Container issues on OpenSpecimen

[pgovindrao]

Posting on behalf of Li Yue:

Dear Sri and Poornima,

I hope this email finds you well. Congratulations to the new release of caTissue recently as the next generation “Open Specimen” and our team is very interested in this project and have installed the instance to our test server and start exploring this. However, we have two questions with regard to this new version and hope to get an answer from your experts.

Firstly, it seemed to us that there is a trouble to “collect” specimen to the available storage facilities:

Above is a screenshot of this that we have a freezer and grid C1 is shown available in green colour. Then when we select collection status to “Collected” and try to submit this collection, there is an error saying “Submission failed since a Specimen Position with the same already exists” and prevents us from saving… The submission is working for virtual locations and in old versions of caTissue with manual storage locations. So we are just wondering if this is a bug? Otherwise could you please advise us why we get this error?

Also we have a general question to all version of caTissue here that if it supports multiple clinical diagnosis per sample? i.e. if the patient has both diabetes and cardiovascular disease, can we keep a record for all of them?

Thanks heaps in advance and hope to hear back from you soon.

Kind regards,
Yue

[pgovindrao]

Hello Yue,

Thanks for showing interest in OpenSpecimen. We have not come across the issue you have mentioned about storing samples. Can you give more details:

1. Error in JBoss log when this error comes- JBOSS/server/default/log/server.log
2. Screenshot of this container from Administration->Storage Container->Edit(look for this NRL_Freezer_1), want to check if there is any restrictions set.

Your question about multiple diagnoses, yes it is supported to have multiple per patient but single value per visit(SpecimenCollectionGroup). Hope that answers your question.

Thanks,
Poornima

[YueLi]

Hi Poornima,

Thank you so much for your prompt reply. Your guys have always been very helpful. Attached are the screenshots of our storage container NRL_Freezer and the specimen collection page which we received an error. Hope this helps!

I’ve also downloaded the error logs from the JBoss server, however it seems that I am unable to attach them here. So I’ve sent you a separate email…

Again, a big thank you for your kind help!

Cheers
Yue

[pgovindrao]

Hi Yue,

Have you done any customizations to the application or done any data changes directly in the database? The reason I am asking is we have not encountered such error and we tried to reproduce with different approaches but could not get to the error. It is not finding the specimen ID being inserted in the catissue_specimen_position table.

Thanks,
Poornima

[YueLi]

Hi Poornima,

Thanks for the investigation. Just confirm that I didn’t customised the code and DB - just the plain installable from http://demo.catissueplus.org/nextgen/ Wondering if you have a demo/test site for the same version that I can test out?

In my instance of OpenSpecimen, I can still save specimens if the location is virtual - guess that’s because there is no write to the catissue_specimen_position table.

Quickly relooked at our specimen records which looks below:

Looks like all of them has got an ID. Is that the same parameter the position table is looking for?

Thanks
Yue

[YueLi]

Hi Poornima,

Here is my catissue_specimen table for your reference (Let me know if you have any problem in loading this image). I’ve also noticed is this due to a failure in foreign key constraint of catissue_specimen_position table which links to catissue_specimen.Identifier. But I was then confused because all specimen in our catissue_specimen table has an id, and I don’t know why this insertion will result an error - and since I haven’t changed any code, so was wondering if your SQL insert statement is referring to the wrong parameter? Just a guess.

Thanks a lot
Yue

.

[pgovindrao]

Hi Yue,

We will not be able to understand the problem just looking at Specimen table. Yes, we have a demo site for OpenSpecimen - http://nextgen.catissueplus.org/catissuecore/
Test login:
site_admin@test.com
Login123

If you can reproduce your problem here, will be useful for us to debug.

Thanks,
Poornima

[YueLi]

Hi Poornima,

Thanks for releasing the test account. Looks like there is no such a problem on your version of OpenSpecimen, big relief for you . Also I’ve noticed a new release on http://demo.catissueplus.org/nextgen/ today, so I installed the new version, however the error persist on my server - I followed the exact same approach as what is specified on the deployment document as well as the same version of JBoss, ANT etc - which was a bit old… i am just wondering if the installable that you released on http://demo.catissueplus.org/nextgen/ is the same version as what you are using for the demo site? Apparently it seems even the build.xml file of the released installable is different from the github - so was very curious to find out if we are using the same version… if possible can I get the stable version of installable for the demo site? Also could I check with you for the version number of JAVA, ANT, JBOSS AND MYSQL that is used for your site? Thanks a lot.

We are very keen to try out and feedback on the new version. Thanks very much for your kindly help and advise.

Thanks
Yue

[YueLi]

Sorry one more question Poornima, does the new version of OpenSpecimen still use the catissue_abstract_specimen table? We’ve got some error saying that the table is missing, wondering if that’s just some legacy code.

Thanks
Yue

[pgovindrao]

Hi Yue,

By next week, we will share new build with you which will be almost the final build. About your current issues, we would like to take a look at it over a call to make sure it is not something specific to your set up. Will set up the call with you offline.

Thanks,
Poornima

[nitesh_marwaha]

Had reviewed the setup over the call, The problem was with the DB engine settings. OpenSpecimen requires it as INNODB, where as it was set to MyISAM. By changing it to INNODB resolves the issue.

Thanks,
Nitesh

[YueLi]

Thanks Poornima and Nitesh. That was very helpful!

[Amy_Brink]

You must assign a specimen label before submitting the specimens and storage location. It cannot store the specimen without know what the label for that specimen is. So two things the error message displayed is incorrect. Its not that the storage container position is not available, its the specimen must have a label.