New 1.7.00 install gives "an error has occurred in the Cell's AJAX library" loging into admin session

[John Milnes]

Hi - I'm putting up i2b2 1.7.00 on Centos with Oracle and I am consistently getting the "An error has occurred in the Cell's AJAX library"  message
whenever I log in as an admin.  A user login to the webclient does not get this message.  I found some posts that say a typo in a path to the cells can cause this so I reviewed the config and tried changing things but I still can't get this message to go away. I can see my services deployed in jboss, my db connection strings are working..  I have tried IP, hostname,  localhost and  loopback address in the properties files, nothing seems to make an impact.

Can anyone let me know what else to look for or how to see exactly what is triggering this message?

Here is a rundown of my settings:
i2b2_config_data.js:
    urlCellPM: "http://localhost:9090/i2b2/services/PMService/",

crcapp/crc.properties:
    queryprocessor.ws.pm.url=http://localhost:9090/i2b2/services/PMService/getServices
    queryprocessor.ws.ontology.url=http://localhost:9090/i2b2/services/OntologyService/getTermInfo
    edu.harvard.i2b2.crc.delegate.ontology.url=http://localhost:9090/i2b2/services/OntologyService

crcapp/edu.harvard.i2b2.crc.loader.properties:
    edu.harvard.i2b2.crc.loader.ws.fr.url=http://localhost:9090/i2b2/services/FRService/
    edu.harvard.i2b2.crc.loader.ws.pm.url=http://localhost:9090/i2b2/rest/PMService/getServices

frapp/edu.harvard.i2b2.fr.properties:
    edu.harvard.i2b2.fr.ws.pm.url=http://localhost:9090/i2b2/services/PMService/getServices

imapp/im.properties:
    im.ws.pm.url=http://localhost:9090/i2b2/services/PMService/getServices

ontologyapp/ontology.properties:
    ontology.ws.pm.url=http://localhost:9090/i2b2/services/PMService/getServices
    edu.harvard.i2b2.ontology.ws.fr.url=http://localhost:9090/i2b2/services/FRService/
    edu.harvard.i2b2.ontology.ws.crc.url=http://localhost:9090/i2b2/services/QueryToolService

workplaceapp/workplace.properties:
    workplace.ws.pm.url=http://localhost:9090/i2b2/services/PMService/getServices

Hive paths in db are:
id    name    method    url
----------------------------
CRC    Data Repository    REST    http://localhost:9090/i2b2/services/QueryToolService/
FRC    File Repository    SOAP    http://localhost:9090/i2b2/services/FRService/
ONT    Ontology Cell    REST    http://localhost:9090/i2b2/services/OntologyService/
WORK    Workplace Cell    REST    http://localhost:9090/i2b2/services/WorkplaceService/
IM    IM Cell    REST            http://localhost:9090/i2b2/services/IMService/

hostname:   dbmi-i2b2-dev02.dbmi.pitt.edu

grep localhost /etc/hosts:
    127.0.0.1       localhost.localdomain localhost       dbmi-i2b2-dev02

Thanks

John

[Karl Burke]

John,

Check your JBoss logs, particularly looking for [ERROR] entries.  The error messages seen in the web clients are how the Ajax app perceives the problem, but I've usually found the root cause in my i2b2-server configuration.

The message you're seeing is one I saw when I did not have the database drivers in my WEB-INF/lib directory with 1.7.00.  This has been addressed in 1.7.01, but you can try manually copying them to finish the effort you've put in so far.  See the topic "Once more?" in this group from the beginning of February.

Karl

[John Milnes]

Thanks Karl!

I have the db drivers in place but checking server.log I see: 
                              edu.harvard.i2b2.common.exception.I2B2Exception: User not registered to the project

In my i2b2pm schema I do have a record in the pm_project_user_roles table that sets i2b2 account with the role admin and  for projects "@" which looks right.  Any experience with that error?

Thanks

John

[Natus]

Hello,

I have the same (minor) problem,
Under Ubuntu 12.04 / Postgresql / 1701 I2B2

[Wei]

I have the same problem. Any solutions?

[Mahbub Guljari Alam]

Could anybody solve the problem ?
I have the same issue in webclient, stuck there for three days.

Any kind of help will be highly appreciable.

Thanks.
Mahbub

[Peter Beninato]

Hi,

 

See an attached OLD email thread, it might be relevant.

