Updating all symlinks in a project (error in documentation?)

Data Management
1

Hi,

we are currently in the process of moving our cryosparc data from 3 different space to one single storage space. For that I’d lilke to move individual Projects slowly to the new storage. While this works great for the the project file (archive / move / unarchive). I have trouble finding the correct script for changing all symlinks in a particular project.
I thought the easiest way would be to run through all jobs of a project but I don’t find any way to list all jobs from particular project (like get_jobs_by_project().

My second attempt was to alter the existing script, which iterates over all jobs and only skip those not in my Project:

failed_jobs = 


for job in jobs:
# skip jobs not in our target projects
if job.get(“project_uid”) not in P:
continue

try:
    print("Repairing %s %s" % (job["project_uid"], job["uid"]))
    modified_count = cli.job_import_replace_symlinks(
        job["project_uid"],
        job["uid"],
        old,
        new,
    )
...

To my surpise this failed with “NameError: name ‘jobs’ is not defined” - although this script is nearly literally from the documentation:

What do I miss? Do I have to populate the “job” variable - I assumed it would be present in an cryosparc-cli…

Best,
Jan

2

You have to first define a list of jobs, e.g., sing get_job or get_project_jobs_by_status functions (cryosparcm cli reference (≤v4.7) | CryoSPARC Guide)

3

Hi,

Thank you for the answer.

However, the script form the documentation should change all jobs in all projects… with get_job you only get a specific job and not a list if all jobs (from a specific project) as far as I understand….

Best

Jan

4

I think I managed. It feels a little bit clunky, as I couldn’t find the correct methods, and the job object seem not to be descibred somewhere (?); but it works:

### Settings 
ProjectID = "P14"
old= "/mnt/Data/CryoEM_Data"
new=  "/mnt/CryoEM-Data"

failed_jobs = []


CRYOSPARC_DONE = [
    "completed", "failed", "killed", "aborted"
]

jobs = cli.get_project_jobs_by_status(ProjectID,None,CRYOSPARC_DONE)


for job in jobs:
    
    try:
        print("Repairing %s %s" % (ProjectID, job["uid"]))
        modified_count = cli.job_import_replace_symlinks(
            ProjectID,
            job["uid"],
            old,
            new,
        )
        print("Finished. Modified %d links." % (modified_count))
    except Exception as e:
        failed_jobs.append((ProjectID, job.get("uid")))
        print("Failed to repair %s %s: %s" % (job.get("project_uid"), job.get("uid"), str(e)))

symlinks = cli.get_project_symlinks (ProjectID)

broken_links = 0
total_links = 0 
for link in symlinks:
    total_links = total_links+1
    if link["exists"] != True:
        broken_links = broken_links+1

print (broken_links, "broken symlinks out off ",total_links," total links.")    

failed_jobs

Best

Jan

5

Thankfully API in CS 5 is much more complete and better documented: api — CryoSPARC Tools