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BioStudies CLI

BioStudies CLI is a tool that allows interacting with the BioStudies web application in order to perform operations over submissions.

Build

In order to build the CLI, execute the command gradle :client:bio-commandline:shadowJar. This will generate the command line jar under build/libs folder.

Usage

Submit

Make a submission to BioStudies

java -jar build/libs/BioStudiesCLI-2.0.jar submit -s <server> -u <user> -p <password> -i <page tab input> -a <files>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: User that will perform the submission.
  • p or --password: The user password.
  • b or --onBehalf: Allows to perform a submission on behalf of the user with the given e-mail.
  • i or --input: Path to the file containing the submission page tab.
  • a or --attach: Comma separated list of paths to the files referenced in the submission.
  • ps or --preferredSource: Comma separated list of file sources. Valid values are FIRE, SUBMISSION and USER_SPACE. The order of the list indicates the priority in which the sources will be used
  • sm or --storageMode: Submission storage mode. Determines where submission need to be saved FIRE/NFS
  • aw or --await: Indicates whether to wait for the submission processing
  • sj or --splitJobs: Indicates whether the submission should be processed in individual jobs per each stage

Notes:

  • The parameter to attach files is optional. If no files are attached, the files referenced in the submission page tab will be retrieved from the user folder.
  • If one of the paths provided to the attached argument is a directory, all files inside it will be used as attachments.
  • The submission format doesn't need to be specified since it'll be inferred from the input file's extension.
  • TSV submissions can be submitted using a XLSX file.

Submission Request Status

Get the status of a submission request

java -jar build/libs/BioStudiesCLI-2.0.jar requestStatus \
-s <server> \
-u <user> \
-p <password> \
-ac <accNo> \
-v <version>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: BioStudies user with privileges to get the submission request.
  • p or --password: The user password.
  • ac or --accNo: Accession number of the submission request to check the status.
  • v or --version: Version of the submission request to check the status.

Delete

Delete a submission

java -jar build/libs/BioStudiesCLI-2.0.jar delete -s <server> -u <user> -p <password> -ac <accNo>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: BioStudies user with privileges to delete the submission.
  • p or --password: The user password.
  • ac or --accNo: Accession number of the submission to delete.
  • b or --onBehalf: Allows to delete a submission on behalf of the user with the given e-mail.

Migrate

Migrate a submission from one environment to another

java -jar build/libs/BioStudiesCLI-2.0.jar migrate \
-ac <accNo> \
-s <source> \
-su <source user> \
-sp <source password> \
-t <target> \
-tu <target user> \
-tp <target password> \
-as <true / false>

Arguments

  • ac or --accNo: Accession number of the submission to migrate.
  • s or --server: BioStudies environment to take the submission from.
  • su or --sourceUser: BioStudies user in the source environment. (Only superusers can perform this operation)
  • sp or --sourcePassword: Password for the BioStudies user in the source environment.
  • t or --target: BioStudies environment to migrate the submission to.
  • tu or --targetUser: BioStudies user in the target environment. (Only superusers can perform this operation)
  • tp or --targetPassword: Password for the BioStudies user in the target environment.
  • to or --targetOwner: New owner for the submission in the target environment. This is an optional parameter. If it isn't provided, the current submission owner should exist in the target environment.
  • as or --async: Indicates whether the migration should be processed in async mode.

Transfer

Transfers a submission to the given target storage mode

java -jar build/libs/BioStudiesCLI-2.0.jar transfer -s <server> -u <user> -p <password> -ac <accNo> -t <target>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: BioStudies user with privileges to delete the submission.
  • p or --password: The user password.
  • ac or --accNo: Accession number of the submission to be transferred.
  • t or --target: Determines where submission need to be transferred to. Valid values are: FIRE/NFS

Validate File List

Validates the given file list contains valid pagetab and the referenced files exist either in the user folder or in the submission files of the given accession.

java -jar build/libs/BioStudiesCLI-2.0.jar validateFileList \
-s <server> \
-u <user> \
-p <password> \
-b <onBehalf> \
-f <fileListPath> \
-ac <accNo> \
-rp <rootPath>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: BioStudies user with privileges to delete the submission.
  • p or --password: The user password.
  • b or --onBehalf: Allows to delete a submission on behalf of the user with the given e-mail.
  • f or --fileListPath: Path to the file list to be validated. The path is relative to the user folder.
  • ac or --accNo: The accNo for the submission which files will be included in the search.
  • rp or --rootPath: Base path to search for the files in the user folder.

Grant Permission

Grants the specified permissions for the given user in the given collection.

java -jar BioStudiesCLI-2.0.jar grantPermission \
-s <server> \
-u <user> \
-p <password> \
-at <access type> \
-tu <target user> \
-ac <collection accNo>

Arguments

  • s or --server: BioStudies instance URL.
  • u or --user: BioStudies user with privileges to delete the submission.
  • p or --password: The user password.
  • at or --accessType: Access type to be granted to the user. Valid values are: ADMIN, ATTACH, UPDATE, READ, DELETE
  • tu or --targetUser: User to whom the access permission will be provided.
  • ac or --accNo: The accession to grant the permission to. The accession must exist.