From c5d8bf9e42de54d590b0c3bcdb5f822a1fecb4a2 Mon Sep 17 00:00:00 2001
From: Diane Adjavon <diane.adjavon@ed.ac.uk>
Date: Fri, 7 Feb 2020 15:54:49 +0000
Subject: [PATCH] Begin testing suite
---
README.md | 25 +++++++++++++--
config.json | 1 +
core/__init__.py | 1 +
core/{omero.py => connect.py} | 42 ++++++++++---------------
install.sh | 6 ++++
omero_py/__init__.py | 5 +++
test/__init__.py | 0
test/connect_to_omero.py | 54 ++++++++++++++++----------------
test/test_connections.py | 59 +++++++++++++++++++++++++++++++++++
9 files changed, 138 insertions(+), 55 deletions(-)
create mode 100644 config.json
rename core/{omero.py => connect.py} (64%)
create mode 100644 install.sh
create mode 100644 omero_py/__init__.py
create mode 100644 test/__init__.py
create mode 100644 test/test_connections.py
diff --git a/README.md b/README.md
index 0f6d0e0d..73ab9ee6 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,26 @@
The core classes and methods for the python microfluidics, microscopy, and analysis pypline pipeline.
-References:
-* OMERO python bindings : https://docs.openmicroscopy.org/omero/5.4.0/developers/Python.html
-* Ice3.5 : https://zeroc.com/downloads/ice/3.5#macos
+## References
+* [OMERO python bindings](https://docs.openmicroscopy.org/omero/5.4.0/developers/Python.html)
+* [Zeroc-ice python](https://pypi.org/project/zeroc-ice/3.6.5/)
+
+## Installation
+How to set up access to OMERO from python:
+* Install openssl headers version 1.0.2: `sudo apt-get install libssl1.0-dev`
+* Install the corresponding openssl (as default is 1.1.1): `conda install openssl==1.0.2k`
+* Install bzip headers : `sudo apt-get install libbz2-dev`
+* Install zeroc-ice from PyPI, which includes Ice: `pip install zeroc-ice==3.6.0`
+* Run `connect_to_omero.py` as a test (TODO TESTS)
+
+## Disclaimers
+TLDR: Most of this stuff is depcrecated.
+Using OMERO 5.2.5 means that we need to use depreacted python 2.7 (EOL 2020.01.01),
+and we need to use `zeroc-ice` version 3.6 which is also dropped in the newer version of OMERO.
+The local version of `openssl` (`conda`) needs to fit the headers of `libssl-dev` (`apt-get`).
+By default conda will install OpenSSL version 1.1.1 as all the others are no longer maintained.
+However, using the headers of verions 1.0.2 means that we have to downgrade OpenSSL to version 1.0.2 also.
+
+It is highly recommended that we upgrade OMERO to 5.6 in order to use Python 3, in which case it will even
+be possible to get OMERO.py directly from PyPI with easy installation, [omero-py](https://pypi.org/project/omero-py/)
diff --git a/config.json b/config.json
new file mode 100644
index 00000000..2cadfef2
--- /dev/null
+++ b/config.json
@@ -0,0 +1 @@
+{"host": "sce-bio-c04287.bio.ed.ac.uk", "password": "***REMOVED***", "port": 4064, "user": "upload"}
