Search for OMERO Images with key-value pairs in Original Metadata

Search_Orig_Metadata.py

#!/usr/bin/python
# -*- coding: utf-8 -*-

# Sript to look for images with key-value pairs in Original Metadata
# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=1226

import omero
import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import *


def check_image(conn, img, params) :
    """
    Check image metadata for matches

    @param conn:   The BlitzGateway connection
    @param img:    The ImageWrapper object
    @param params: The script parameters
    """

    key = params["Key"]     # Key the user is looking for
    value = params["Value"] # Value (may end with * wildcard)

    om = img.loadOriginalMetadata()

    if om is not None:
      #global_metadata : om[1]
      #series_metadata : om[2]
      for keyValue in (om[1] + om[2]):

        if len(keyValue) > 1:
          if keyValue[0] == key:
            
            if value[-1] == "*":
                if keyValue[1].startswith(value):
                    return True
            else:
                if keyValue[1] == value:
                    return True


def search_images(conn, params):
    """
    Parse each image for metadata
    
    @param conn:   The BlitzGateway connection
    @param params: The script parameters
    """

    images = []
    
    all_imgs = conn.getObjects("Image")
    
    for img in all_imgs:
        print "Checking Image: %s ID: %s" % (img.getName(), img.getId())
        if check_image(conn, img, params):
            images.append(img)
    
    return images


def runAsScript():
    """
    The main entry point of the script, as called by the client via the 
    scripting service, passing the required parameters. 
    """
    
    client = scripts.client('Search_Orig_Metadata.py', """\
    Look for images that have key-value matches in their Original Metadata
    """, 
    
    scripts.String("Key", optional=False, grouping="1.1",
        description="The name of the Metadata value."),

    scripts.String("Value", optional=False, grouping="1.2",
        description="Value you're looking for. End with * for wild-card"),

    ) 
    
    conn = BlitzGateway(client_obj=client)
    
    # Process the list of args above. 
    params = {}
    for key in client.getInputKeys():
      if client.getInput(key):
        params[key] = client.getInput(key, unwrap=True)
    print params
    
    # Call the main script - returns the number of images and total bytes
    results = search_images(conn, params)
    
    msg = "Found %s images" % len(results)
    print msg
    client.setOutput("Message", rstring(msg))
    
    if len(results) > 0:
      client.setOutput("Image", robject(results[0]._obj))

if __name__ == "__main__":
    """
    Python entry point
    """
    runAsScript()