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Hi Eilidh,
<div class=""><br class="">
</div>
<div class=""> Yes, I’m afraid the output from conn.connect() is not very helpful.</div>
<div class=""><br class="">
</div>
<div class="">You can try the underlying omero.client connection like this:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">>>> c = omero.client(host=‘<a href="http://demo.openmicroscopy.org" class="">demo.openmicroscopy.org</a>', port=4064)</div>
<div class="">>>> c.createSession(‘username', ‘password’)</div>
<div class=""><br class="">
</div>
<div class="">which should give you an exception if this fails.</div>
<div class=""><br class="">
</div>
<div class="">e.g.</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
$ omero script launch 87923</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
Using session 009e7c47-5b59-4156-a664-21bd8d84ea68 (root@localhost:4064). Idle timeout: 10 min. Current group: system</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
Enter value for "IDs": 1</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
Job 89261 ready</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
Waiting....</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
Callback received: FINISHED</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196); min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>*** start stderr (id=89762)***</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* Traceback (most recent call last):</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* File "./script", line 394, in <module></div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* run_script()</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* File "./script", line 369, in run_script</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* ok = c.createSession('user', ‘password')</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* File "/Users/wmoore/Desktop/OMERO/openmicroscopy/dist/lib/python/omero/clients.py", line 569, in createSession</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* prx = rtr.createSession(username, password, ctx)</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* File "/usr/local/lib/python2.7/site-packages/Glacier2_Router_ice.py", line 258, in createSession</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, password), _ctx))</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* Glacier2.PermissionDeniedException: exception ::Glacier2::PermissionDeniedException</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* {</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* reason = Password check failed for 'user': []</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* }</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>* !! 10/31/17 21:30:57.788 error: communicator not destroyed during global destruction.</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>*** end stderr ***</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196); min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196); min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>*** out parameters ***</div>
<div style="margin: 0px; font-family: Courier; color: rgb(76, 47, 45); background-color: rgb(223, 219, 196);" class="">
<span class="Apple-tab-span" style="white-space:pre"></span>*** done ***</div>
</div>
<div class=""><br class="">
</div>
<div class="">In fact, I’ve found the same issue as you - Connection to a different server doesn’t work from within an OMERO.script</div>
<div class="">but does work locally.</div>
<div class="">Not sure what is going on here but I’ll ask others on the OME team.</div>
<div class=""><br class="">
</div>
<div class="">You shouldn’t be seeing a "ValidationException Can’t find params…” when</div>
<div class="">you run the script.</div>
<div class=""><br class="">
</div>
<div class="">Do you see any errors when uploading the script with $ omero script upload ?</div>
<div class="">Or are you simply putting the script into the lib/scripts directory?</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div>
<blockquote type="cite" class="">
<div class="">On 31 Oct 2017, at 16:15, Eilidh Troup <<a href="mailto:e.troup@epcc.ed.ac.uk" class="">e.troup@epcc.ed.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi,<br class="">
<br class="">
Thank you very much for your thoughtful response to my question on how to transfer data from one OMERO to another.