diff --git a/core/__init__.py b/core/__init__.py
index e69de29b..d28ccbde 100644
--- a/core/__init__.py
+++ b/core/__init__.py
@@ -0,0 +1 @@
+import omero_py
diff --git a/core/omero.py b/core/connect.py
similarity index 64%
rename from core/omero.py
rename to core/connect.py
index 1f148c3a..3389fcda 100644
--- a/core/omero.py
+++ b/core/connect.py
@@ -5,68 +5,56 @@
# Copyright (C) 2014 University of Dundee & Open Microscopy Environment.
# All Rights Reserved.
# Use is subject to license terms supplied in LICENSE.txt
+import itertools
-
-USERNAME = 'upload'
-PASSWORD = '***REMOVED***'
-HOST = 'sce-bio-c04287.bio.ed.ac.uk'
-PORT = 4064
from omero.gateway import BlitzGateway
from utils import repr_obj
class Database:
- def __init__(self):
- self.conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
+ def __init__(self, username, password, host, port):
+ self.conn = BlitzGateway(username, password, host=host, port=port)
def __repr__(self):
return repr_obj(self.conn)
_
- def connect(self):
+ def connect(self, secure=False):
connected = self.conn.connect()
-
- # Check if you are connected
- # ==========================
- if not connected:
- import sys
- sys.stderr.write(
- "Error: Connection not available, please check your user name and"
- " password.\n")
- sys.exit(1)
-
- # Using secure connection
- # =======================
- # By default, once we have logged in, data transfer is not encrypted
- # (faster)
- # To use a secure connection, call setSecure(True):
-
- #self.conn.setSecure(True) # <--------- Uncomment this
+ self.conn.setSecure(secure)
+ return connected
def disconnect(self):
self.conn.seppuku()
@property
def user(self):
+ # TODO cache
user = self.conn.getUser()
return dict(ID=user.getId(), Username=user.getName())
@property
def groups(self):
+ # TODO cache
return [dict(ID=g.getId(), Name=g.getName()) for g in
self.conn.getGroupsMemberOf()]
@property
def current_group(self):
+ # TODO cache
g = self.conn.getGroupFromContext()
return dict(ID=g.getId(), Name=g.getName())
def isAdmin(self):
+ # TODO cache
return self.conn.isAdmin()
def getDataset(self, dataset_id):
ds = self.conn.getObject("Dataset", dataset_id)
return Dataset(ds)
+ def getDatasets(self, n):
+ top_n = itertools.islice(self.conn.getObjects("Dataset"), n)
+ return [Dataset(ds) for ds in top_n]
class Dataset:
def __init__(self, dataset_wrapper):
@@ -75,6 +63,10 @@ class Dataset:
def __repr__(self):
return repr_obj(self.dataset)
+ def getImages(self, n):
+ top_n = itertools.islice(self.dataset.listChildren(), n)
+ return [Image(im) for im in top_n]
+
class Image:
def __init__(self, image_wrapper):
self.image = image_wrapper
diff --git a/install.sh b/install.sh
new file mode 100644
index 00000000..638039e7
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,6 @@
+sudo apt-get install libbz2-dev # Install bzip headers
+sudo apt-get install libssl1.0-dev # Install openssl headers
+conda install openssl==1.0.2n # Install local openssl to match
+pip install --no-cache-dir zeroc-ice==3.6.5
+python connect_to_omero.py
+
diff --git a/omero_py/__init__.py b/omero_py/__init__.py
new file mode 100644
index 00000000..d7648721
--- /dev/null
+++ b/omero_py/__init__.py
@@ -0,0 +1,5 @@
+import os
+THISPATH = os.path.dirname(os.path.abspath(__file__))
+
+import sys
+sys.path.insert(0, THISPATH)
diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/test/connect_to_omero.py b/test/connect_to_omero.py
index 92a56da7..d91eece9 100644
--- a/test/connect_to_omero.py
+++ b/test/connect_to_omero.py
@@ -7,13 +7,13 @@
# All Rights Reserved.
# Use is subject to license terms supplied in LICENSE.txt
#
+from __future__ import print_function
-"""
-FOR TRAINING PURPOSES ONLY!
-"""
-import sys
-sys.path.insert(0, './omero_py')
-
+# TODO remove and use unittest to run tests
+import os
+import sys
+sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
+import omero_py
USERNAME = 'upload'
PASSWORD = '***REMOVED***'
@@ -26,12 +26,12 @@ def print_obj(obj, indent=0):
Helper method to display info about OMERO objects.
Not all objects will have a "name" or owner field.
