+ "cd #{self.real_remote_dir.to_s.bash_escape} && singularity -s exec #{self.local_bind_opt} #{APPTAINER_IMAGE_BASENAME}"
  end
 
  def local_bind_opt #:nodoc:
  "-B #{self.filesystem_image_basename.bash_escape}:/cbrain:image-src=/,ro"
  end
 
  def remote_rsync_command #:nodoc:
- "#{singularity_exec_prefix} rsync"
+ "#{apptainer_exec_prefix} rsync"
  end
 
  def real_remote_dir #:nodoc:
@@ -333,12 +333,12 @@ def rsync_over_ssh_prefix
  rsync
  end
 
- def remote_in_sing_bash_this(com) #:nodoc:
- newcom = "#{singularity_exec_prefix} bash -c #{com.bash_escape}"
+ def remote_in_apptainer_bash_this(com) #:nodoc:
+ newcom = "#{apptainer_exec_prefix} bash -c #{com.bash_escape}"
  remote_bash_this(newcom)
  end
 
- def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
+ def remote_in_apptainer_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
  max_depth = one_level ? "-maxdepth 1" : ""
  type_opt = find_type ? "-type #{find_type}" : ""
  # Linux 'stat' command formats:
@@ -354,7 +354,7 @@ def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil)
  # Linux 'find' command format:
  find_format = "E=%y,%m,%s,%U,%u,%G,%g,%A@,%T@,%C@,%p\\n"
  com = "cd #{basedir.to_s.bash_escape} && find #{subdir.to_s.bash_escape} #{max_depth} #{type_opt} -printf \"#{find_format}\""
- remote_in_sing_bash_this(com)
+ remote_in_apptainer_bash_this(com)
  end
 
  # Given a text file report such as this: