Merge pull request #1 from moisbo/master

Run scripts with environment variables

Author: evenhuis

omero/annotation_scripts/.gitignore

@@ -33,3 +33,10 @@ nosetests.xml
 .mr.developer.cfg
 .project
 .pydevproject
+
+
+downloads/OMERO.py-5.4.1-ice36-b75.zip
+downloads/OMERO.py-5.4.1-ice36-b75
+cli_scripts/downloads
+.idea
+.DS_Store

omero/annotation_scripts/README.md

@@ -19,46 +19,106 @@ The scripts were developed using the following resources:
 # Installing OMERO CLI for 5.4.1
 
 ## 1. Create a virtual env for python 2.7:
-	conda create -n OMERO_CLI python=2.7 anaconda
+
+```
+conda create -n OMERO_CLI python=2.7 anaconda
+```
+
 ## 2. Download the package from: 
 Get the "OMERO python" package download 
 
 * [https://www.openmicroscopy.org/omero/downloads/](https://www.openmicroscopy.org/omero/downloads/)
 
 or directly from this [link](http://downloads.openmicroscopy.org/omero/5.4.1/artifacts/OMERO.py-5.4.1-ice36-b75.zip).	
 ## 3. Install the ICE library
-	pip install zeroc-ice==3.6.4
+
+```
+pip install zeroc-ice==3.6.4
+```
 
 ## 4. Add conda paths
+
 Add the path to the library. Instructions from [conda webpage](https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables)
 
-	cd /Users/evenhuis/anaconda3/envs/OMERO_5.4_CLI
-	mkdir -p ./etc/conda/activate.d
-	mkdir -p ./etc/conda/deactivate.d
-	touch ./etc/conda/activate.d/env_vars.sh
-	touch ./etc/conda/deactivate.d/env_vars.sh
-	
+```
+cd /Users/evenhuis/anaconda3/envs/OMERO_5.4_CLI
+mkdir -p ./etc/conda/activate.d
+mkdir -p ./etc/conda/deactivate.d
+touch ./etc/conda/activate.d/env_vars.sh
+touch ./etc/conda/deactivate.d/env_vars.sh
+```
+
 Add the following to the activate.d/env_vars.sh:
 
+
 ```	
 #!/bin/sh
+
+export OMERO_PREFIX=~/Dropbox/MIF/OMERO/downloads_5.4.1/OMERO.py-5.4.1-ice36-b75
+
 export ORIGPATH=$PATH
 export ORIGPYTHONPATH=$PYTHONPATH
-export OMERO_PREFIX=~/Dropbox/MIF/OMERO/downloads_5.4.1/OMERO.py-5.4.1-ice36-b75
 export PATH=$PATH:$OMERO_PREFIX/lib/python:$OMERO_PREFIX/bin
 export PYTHONPATH=$PYTHONPATH:$OMERO_PREFIX/lib/python:$OMERO_PREFIX/bin
 ```
+
 This appends the OMERO library to the search path.  And the following in deactivate.d/env_vars.sh restores the path variabeles
 
-	export PATH=$ORIGPATH
-	export PYTHONPATH=$ORIGPYTHONPATH
+```
+export PATH=$ORIGPATH
+export PYTHONPATH=$ORIGPYTHONPATH
 
-	unset ORIGPATH
-	unset ORIGPYTHONPATH
-	
+unset ORIGPATH
+unset ORIGPYTHONPATH
+```
 
+5. Examples:
 
+## Run downloads
 
+1. Example
+```bash
+OMERO_USERNAME='USERNAME' OMERO_USER_PASSWORD='PASSWORD' OMERO_APP_URL='omero-app.server.edu' python download_files.py -h
+```
+Result:
+```bash
+usage: download_files.py [-h] [-p PROJECT [PROJECT ...]]
+                         [-d DATASET [DATASET ...]] [-g [GROUP]] [-o] [-t]
+
+Download datasets and projects from OMERO
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -p PROJECT [PROJECT ...], --project PROJECT [PROJECT ...]
+                        IDs of projects to download
+  -d DATASET [DATASET ...], --dataset DATASET [DATASET ...]
+                        IDs of datasets to download
+  -g [GROUP], --group [GROUP]
+                        name of group
+  -o, --orig            download originals
+  -t, --tif             download OME-TIFs
+
+```
+
+2. Example
+```bash
+OMERO_USERNAME='USERNAME' OMERO_USER_PASSWORD='PASSWORD' OMERO_APP_URL='omero-app.server.edu' python download_files.py -d 2071 -p 759 -o
+```
+```bash
+
+omero-app.research.uts.edu.au
+Current user:
+   ID: 2
+   Username: 135553
+   Full Name: Moises Sacal Bonequi
+['2071']
+moises-dataset/
+              /gravatar.jpeg
+['759']
+moises-dataset/
+              /gravatar.jpeg
+
+```
 