 

-Peter

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[Mahbub Guljari Alam]

Hi Peter,

Thanks for your time to look into my problem.

I already solved this issue. It was the problem in i2b2hive schema.

Thanks,

Mahbub

[Anil Pandey]

Hi Mahbub guljari Alam

can you please explain how you solve it. i am experiencing same issue while i login to webclient.

thanks

[Dumestier Johan]

Hi Anil Pandey,

i got the error with the webclient.

It seem to come from a "mistake" (don't know if it's a real mistake) in the hive schema :

In the i2b2hive schema, in the X_db_lookup tables , the column c_db_fullschema is set to "public" by default.

To resolve the "ajax error', you must set it to the right schema (exemple : for work, it's i2b2workdata, for im, it's i2b2im, etc etc)

I hope it will help you (it work for me).

[Jani Heikkinen]

Hi, I have also the AJAX error, doing a fresh installation of i2b2 on CentOS7.
What you mean by in the i2b2hive schema? I have nothing if I connect to i2b2hive schema in postgesql.
I have executed all the commands as told in official i2b2 documentation (using localhost as server name everywhere).
I noticed that the installation never excplicitly instructs to create i2b2 db, however nothing works until a db with that name is created.
I've done the installation at least 5-6 times following instructions and I always get same AJAX error.

Would you have more detailed way of explaining how you edit these tables?

[Dumestier Johan]

Hi,

I mean by 'i2b2hive schema' is  in the database 'i2b2', there is many schema (i2b2metadata,i2b2imdata) and one of them is i2b2hive.

If you use postgresql, you can "browse'" the database by using the software "pgAdmin". Else you can see the schemas by the command \dn. 

You need to create the schemas before the installation. The schemas are created by this command "CREATE SCHEMA i2b2hive AUTHORIZATION i2b2hive ;" ( don't forget to create the user before). ( After for each  schema and user described in the chapter 3.3)(3.3.2 for postgresql)

Else i have some questions :

what do you mean exactly by 'connect' in ' I have nothing if I connect to i2b2hive schema in postgesql.' ?

Do you check if the parameters in the Properties File are corrected ? (else step in the chapter 3)  ?

For editing, you have 2 ways :

You can use PgAdmin (simple, just show the lignes and editing =) ) 

In command :

For exemple :

Update i2b2hive.crc_db_lookup set c_db_fullschema='i2b2demodata where c_db_nicename='Demo';

Update i2b2hive.im_db_lookup set c_db_fullschema='i2b2imdata' where c_db_nicename='IM';

Update i2b2hive.ont_db_lookup set c_db_fullschema='i2b2metadata' where c_db_nicename='Metadata';

Update i2b2hive.work_db_lookup set c_db_fullschema='i2b2workdata'  where c_db_nicename='Workplace';

[Jani Heikkinen]

Hi Johan, and thanks a lot for your reply!
It seems I have not created the schemas, when I connect to i2b2
database and type \dn there is only postgres schema.
The step 3.3.2 only mentions that databases should be created.
I read about the postgresql schemas, yet it is unclear at which stage
I should use "create schema". It is not obvious in the documentation
that BOTH the db and the schema is to be created.
So what is the order of the steps when setting up i2b2 database?

Is the following what you did:

1. create database i2b2
2. create database i2b2demodata etc.
3. create schema i2b2demodata authorization i2b2demodata etc..?
4. create user i2b2demodata password xyz etc.
5. grant all privileges on database i2b2demodata to i2b2demodata etc..

If this is the case, I have always been missing the schema creation
step. That is not clearly stated in the installation documentation and
thus is quite confusing.


"In order for the i2b2 database scripts to work and enable the core
cells to communicate with the database you need to create user
accounts in your i2b2 database. The following table shows what users
will be created for each database / schema that is part of the i2b2
database." - > for me this is not explicitly pointing that I HAVE to
create a schema with the database. More like they are excluding each
other as options?

Thanks, Jani

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[Dumestier Johan]

After reading once more the documention, I agree with you there is no indication about creating the schemas (then, does i miss something too ?)

Also, there is a difference between databases, schemas , and tables.

Tables are in schema, schemas in database.

