database export from IJC to the Web Services

Hello,



We have recently got the Academic license for the Chem Axon
JChem Web service.


We have installed JRE 1.6.0_23 and the JChem Web Services version 5.4.1.1,but now we are
a bit lost what to do next.

Do we need to install on our server beside JChem Web Services as
well other programs, like Marvin, IJC

in order that Web Services will work correctly or not?

How do we actually put/export our database from the IJC on the desktop to the Web?



Thank you for your support.



Best regards,



Agata

Agata,

It is not a requirement to have a database to use non-database related services (Atom-by-atom search, chemical terms, molecular conversion, etc.)  from JChem Web Services.

I believe from your post, that you are trying to understand how to use the database related services (Connection, JChem Search, Related Search, Data Definition, Data Manipulation, etc.) from JChem Web Services.  These database related services operate on a JChem Database. 

Here is a link to the administration guide on how to setup a JChem Database.

http://www.chemaxon.com/jchem/doc/admin/

 

Can you descirbe what type of database you are using in IJC? 

 

 

Hi,

thank you for the hints. I will go through the Administration Guide of JChem and try to solve the difficulties we have.

So, I have built a small database of 120 molecules in IJC.

I have a table with 120 entries and fields are chemical structure (picture), and then integer and text fields (this database will be expanded till couple of thousands mols).

I would like to share it with 3 other groups involved in the same project, but I do not know how to use JChem web services to actually make the databse available for the others. Well now you gave me some hints,

I will read and try them out. I would like that other 3 groups can open database via web, read it and as well insert+save their experimentally measured data through the web to the database. This way we share faster the results we obtained.

Agata

 

 

Agata,

As long as you have a JChem Table (also called structure tables in IJC) holding the data, they should be readable from JChem Web Services. From a simplified perspective, IJC uses two table types (structure tables and standard tables).

Your current table with 120 structures may already be a JChem Table. One way to find out is to open IJC and look in the schema.  From the tree view on the left, the schema should have an icon underneath (one icon per table).  The structure tables are in orange and the standard tables are in green. If your table is in orange, then you should be able to directly connect with JChem Web Services.

Otherwise, you may want put your molecules and data into a new Data tree that uses a structure table (JChem Table). 

To do this, from the Projects tree, select a Schema (aka Database).  Right click on the schema and select the "New Data Tree and structure table...".  This will create a Data Tree that uses a JChem table and the icon should be orange.  Then fill it with the molecules and data you want to share. 

Write back and let us know which type has your data or if you have been able to create a new Data Tree that uses a JChem Table.

Hello,

I am back after almost a year and at the same point as a year ago since I was busy with other things.

Can you please help me, maybe step by step to make a database made in IJC available via web.

I prepared a table in IJC (i believe it is a structure table, orange icon in front of it) in 2 possible views:

grid view and let's say designed view as i would like it to appear on a web. We have a server prepared and web services ( JChem Web Services version 5.4.1.1) installed as well as JRE 1.6.0_23. We use MySQL.

How can I connect or export the database from IJC to the web so that my colleagues can read it, search through it and as well insert and save data for which they will have permission. I would like a database to appear on a web in both views grid view and so called designed view.We tried already to export data from IJC via MySQL, but we could do it only for structure files (sdf, mdl). 

If it will be easier to understand what I would like in direct discussion, we can hear by skype. If this is of course a part of support as well.

Thank you for your help and disponibility,

best regards,

Agata

Agata,

It's great that you have your data in a JChem table.

 

Take a look at our Ajax example on our website.  http://www.chemaxon.com/ajax/

This example enables users to read, search, insert and save data for the example data tables on our server. 

If this fits the features you are looking for then you can follow the setup instructions for your MySQL tables using your own JChem Web Services Server.  http://www.chemaxon.com/webservices/ajax/setup.html

 

Jon

Jon,

thank you for such a fast reply.

i tried to have a look to the ajax example, but the page is not available - i guess is just a temporary problem, so i will try later.

I will follow the other link to set up MySQL tables - web services are installed so i need just to configure everything.

I will come back when other questions raise up.

Cheers,

Agata

Oops! There was an extra space at the end of the link.

http://www.chemaxon.com/ajax/

 

Also corrected it in the earlier post.

Hello,

The ajax example on your web server fits to what I am looking for.

We have set up MySQL tables using our own JChem Web Services Server as described at http://www.chemaxon.com/webservices/ajax/setup.html.

But now I am lost with the next step - getting the db from IJC to the web. I know I am green, but is there any tutorial how to do it?

Will the db then be available for multiple users or only one at the time? If we can make it for multiple would be great.

How do I define permissions - so that user A can enter data and save them in 3 fields, user B in other fields and so on up to 4 excluding me as adminitrator?

Thank you a lot and have a nice w-end,

Agata

 

Agata,

It seems like many of these questions revolve around the design of your own system. I can just offer a few suggestions.

Tips for getting your db to the web (though using the web services server): 

Be sure to read the admin guide.  http://www.chemaxon.com/webservices/adminGuide.html 

This will tell you about things like port numbers and any platform specific configurations due to your web-accessible machine (Unix, windows, etc.).  You may want toget it working on a local machine first and then try it out on a web-accessible machine, then adding users and privileges. 

Tips for users and privileges:

The Mysql database has the ability to have multiple users and certain table or column privileges. 

The Ajax example enables logging into the database using a specific username/password.  This can be achieved by omitting the username and password from the config.xml file which is used for all users of the app.  

The Ajax example does not have field (i.le. column) or row specific authorization built-in.  If you want to customize the example further, you can check out the Developers guide: http://www.chemaxon.com/webservices/ajax/index.html

Jon

Hello,

We have followed the admin
guide at  http://www.chemaxon.com/webservices/adminGuide.html 
and our web server is ready. We succeeded to import on it an sdf file and we
obtained a grid view (fig 1 in attachment).  

But we would like to
have on a web server our database in
grid and form views (fig 2 in attachment). Is there a different way than making always an sdf file?

We tried to export a
dbase from IJC via: File -- new
schema -- connect to
new schema and through this to a remote mysql database. Is this the right way
to get our database in the 2 views on a web server? I guess I need to promote
tables, since otherwise they do not appear on a web.

Or we need to follow
any of the following ways:

1. How to deploy Instant JChem using Java Web
   Start on your server


2.  How to
   access data in Instant JChem using URLs

Thank you,

Agata

Agata,

Congratulations on your current success.  

My colleagues are looking at your other questions.  

 

Jon

Hi Agata,

there is currently no way how to display the IJC forms on the web. We are working on the web client for Instant JChem which will be more sophisticated, but don't expect that before middle of the year.

I suggest to use Instant JChem application with shared project or connecting to MySQL database using Java Web Start for IJC.

Deploying JWS is pretty easy, only web server is needed, and can be done according this guide: http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/jws_deploy.html

Then all users can access the same IJC schema existing in remote MySQL(or Oracle) database using the same IJC version distributed via JWS.

Using shared projects is described on these pages:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/project_deploy.html />http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/ijc_urls.html

Data in shared project can be accessed via generated URLs, but you need to deploy it to an application server such as Tomcat. As an example of working demo, see http://www.chemaxon.com/urldemo/

Using shared project all users use the same IJC project uploaded on the server.

User policy for both options can be defined directly in IJC.

Let us know if you have further questions.

Filip

Agata,

I have moved your post to the IJC forum.

https://www.chemaxon.com/forum/ftopic8764.html

 

Thanks,

Jon