 Legal
 -----

omero/annotation_scripts/cli_scripts/Parse_OMERO_Properties.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python2
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Nov 20 14:16:53 2017
+
+@author: evenhuis
+
+FOR TRAINING PURPOSES ONLY!
+
+Change this file to Parse_OMERO_Properties.py and enter your ID/username 
+"""
+
+import omero
+import os
+import sys
+
+try:
+    omero_app_url = os.environ["OMERO_APP_URL"]
+    omero_username = os.environ["OMERO_USERNAME"]
+    omero_user_password = os.environ["OMERO_USER_PASSWORD"]
+except KeyError:
+    print "Please set the environment variable OMERO_USERNAME, OMERO_USER_PASSWORD and OMERO_APP_URL"
+    sys.exit(1)
+
+client = omero.client(omero_app_url)
+
+omeroProperties = client.getProperties().getPropertiesForPrefix('omero')
+
+# Configuration
+# =================================================================
+# These values will be imported by all the other training scripts.
+HOST = omeroProperties.get('omero.host', omero_app_url)
+PORT = omeroProperties.get('omero.port', 4064)
+USERNAME = omeroProperties.get('omero.user', omero_username)
+PASSWORD = omeroProperties.get('omero.pass', omero_user_password)
+OMERO_WEB_HOST = omeroProperties.get('omero.webhost')
+SERVER_NAME = omeroProperties.get(omero_app_url)
+# projectId = omeroProperties.get('omero.projectid')
+# datasetId = omeroProperties.get('omero.datasetid')
+# imageId = omeroProperties.get('omero.imageid')

omero/annotation_scripts/cli_scripts/download_files.py

@@ -5,123 +5,131 @@
 
 @author: evenhuis
 """
-#from Parse_OMERO_Properties import datasetId, imageId, plateId
+# from Parse_OMERO_Properties import datasetId, imageId, plateId
 
 import sys
 import argparse
 import os
 
+
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-def download_dataset( conn, Id, path, orig=False, tif=False ):
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-    ''' download a dataset from OMERO
-    INPUT : conn   : the connection needs to be open
-        Id     : ID of the dataset
-        path   : location of local filesystem
-        fmt    : "o" is orginal , "t" is tiff
-    '''
-   
+def download_dataset(conn, Id, path, orig=False, tif=False):
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+    """
+    download a dataset from OMERO
+        INPUT : conn, the connection needs to be open
+        Id    : ID of the dataset
+        path  : location of local filesystem
+        fmt   : "o" is original , "t" is tiff
+    """
+
     # get the data set
-    dataset = conn.getObject('Dataset',Id)
-    if( dataset==None ):
+    dataset = conn.getObject('Dataset', Id)
+    if (dataset == None):
         print("Dataset ID {} not found in group".format(Id))
         sys.exit(1)
     print("here")
 
     # get the images
-    imgs    = list(dataset.listChildren())
-   
+    imgs = list(dataset.listChildren())
+
     # this is the directory to place the data in
     ds_name = dataset.getName()
-    print("{}/".format(ds_name) )
-    reldir  = os.path.join( path, ds_name)
-    if( not os.path.isdir(reldir) ):
+    print("{}/".format(ds_name))
+    reldir = os.path.join(path, ds_name)
+    if (not os.path.isdir(reldir)):
         os.makedirs(reldir)
-    
+
     for img in imgs:
-        print(" "*len(ds_name)+"/{}".format(img.getName()))
-    
-        if( orig ):
+        print(" " * len(ds_name) + "/{}".format(img.getName()))
+
+        if (orig):
             for orig in img.getImportedImageFiles():
                 name = orig.getName()
-                file_path = os.path.join( reldir, name)
+                file_path = os.path.join(reldir, name)
 