In postgres, we use the term of 'schema', but , for SQL server, it seem to be 'database', if think this is why there is a '/' in "The following table shows what users 

will be created for each database / schema that is part of the i2b2".

The command in the chapter 3.3 create and load the tables. But it seem (for me at least) the schema aren't created.

Then, what i did is more likely :

1- create database i2b2

2- create the user (i2b2demodata ,i2b2hive) with their password

3- create the schema with the authorization

4- grant privliges

5- enjoy =)

You don't have create databases "i2b2demodata" etc etc, and the authorization (your step 3) must be after creating the users :

create schema nameofschema authorization username ;

if you want a example in command :

#I supose you freshly install pgsql:

#first create the data base (step 1)

#log to pgsql ("psql -U postgres" for example ) 

Create database i2b2

#delog and relog to i2b2 (quit : "\q" . log to i2b2 :"psql -U postgres -d i2b2) (step 2)

#Now create the user by this command : "Create user IDENTIFIED BY PASSWORD"

#Example from the documentation :

CREATE USER i2b2demodata WITH PASSWORD 'demouser' ;

CREATE USER i2b2hive WITH PASSWORD 'demouser' ;

CREATE USER i2b2imdata WITH PASSWORD 'demouser' ;

CREATE USER i2b2metadata WITH PASSWORD 'demouser' ;

CREATE USER i2b2pm WITH PASSWORD 'demouser' ;

CREATE USER i2b2workdata WITH PASSWORD 'demouser' ;

#Now , create the schema (step 3)

CREATE SCHEMA i2b2demodata AUTHORIZATION i2b2demodata ;

CREATE SCHEMA i2b2hive AUTHORIZATION i2b2hive ;

CREATE SCHEMA i2b2imdata AUTHORIZATION i2b2imdata; 

CREATE SCHEMA i2b2metadata AUTHORIZATION i2b2metadata ;

CREATE SCHEMA i2b2pm AUTHORIZATION i2b2pm ;

CREATE SCHEMA i2b2workdata AUTHORIZATION i2b2workdata;

#You can grant privilges here, but it seem i didn't do (i didn't take note of that step, then i can't remember if i did or not this step)

#End (step 5)

I hope i didn't miss something in the documention (a command which create the schema ).

I hope it will work for you too.

When you use the command in the chapter 3.3 of the documentation ( create the table), do you have some errors?

Dumestier Johan

[Donahoe, Janice M]

Hi Johan,

Thank you for this information on the i2b2 installation guide. You are correct in your thinking as to why there is a '/' between database and schema. Knowing that Oracle and PostgreSQL use the term "schema" and SQLServer uses "database" I was trying to make the documentation accommodating to all users. However, I can see how this can create confusion.

I recently took a look at the installation guide and feel it needs to be updated and more clarification needs to be documented. I will be updating this document over the coming months. I welcome all feedback from you and the rest of the community on ways to improve this document.

Thanks again for taking the time to send this information.

Janice Donahoe

Sr. Project Specialist

Partners HealthCare

Research Information Sciences & Computing

i2b2 - Informatics for Integrating Biology & the Bedside

399 Revolution Drive, Suite 725, Somerville, MA 02145

857-282-3754

jdon...@partners.org

http://www.partners.org | http://www.i2b2.org

---

From: i2b2-ins...@googlegroups.com [i2b2-ins...@googlegroups.com] on behalf of Dumestier Johan [johan.d...@outlook.fr]
Sent: Monday, April 03, 2017 8:56 AM
To: i2b2 Install Help

Subject: Re: New 1.7.00 install gives "an error has occurred in the Cell's AJAX library" loging into admin session

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[Jani Heikkinen]

I did a fresh i2b2 installation once again. No matter what I do, I get
AJAX errors when I first time log in into the webclient.
currently my database creation procedure is:

1. create i2b2 db
2. create users with demouser password.
3. I create schemas with authorization to each schema user
4. I set privileges for the schema for each user (grant all privileges)

And I do the rest of the installation all the way until I have admin
web interface and webclient web interface (after PM cell setup).
All the steps are succesfull. I know that after installing PM cell I
do not have all other modules yet present.
I get 5 AJAX errors after logging in to webclient first time.

I am using postgresql 9.2 on CentOS 7 with all recommended packages
(wildfly, axis, ant) from i2b2 community wiki.