<br class="">
<br class="">
I was able to create a script to take an Image ID as input, along with username & password of central server, and could list the files belonging to the image too.<br class="">
<br class="">
I got stuck when I tried to create a BlitzGateway connection to central server. I’m using the demo OMERO server as my remote OMERO.<br class="">
<br class="">
This is a short script that reproduces the problem. I can connect to a local or remote OMERO.server using the following script when I run it as a python script directly from the command line, but when I run it as an omero script, it will connect to the local
server (itself), but not to the remote server: remote_conn.connect() returns False. Is there a way to get more information about why it won’t connect? I’m at a loss as to how to debug this.<br class="">
<br class="">
--------------------------------------------------<br class="">
Connect_to_remote_omero.py<br class="">
<br class="">
from omero.gateway import BlitzGateway<br class="">
<br class="">
# remote<br class="">
username = "etroup"<br class="">
password = “redacted"<br class="">
host = '<a href="http://demo.openmicroscopy.org" class="">demo.openmicroscopy.org</a>'<br class="">
<br class="">
# local<br class="">
# username = "root"<br class="">
# password = “redacted"<br class="">
# host = 'localhost'<br class="">
port = 4064<br class="">
<br class="">
# Connect to remote server.<br class="">
remote_conn = BlitzGateway(username, password, host=host, port=port)<br class="">
connected = remote_conn.connect() # returns true if connected<br class="">
<br class="">
if (connected):<br class="">
print "connected"<br class="">
for p in remote_conn.listProjects():<br class="">
print p.getName()<br class="">
else:<br class="">
print "not connected"<br class="">
<br class="">
remote_conn.close()<br class="">
—————————————————————————<br class="">
<br class="">
Running from python (works for local or remote server):<br class="">
<blockquote type="cite" class="">python Connect_to_remote_omero.py<br class="">
</blockquote>
connected<br class="">
Project1<br class="">
<br class="">
Running as OMERO script, fails to connect to remote server:<br class="">
<blockquote type="cite" class="">bin/omero script list<br class="">
</blockquote>
623 | /rdm/Connect_to_remote_omero.py <br class="">
524 | /rdm/Export_to_other_omero.py <br class="">
547 | /rdm/ping.py <br class="">
(20 rows)<br class="">
<blockquote type="cite" class="">bin/omero script launch 623 <br class="">
</blockquote>
Using session 5f02548b-6655-490b-981a-85edec1e70c4 (root@localhost:4064). Idle timeout: 10 min. Current group: system<br class="">
ValidationException: Can't find params for 623!<br class="">
stdout is in file 624:<br class="">
---------------------------------<br class="">
not connected<br class="">
<br class="">
---------------------------------<br class="">
No stderr.<br class="">
<br class="">
Running as OMERO script, does connect to local server:<br class="">
bin/omero script launch 625 <br class="">
Using session 5f02548b-6655-490b-981a-85edec1e70c4 (root@localhost:4064). Idle timeout: 10 min. Current group: system<br class="">
ValidationException: Can't find params for 625!<br class="">
stdout is in file 626:<br class="">
---------------------------------<br class="">
connected<br class="">
project2<br class="">
project1<br class="">
<br class="">
————————————————<br class="">
<br class="">
Thanks,<br class="">
Eilidh<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On 17 Oct 2017, at 12:00, <a href="mailto:ome-devel-request@lists.openmicroscopy.org.uk" class="">
ome-devel-request@lists.openmicroscopy.org.uk</a> wrote:<br class="">
<br class="">
Send ome-devel mailing list submissions to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>ome-devel-request@lists.openmicroscopy.org.uk<br class="">
<br class="">
You can reach the person managing the list at<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>ome-devel-owner@lists.openmicroscopy.org.uk<br class="">
<br class="">
When replying, please edit your Subject line so it is more specific<br class="">
than "Re: Contents of ome-devel digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Re: Plan for transferring data from one OMERO to another<br class="">
(William Moore (Staff))<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Tue, 17 Oct 2017 10:18:18 +0000<br class="">
From: "William Moore (Staff)" <W.Moore@dundee.ac.uk><br class="">
To: OME External Developer List<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><ome-devel@lists.openmicroscopy.org.uk><br class="">
Subject: Re: [ome-devel] Plan for transferring data from one OMERO to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>another<br class="">
Message-ID: <818C04E1-B318-472F-AEF4-16F998AEB015@dundee.ac.uk><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hi,<br class="">
<br class="">
This could be quite a bit of work, so you will need to start small and build-up functionality as you go. Some investigation will be required - Some things will depend on the type of images you?ll be transferring. You?ll also need to have both OMERO servers
using the same major version. E.g. 5.3.x.<br class="">
<br class="">
You?ll really need to re-import the images to the central server instead of manually creating new DB entries for all image metadata etc. This can be acheived from the command line, with your OMERO.script invoking ?bin/omero import ?? to the central server.<br class="">