-                if( not os.path.exists( file_path)  ):
+                if (not os.path.exists(file_path)):
                     with open(str(file_path), 'w') as f:
                         for chunk in orig.getFileInChunks():
                             f.write(chunk)
 
-        if( tif ):
-            name = os.path.basename(img.getName())+".ome.tif"
+        if (tif):
+            name = os.path.basename(img.getName()) + ".ome.tif"
             file_path = os.path.join(reldir, name)
             file_size, block_gen = img.exportOmeTiff(bufsize=65536)
             with open(str(file_path), "wb") as f:
                 for piece in block_gen:
                     f.write(piece)
-         
-    return 
+
+    return
+
 
 """
 start-code
 """
 
-
 parser = argparse.ArgumentParser(description='Download datasets and projects from OMERO')
-parser.add_argument('-p','--project', nargs="+", default=[],help="IDs of projects to download")
-parser.add_argument('-d','--dataset', nargs="+", default=[],help="IDs of datasets to download")
-parser.add_argument('-g','--group'  , nargs="?", help="name of group")
-parser.add_argument('-o','--orig'   , action="store_true", default=False, help="download originals")
-parser.add_argument('-t','--tif'    , action="store_true", default=False, help="download OME-TIFs" )
+parser.add_argument('-p', '--project', nargs="+", default=[], help="IDs of projects to download")
+parser.add_argument('-d', '--dataset', nargs="+", default=[], help="IDs of datasets to download")
+parser.add_argument('-g', '--group', nargs="?", help="name of group")
+parser.add_argument('-o', '--orig', action="store_true", default=False, help="download originals")
+parser.add_argument('-t', '--tif', action="store_true", default=False, help="download OME-TIFs")
 
 args = parser.parse_args()
 
 # Create a connection
 # ===================
+
+
+from omero.gateway import BlitzGateway
+from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
+
+print(HOST)
+
+conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
+
 try:
-    from omero.gateway import BlitzGateway
-    from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
-    print(HOST)
-    conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
     conn.connect()
-    
+
     user = conn.getUser()
     print "Current user:"
     print "   ID:", user.getId()
     print "   Username:", user.getName()
     print "   Full Name:", user.getFullName()
 
-    if( args.group is not None ):
+    if args.group is not None:
         print("change group")
         new_group = args.group
-        groups = [ g.getName() for g in conn.listGroups() ]
+        groups = [g.getName() for g in conn.listGroups()]
         print(groups)
-        if( new_group not in groups ):
+        if new_group not in groups:
             print("{} not found in groups:".format(new_group))
             for gn in groups:
                 print("    {}".format(gn))
             sys.exit(1)
         else:
             conn.setGroupNameForSession(new_group)
-   
-    path    = os.getcwd()
-    print( args.dataset )
+
+    path = os.path.join(os.getcwd(), 'downloads')
+    print(args.dataset)
     for d_id in args.dataset:
-        download_dataset( conn, d_id, path, orig=args.orig, tif=args.tif )
+        download_dataset(conn, d_id, path, orig=args.orig, tif=args.tif)
 
     print(args.project)
     for p_id in args.project:
-        project = conn.getObject('Project',p_id)
-        path_p = os.path.join(path,project.getName())
-        if( project==None ):
+        project = conn.getObject('Project', p_id)
+        path_p = os.path.join(path, project.getName())
+        if project is None:
             print("project ID {} not found in group {}".format(p_id, orig=args.orig, tif=args.tif))
             sys.exit(1)
 
         for ds in list(project.listChildren()):
-            download_dataset( conn, ds.getId(), path_p, orig=args.orig, tif=args.tif )
+            download_dataset(conn, ds.getId(), path_p, orig=args.orig, tif=args.tif)
+
+except Exception:
+    print "There was a problem trying to connect"
+    sys.exit(1)
 
-        
-finally:    
+finally:
     # When you are done, close the session to free up server resources.
     conn.close()
-
-