We are also evaluating other solutions for data management, but would
feel sad to abandon i2b2 just because it seems to be technically very
hard to set up.

Another note on the instructions: on parts where it says for opening
the config file x or y, it would better to say something like "use
your favourite editor to open the file" than just "open xyz" since
that can be misleading to not so technically advanced users or with
little experience on Linux. I could understand that this step means
"use vi" or something else preferred, but not all can.

Jani Heikkinen

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[Dumestier Johan]

Can you now check the value of the c_db_fullschema's column of the Hive schema ?

by doing (for example) :

select c_db_fullsschema from i2b2hive.crc_db_lookup ; 

if it set to 'public', try what i said :

Update i2b2hive.crc_db_lookup set c_db_fullschema='i2b2demodata where c_db_nicename='Demo';

Update i2b2hive.im_db_lookup set c_db_fullschema='i2b2imdata' where c_db_nicename='IM';

Update i2b2hive.ont_db_lookup set c_db_fullschema='i2b2metadata' where c_db_nicename='Metadata';

Update i2b2hive.work_db_lookup set c_db_fullschema='i2b2workdata'  where c_db_nicename='Workplace';

If you already did,  i'm out of ideas sorry :s (may be double check all configurations file ?).

[Jani Heikkinen]

Hi, I did the installation (in the end created Ansible role to make it
easily repeatable) :)

I do not have anything in i2b2hive.crc_db_lookup table, it is empty.
Even I ran the update commands there are 0 rows in the lookup table.

The schemas look okay, I have them created and they are owned by their
respective users.
Grants seem to be fine too.

I recal that the step when I loaded the demo data seemed quite fast,
given that I got warning it should take 10 minutes. For me it was over
more like 0.5 seconds. But the script stated that the load was
succesfull.

Tables look quite empty though.

Not sure if it is related to the other problems with installation.

I can access admin interface, all the URLs are okay and services can
be listed on the service url.

[Dumestier Johan]

This is weird if these tables are empty.

It look like you miss a step.

In the capter 3.4-9, you create and load these table.

I made this mistake that I forgot to run the load command line.

In each of these chapter, you are the "create" command line :

ant –f data_build.xml create_hivedata_tables_release_1-7

and you have the "load" command line :

ant –f data_build.xml db_hivedata_load_data

did you run these "load" command (for each schema)? 

If yes, and the table(s) stay empty, check how many lines are run (if i remember well, at the end of each "ant", there is a message like "X SQL statement on Y)")

if X  < Y, try to check in the console if some SQLs statements are not run or seem weird.

I remember when i tried to custom my I2B2 instance, there was a problem that the script try to load in a dbo database (or schema) instead the right one (i2b2hive for exemple). 

But i don't think there is a link with your problem.

Does the I2B2 Jboss server is on or off while these step ? If on,  try to put it off ?

[Jani Heikkinen]

I can see from i2b2 webclient that the cells cannot communicate
properly with the database. So it seems at least that the error is to
do with the database creation.

Is it possible to increase wildfly logging level? The instruction on
the wiki was not working (wildfly config was different than what they
describe in their webpage). I would need something to get a hold on
where things go wrong.

i2b2 is quite much harder to setup than say, Transmart.

[Jani Heikkinen]

Ok, just a brief notice... in the build.properties it is very
important not to have extra characters in the end of lines. The ant
build scripts will get confused and insert statements will fail when
creating the dbs. Checking now if going through all my configs will
help resolving the issue.

[Jani Heikkinen]

Ok that was it. I needed to have all the db creation scripts
_absolutely_ correct without whitespaces in the end + add your
commands:

>
> Update i2b2hive.crc_db_lookup set c_db_fullschema='i2b2demodata' where c_db_nicename='Demo';
> Update i2b2hive.im_db_lookup set c_db_fullschema='i2b2imdata' where c_db_nicename='IM';
> Update i2b2hive.ont_db_lookup set c_db_fullschema='i2b2metadata' where c_db_nicename='Metadata';
> Update i2b2hive.work_db_lookup set c_db_fullschema='i2b2workdata' where c_db_nicename='Workplace';

In addition I granted the schema privileges as separate step as
instructed in the documentation.

Hopefully if anyone else needs help these findings can clarify things.

Thanks a lot for your help!



On Thu, Apr 6, 2017 at 5:10 PM, Jani Heikkinen