"""
- print """%s%s:%s Name:"%s" (owner=%s)""" % (
+ print("""%s%s:%s Name:"%s" (owner=%s)""" % (
" " * indent,
obj.OMERO_CLASS,
obj.getId(),
obj.getName(),
- obj.getAnnotation())
+ obj.getAnnotation()))
if __name__ == '__main__':
@@ -74,40 +74,40 @@ if __name__ == '__main__':
# clients.
user = conn.getUser()
- print "Current user:"
- print " ID:", user.getId()
- print " Username:", user.getName()
- print " Full Name:", user.getFullName()
+ print( "Current user:")
+ print( " ID:", user.getId())
+ print( " Username:", user.getName())
+ print( " Full Name:", user.getFullName())
# Check if you are an Administrator
- print " Is Admin:", conn.isAdmin()
+ print( " Is Admin:", conn.isAdmin())
- print "Member of:"
+ print( "Member of:")
for g in conn.getGroupsMemberOf():
- print " ID:", g.getId(), " Name:", g.getName()
+ print( " ID:", g.getId(), " Name:", g.getName())
group = conn.getGroupFromContext()
- print "Current group: ", group.getName()
+ print( "Current group: ", group.getName())
# List the group owners and other members
owners, members = group.groupSummary()
- print " Group owners:"
+ print( " Group owners:")
for o in owners:
- print " ID: %s UserName: %s Name: %s" % (
- o.getId(), o.getOmeName(), o.getFullName())
- print " Group members:"
+ print( " ID: %s UserName: %s Name: %s" % (
+ o.getId(), o.getOmeName(), o.getFullName()))
+ print( " Group members:")
for m in members:
- print " ID: %s UserName: %s Name: %s" % (
- m.getId(), m.getOmeName(), m.getFullName())
+ print( " ID: %s UserName: %s Name: %s" % (
+ m.getId(), m.getOmeName(), m.getFullName()))
- print "Owner of:"
+ print( "Owner of:")
for g in conn.listOwnedGroups():
- print " ID: ", g.getId(), " Name:", g.getName()
+ print( " ID: ", g.getId(), " Name:", g.getName())
# New in OMERO 5
- print "Admins:"
+ print( "Admins:")
for exp in conn.getAdministrators():
- print " ID: %s UserName: %s Name: %s" % (
- exp.getId(), exp.getOmeName(), exp.getFullName())
+ print( " ID: %s UserName: %s Name: %s" % (
+ exp.getId(), exp.getOmeName(), exp.getFullName()))
# The 'context' of our current session
ctx = conn.getEventContext()
diff --git a/test/test_connections.py b/test/test_connections.py
new file mode 100644
index 00000000..27923029
--- /dev/null
+++ b/test/test_connections.py
@@ -0,0 +1,59 @@
+"""
+Testing suite for connection to OMERO
+"""
+# TODO use omero.gateway.scripts.testdb_create module
+from __future__ import print_function
+
+import sys
+print(sys.path)
+
+import unittest
+import json
+
+import omero_py
+from core.connect import Database, Dataset
+
+class TestConnections(unittest.TestCase):
+
+ @classmethod
+ def setUpClass(cls):
+ with open('config.json', 'r') as fd:
+ config = json.load(fd)
+ cls._config = config
+ cls._db = Database(cls._config['user'],
+ cls._config['password'],
+ cls._config['host'],
+ cls._config['port'])
+
+ @classmethod
+ def tearDownClass(cls):
+ cls._db.disconnect()
+
+ def testConnection(self):
+ self.assertTrue(self._db.connect())
+
+ def testUser(self):
+ self.assertEquals(self._db.user['Username'], self._config['user'])
+
+ def testDataset(self):
+ dataset = self._db.getDatasets(1)
+ self.assertTrue(dataset is not None)
+ # FIXME cannot do this as it is instanciated anew.
+ # self._ds = dataset
+
+ def testImage(self):
+ dataset = self._db.getDatasets(1)
+ self.assertTrue(dataset is not None)
+
+ #FIXME return single dataset
+ image = dataset[0].getImages(1)
+ self.assertTrue(image is not None)
+ # FIXME cannot do this as it is instanciated anew.
+ self._im = image
+
+ def testRenderImage(self):
+ pass
+
+
+if __name__ == "__main__":
+ unittest.main()
--
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