list_submissions.py

import omero.cli
import pandas as pd 
from omero.rtypes import rint

data = {
    "id": [],
  "name": [],
  "type": [],
  "imported_from_path": [],
  "download_location": [],
  "zarr": []
}
df = pd.DataFrame(data)


def get_import_from_path(conn, imageId):
    query = "select fse from Fileset f \
        join f.usedFiles as fse \
        join f.images as imgs \
        where :id in imgs"
    params = omero.sys.ParametersI()
    params.addId(imageId)
    res = conn.getQueryService().findAllByQuery(query, params)
    if res and len(res) > 0:
        return res[0].clientPath._val
    return None
    

def get_image_info(conn, image):
    path = get_import_from_path(conn, image.getId())
    if path:
        kind = "NA"
        if path.startswith("uod/idr/filesets") or \
            path.startswith("nfs/bioimage") or \
            path.startswith("idr/filesets") or \
            path.startswith("idr/tmp") or \
            path.startswith("idr/incoming"):
            kind = "IDR"
        elif path.startswith("uod/idr/metadata"):
            kind = "Github"
        elif path.startswith("bia"):
            kind = "Embassy_S3_2"
        elif path.startswith("https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data"):
            kind = "Embassy_S3"
        zarr = "No"
        if ".zarr" in path:
            zarr = "Yes"
        return (path, kind, zarr)
    return (None, None, None)


def get_container_info(container, is_screen):
    try:
        if is_screen:
            for plate in container.listChildren():
                for well in plate.listChildren():
                    for wellsample in well.listChildren():
                        path, kind, zarr = get_image_info(conn, wellsample.getImage())
                        return (container.getId(), container.getName(), "Screen", path, kind, zarr)
        else:
            for dataset in container.listChildren():
                for image in dataset.listChildren():
                    path, kind, zarr = get_image_info(conn, image)
                    return (container.getId(), container.getName(), "Project", path, kind, zarr)
    except Exception as e:  
        print(e)
        return None


with omero.cli.cli_login() as c:
    conn = omero.gateway.BlitzGateway(client_obj=c.get_client())
    for project in conn.listProjects():
        print("Checking: ", project.getName())
        info = get_container_info(project, False)
        if info:
            df.loc[len(df)] = info
    
    for screen in conn.listScreens():
        print("Checking: ", screen.getName())
        info = get_container_info(screen, True)
        if info:
            df.loc[len(df)] = info
df.sort_values(by=['name'], inplace=True)
df.to_csv('list_submissions.csv', index=False)
print(df)