OMERO.server creation questions

[shaneklumpp]

"./omero db script --password root"

is what I typed

when I run:

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero db password
Please enter password for OMERO root user:
Please re-enter password for OMERO root user:
UPDATE password SET hash = 'EKll2AhGGwCtj52nFobz1Q==' WHERE experimenter_id = 0;

I get nothing about updating the psql database which on other examples happens (see thread: http://www.openmicroscopy.org/community ... 42&start=0)

[atarkowska]

if you typed root then your login is root and password root as well

Ola

[shaneklumpp]

when I run:

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero db password
Please enter password for OMERO root user:
Please re-enter password for OMERO root user:
UPDATE password SET hash = 'EKll2AhGGwCtj52nFobz1Q==' WHERE experimenter_id = 0;

I get nothing about updating the psql database which on other examples happens (see thread: http://www.openmicroscopy.org/community ... ?f=5&t=642)

Could this be causing a problem in why I cannot login with root root on OMERO.web?

[atarkowska]

You have to log in to postgres and then paste that in your PSQL console to update password table in the db

Code: Select all

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME"
psql (9.5.3)
Type "help" for help.

omero=> UPDATE password SET hash = 'EKll2AhGGwCtj52nFobz1Q==' WHERE experimenter_id = 0;


$OMERO_DB_USER and $OMERO_DB_NAME is the same you used in viewtopic.php?f=4&t=8163&p=17667&hilit=psql#p17667

Ola

[shaneklumpp]

Okay. I actually figured out how to log into OMERO.web using my OMERO_ROOT_PASS that i set in the step

Configure:

ln -s OMERO.server-*/ OMERO.server
OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
OMERO.server/bin/omero config set omero.db.name "$OMERO_DB_NAME"
OMERO.server/bin/omero config set omero.db.user "$OMERO_DB_USER"
OMERO.server/bin/omero config set omero.db.pass "$OMERO_DB_PASS"
OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS"
psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < OMERO.server/db.sql

At this point I am going to leave everything how it is because I need to be able to use OMERO.web so I won't be trying to change the password, but why didn't

" ./omero db password"

change the root password? It stayed the same from "OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS""

Is it because I didn't change it directly in the database like you suggested with this:

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME"
psql (9.5.3)
Type "help" for help.

omero=> UPDATE password SET hash = 'EKll2AhGGwCtj52nFobz1Q==' WHERE experimenter_id = 0;

[jmoore]

At this point I am going to leave everything how it is because I need to be able to use OMERO.web so I won't be trying to change the password,

Ok, but if the password is "root", I'd strongly suggest you change it

but why didn't

" ./omero db password"

change the root password? It stayed the same from "OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS""

Is it because I didn't change it directly in the database like you suggested with this:

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME"
psql (9.5.3)
Type "help" for help.

omero=> UPDATE password SET hash = 'EKll2AhGGwCtj52nFobz1Q==' WHERE experimenter_id = 0;

Correct. The command `db password` simply prints a command that you can use on your database.

Alternatively, once you can successfully login, you can either use OMERO.web to change the root password, or you can use the OMERO CLI:

Code: Select all

bin/omero login root@localhost
bin/omero user password


Cheers,
~Josh.

[shaneklumpp]

Hi everyone.

OMERO is up an running and we have images uploaded now which is awesome.

We're now tagging/adding key value pairs to images. Is there a way to have a data dictionary of sorts that a user can select from in the key region? For example, we're going to enter a key of "Stroma_Area" into they key field. Is there something that can store Stroma_Area key so the next time someone wants to use the Stroma_Area key it can autofill/be preselected for?

Reasoning behind this is that we're going to have multiple users uploading images and adding key value pairs to images. They're going to be using the same set of key's and want them to consistently use the same key's so we can have a standardized operation when using OMERO.

I've looked into OMERO.tables would this work for this function?

Shane

[jmoore]

Hi Shane,

at the moment, there's no auto-complete functionality in the standard clients though the idea has definitely been discussed. I know others have been looking into partially similar ideas, e.g. https://github.com/sorgerlab/OMERO.forms which hard-codes the expected responses or https://github.com/ome/omero-mapr which auto-completes searches for key/value pairs. It might be possible to use one of them as a starting point to build your own. If you're interested in that, let's start another thread specifically on the forums or ome-devel for it. Regardless, I've captured the idea as https://trello.com/c/IVeN02uU/110-auto- ... uick-entry

All the best,
~Josh.

[shaneklumpp]

Thanks for the input jmoore. Glad I put it on your guy's radar then. I think it would be a great addition to the key value pair system. I'll look into the other links to look at what others are doing.

I am trying to add scripts now to OMERO and was going to use OMERO.insight upload to do this. When I have my scripts to upload, do I need to upload each .py file individually?

For example I have downloaded webtagging-2.0.0 which comes with two folders: autotag and tagsearch that have many .py files inside of them. How do I go about uploading webtagging-2.0.0 correctly? Do i need to do each .py file at a time or can I do an entire folder at once?

Shane

[jmoore]

I am trying to add scripts now to OMERO and was going to use OMERO.insight upload to do this. When I have my scripts to upload, do I need to upload each .py file individually?

When uploading scripts, yes, insight can only do one at a time. But the .py files in webtagging & autotag aren't scripts but rather a plugin that needs to be installed into OMERO.

For example I have downloaded webtagging-2.0.0 which comes with two folders: autotag and tagsearch that have many .py files inside of them. How do I go about uploading webtagging-2.0.0 correctly? Do i need to do each .py file at a time or can I do an entire folder at once?

You will need to make sure that the directory you downloaded is on your PYTHONPATH as described in https://github.com/MicronOxford/webtagging/blob/master/README.md#installation (where you can skip the `git clone` command).

Cheers,
~Josh