<br class="">
Are these images imported in OMERO 5.0 or later (original files will be in managed repo)?<br class="">
Your script, running on the source OMERO server *may* be able to access the managed repository directly, and call e.g. ?bin/omero import /OMERO/ManagedRepository/will_3/2017-10/05/15-31-34.090/control.lsm?<br class="">
This is certainly the easiest solution.<br class="">
<br class="">
Alternatively, if the managed repo is not available then you can download the original images to the folder where the OMERO.script is running and import the images from there.<br class="">
In the simplest case, a single OMERO Image has a single image file. However, some Images are stored as multiple original files in the managed repo, which means they will all need to be downloaded to the script before they can be imported if you go for that
option.<br class="">
<br class="">
In some cases, a single original file (or set of original files) will generate multiple OMERO Images when imported. So you may find that multiple images in your source server come from the same original file(s). In that case, you will have to be careful when
you iterate through these images that you don?t import the same original file multiple times.<br class="">
<br class="">
It?s not really possible for OMERO.scripts to be ?interactive?. The easiest option for choosing a target is to have your users log in to the webclient (or Insight) in the central server and pick a Project or Dataset ID to enter into the script dialog in the
other server.<br class="">
<br class="">
Traversing the graph of linked objects Dataset -> Image and handling of file Annotations / duplicate tags etc should be pretty straight-forward once you have the re-import of images working.<br class="">
<br class="">
Please put your script in github and commit all changes as you go. This will allow us to see what you have working and to help or contribute much easier. One option if you don?t already have a repo is to fork https://github.com/ome/omero-user-scripts which
allows us and the community to find your repo from there.<br class="">
<br class="">
Be careful when handling usernames and passwords in your OMERO.script. Make sure you?re not logging these etc.<br class="">
<br class="">
Initial goals:<br class="">
- Create an script that can take an Image ID as input, along with username & password of central server. Can use https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Scripting_Service_Example.py<br class="">
- List original files from source Image<br class="">
for f in image.getImportedImageFiles():<br class="">
print f.path, f.name<br class="">
- Create a BlitzGateway connection to central server<br class="">
- You can get a ?client? object using client = conn.c<br class="">
- Command line import using code similar to that in our python test framework (using ?client? from above as in the example) :https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/src/omero/testlib/__init__.py#L277<br class="">
<br class="">
<br class="">
Let us know how this goes,<br class="">
<br class="">
Regards,<br class="">
<br class="">
Will.<br class="">
<br class="">
<br class="">
On 12 Oct 2017, at 12:46, Eilidh Troup <e.troup@epcc.ed.ac.uk<mailto:e.troup@epcc.ed.ac.uk>> wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
I?m a software engineer working on data management in biology. Our use case is that lab groups have their own instances of OMERO, and there is also a centrally-hosted university OMERO server which they would like to transfer data to. I?m planning to write a
script to allow users to transfer data from one OMERO to another. I wanted to run the plans by this forum to see what you thought of the idea, and whether my planned implementation seems sensible.<br class="">
<br class="">
I plan to write a script (OMERO.scripts) to run on the local instances of OMERO and be used through OMERO.server or OMERO.web. This will let the user choose the image, dataset or project that they want to move, and enter their credentials for the central OMERO
server. Then the script will use the Blitz Gateway to read data from the local server, and then to write to the remote server.<br class="">
<br class="">
issues:<br class="">
<br class="">
- How will users choose where to put data? It will have to be either in a default project on the central server, or the script would have to be interactive, where the user enters their credentials, and then the central server is contacted so that a list of
projects and datasets belonging to that user can be presented.<br class="">
<br class="">
- There will be a graph of objects linked to any given one, for example, a dataset with images, tags and attachments. Need to traverse this to transfer all associated data.<br class="">
<br class="">
- Some IDs will need to be mapped from one OMERO to the other, for example tags - shouldn?t create a new one, but link to existing tag with same name on the other OMERO.<br class="">
<br class="">
I?m planning to write the code in Python and use OMERO.scripts and the Blitz Gateway. Please let me know what you think.<br class="">
--<br class="">
The University of Edinburgh is a charitable body, registered in<br class="">
Scotland, with registration number SC005336.<br class="">
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<br class="">
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