cryosparc2.utils module

cryosparc2.utils.addComputeSectionParams(form, allowMultipleGPUs=True)[source]

Add the compute settings section

cryosparc2.utils.addSymmetryParam(form)[source]

Add the symmetry param with the conventions :param form: :return:

cryosparc2.utils.calculateNewSamplingRate(newDims, previousSR, previousDims)[source]
Parameters:
  • newDims
  • previousSR
  • previousDims
Returns:

cryosparc2.utils.clearJob(projectName, job)[source]
Clear a Job (if queued) to get it back to builing state (do not clear params or inputs)
Parameters:
  • projectName – the uid of the project that contains the job to clear
  • job – the uid of the job to clear

** IMPORTANT: This method can be launch only if the job is queued

cryosparc2.utils.createEmptyProject(projectDir, projectTitle)[source]
create_empty_project(owner_user_id, project_container_dir, title=None,
desc=None)
cryosparc2.utils.createEmptyWorkSpace(projectName, workspaceTitle, workspaceComment)[source]
create_empty_workspace(project_uid, created_by_user_id,
created_by_job_uid=None, title=None, desc=None)

returns the new uid of the workspace that was created

cryosparc2.utils.createProjectDir(project_container_dir)[source]
Given a “root” directory, create a project (PXXX) dir if it doesn’t already
exist
Parameters:project_container_dir – the “root” directory in which to create the project (PXXX) directory
Returns:str - the final path of the new project dir with shell variables still in the returned path (the path should be expanded every time it is used)
cryosparc2.utils.cryosparcExists()[source]

Determine if scipion can find cryosparc :returns True if found, False otherwise

cryosparc2.utils.cryosparcValidate()[source]

Validates some cryo properties that must be satisfy

cryosparc2.utils.doImportParticlesStar(protocol)[source]
do_import_particles_star(puid, wuid, uuid, abs_star_path,
abs_blob_path=None, psize_A=None)

returns the new uid of the job that was created

cryosparc2.utils.doImportVolumes(protocol, refVolume, volType, msg)[source]
Returns:
cryosparc2.utils.doJob(jobType, projectName, workSpaceName, params, input_group_conect)[source]
do_job(job_type, puid=’P1’, wuid=’W1’, uuid=’devuser’, params={},
input_group_connects={})
cryosparc2.utils.enqueueJob(jobType, projectName, workSpaceName, params, input_group_conect, lane, gpusToUse=False, group_connect=None)[source]
make_job(job_type, project_uid, workspace_uid, user_id,
created_by_job_uid=None, params={}, input_group_connects={})
cryosparc2.utils.getCryosparcDir()[source]

Get the root directory where cryoSPARC code and dependencies are installed.

cryosparc2.utils.getCryosparcEnvInformation(envVar='version')[source]

Get the cryosparc installed version

cryosparc2.utils.getCryosparcProgram(mode='cli')[source]

Get the cryosparc program to launch any command

cryosparc2.utils.getCryosparcProjectsDir()[source]

Get the path on the worker node to a writable directory

cryosparc2.utils.getCryosparcUser()[source]

Get the full name of the initial admin account

cryosparc2.utils.getJobLog(projectDirName, projectName, job)[source]

Return the job log

cryosparc2.utils.getJobStatus(projectName, job)[source]

Return the job status

cryosparc2.utils.getProjectName(scipionProjectName)[source]

returns the name of the cryosparc project based on scipion project name and a hash based on the user name

cryosparc2.utils.getProjectPath(projectDir)[source]

Gets all projects of given path . projectDir: Folder path to get subfolders. returns: Set with all subfolders.

cryosparc2.utils.getSymmetry(symmetryGroup, symmetryOrder)[source]

Get the symmetry(string) taking into account the symmetry convention

cryosparc2.utils.getSystemInfo()[source]

Returns system-related information related to the cryosparc app :returns: dict – dictionary listing information about cryosparc environment {

‘master_hostname’ : master_hostname, ‘port_webapp’ : os.environ[‘CRYOSPARC_HTTP_PORT’], ‘port_mongo’ : os.environ[‘CRYOSPARC_MONGO_PORT’], ‘port_command_core’ : os.environ[‘CRYOSPARC_COMMAND_CORE_PORT’], ‘port_command_vis’ : os.environ[‘CRYOSPARC_COMMAND_VIS_PORT’], ‘port_command_proxy’ : os.environ[‘CRYOSPARC_COMMAND_PROXY_PORT’], ‘port_command_rtp’ : os.environ[‘CRYOSPARC_COMMAND_RTP_PORT’], ‘port_rtp_webapp’ : os.environ[‘CRYOSPARC_HTTP_RTP_PORT’], ‘version’ : get_running_version(),

}

cryosparc2.utils.get_job_streamlog(projectName, job, fileName)[source]
cryosparc2.utils.gpusValidate(gpuList, checkSingleGPU=False)[source]

Validate a gpu list

cryosparc2.utils.isCryosparcRunning()[source]

Determine if cryosparc services are running :returns True if running, false otherwise

cryosparc2.utils.killJob(projectName, job)[source]
Kill a Job (if running)
Parameters:
  • projectName – the uid of the project that contains the job to kill
  • job – the uid of the job to kill
cryosparc2.utils.runCmd(cmd, printCmd=True)[source]

Runs a command and check its exit code. If different than 0 it raises an exception :parameter cmd command to run

cryosparc2.utils.waitForCryosparc(projectName, jobId, failureMessage)[source]

Waits for cryosparc to finish or fail a job :parameter projectName: Cryosparc project name :parameter jobId: cryosparc job id :parameter failureMessage: Message for the exception thrown in case job fails :returns job Status :raises Exception when parsing cryosparc’s output looks wrong

cryosparc2.utils.waitJob(projectName, job)[source]

Wait while the job not finished