missing tables from the list accessing to remote database

Hi

I just started evaluating IJC, so I am a novice user.   

I accessed to the remote database server from my IJC client and got a
warning message about the discrepancy of cartridge as follows. 

JChem table versions in IJC and the JChem Cartridge are different.

Many operations on cartridge indexes on JChemBase tables will fail.

If you use these sorts of table the your administrator should update IJC and/or
the JChem Cartridge so that they use the same JChem version.

Anyway, I continued to access and the connection was successfully
established.  However, it only displayed 20 tables, but is missing a lot
of tables/views.  Could you tell me what is controlling the list under
database on project pane. Is this due to the warning message I am
getting?  Or is there any way to expand the list?

By the way, I created IJC schema that contains no table/view. When I accessed to this
schema, it displayed pick-up schema window, but I see a blank text area on this. I would like to know how to configure this function to pick-up schemas from the list.  If I choose to directly access to
the schema that contains structure table with multi-user mode, it dose not
display this pick-up schema window anymore, but I only see the limited number of tables as mentioned above.

Thanks,

yasushi

Hi,

I have moved your question to the Instant JChem forum, my colleagues will answer here soon.

Best regards,

Szilard

Hi Yasushi

I accessed to the remote database server from my IJC client and got a

warning message about the discrepancy of cartridge as follows.  


JChem table versions in IJC and the JChem Cartridge are different.

...

This is a warning notifying you that the JChem version in IJC is different to that used by JChem cartridge. There are two ways in which JChem cartridge can be used, and a difference in the JChem versions impacts on of these:

1. cartridge indexes added to normal tables. These just have a cartridge index added to a column in a table that contains structures. For these types the interface between IJC and the cartridge is just plain SQL and the JChem versions in IJC and cartridge can be different. So these tables will work fine, even if the JChem versions are different.

2. cartridge indexes added to the structure column of a JChemBase table. For these the JChem API needs to be used and so the JChem versions must be the same in IJC and the cartridge. So for this reason, when the JChem versions are different this type of table/index is disabled, and you are warned about this.

Other than disabling the second type of table/index, this warning can be ignored. The first type is prefered anyway, and I believe that Takeda are only using the first type, but I can't be sure about this.

Anyway, I continued to access and the connection was successfully


established.  However, it only displayed 20 tables, but is missing a lot


of tables/views.  Could you tell me what is controlling the list under


database on project pane. Is this due to the warning message I am


getting?  Or is there any way to expand the list?

All tables and views in the default schema will be generally be displayed. You will see these in the Tables and Views tabs of the schema editor. There are some exceptions:

1. tables that are disabled due to a difference in the JChem version in IJC and cartridge, as explained above

2. tables that are part of set of tables associated a JChemBase of JChem cartridge index. e.g. the *_UL table associated with a JChemBase table, and the similar ones associated with a cartridge index. As these are "secondary" tables it never makes sense for the user to work with them

3. tables or views for when the oracle used does not have privileges.

By default only tables from the Oracle user's default scheme are present, but ones from additional schemas can be added using the ''Manage DB schemas' button in tables tab.

Do note however that although the tables and views may be present on the Tables and Views tab of the schema editor, they cannot be used in IJC until they are promoted to Entities and appear on the Entities tab. It may be the contents of the Entities tab you are referring to when you say that tables or views are missing. An Entity is IJC's representation of a table (or view), and has the additional information associated with it needed for IJC to work with it.

By the way, I created IJC schema that contains no table/view. When I accessed to this


schema, it displayed pick-up schema window, but I see a blank text 

area on this. I would like to know how to configure this function to 

pick-up schemas from the list. 

The term schema is used with two different meanings, which can be a bit confusing:

1. Database schema (as in a schema within oracle)

2. IJC schema, which means a connection to the database as a particular user.

What you did is to connect  to a new empty oracle schema, but the IJC schema had not yet been created in it, so there was no IJC schema to 'pick up'. What you need to do is to use the 'New schema' wizard rather than the 'Connect to schema' wizard. This will create a new IJC schema in that oracle schema (and in doing so create the IJC_* metadata tables that are used by IJC and initialise the IJC schema). Had that IJC schema already been created then you could have used 'Connect to schema' to start to use it (e.g. if you were wanting to use it from a different computer).

If in fact you are wanting to add an additional Oracle schema to the IJC schema that you are already using (so that IJC can use tables from both of the Oracle schemas) then you should instead use the ''Manage DB schemas' function in the schema editor wich wil allow you to access a second (or third...) oracle schema. If doing this you need to pay particualr attention to the privileges on those tables in the secondary schemas, particulalry for cartridge indexes. More information on this is contained in the Admin guide:
https://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/index.html

If any of this is not clear then please let us know, and we can arrange a webex to help explain this further.

Tim

I accessed to the remote database server from my IJC client and got a

warning message about the discrepancy of cartridge as follows.  


JChem table versions in IJC and the JChem Cartridge are different.

...

Anyway, I continued to access and the connection was successfully


established.  However, it only displayed 20 tables, but is missing a lot


of tables/views.  Could you tell me what is controlling the list under


database on project pane. Is this due to the warning message I am


getting?  Or is there any way to expand the list?

By the way, I created IJC schema that contains no table/view. When I accessed to this


schema, it displayed pick-up schema window, but I see a blank text 

area on this. I would like to know how to configure this function to 

pick-up schemas from the list. 

Hi Tim

Okay, I created ijc schema: tables contain IJC_ * tables and jchemproperties by  new schema function.  Then, used the same schema name to connect to database: db user/db password, then I tried to import an SDF file, but it does not allows me to import it by  telling me that insufficient access rights.  I do not see any tables/views in any tabs after connecting to ijc.

What kind of access rights are quired to import an SDF file? And then, is there any scripts I need to run to create tables to import SDF (nci_drugs.sdf) for demo?  And also, I do not see "Manage schema" function.

Could you tell where I can find a info to replicate demo tables into remote database?

Thanks,

ok, I created my own structure table and tried to promote it to entity, but again it is generating the error saying:

New entity creation failed: Cannot perform adding new entity. You have insufficient access rights to modify database model. 

So, could you tell me what kind of access required for this operation? 

Thanks,

yasushi

Hi,

this is all a bit complicated as its not exactly clear what you have done. I think setting up a  webex to look at this directly will be the fastest approach. I will contact you separately about this.

But the problem is that the IJC user you are using does not have sufficient rights to modify the database model. I expect you are not getting the prompt when you connect which lets you enter "single user mode" as you do not have sufficient rights to enter this mode. Only with these rights and in "single user mode" can you modify the database model (e.g create or delete tables etc.). This is to prevent one user deleting a table that is in use by another user, and other equally nasty things.

You should look at the way security is implemented for the IJC schema, and make sure that the IJC user you are using has ROLE_EDIT_SCHEMA role.

But I think there may be other issues related to how the IJC schema was created in the first place ('New schema' vs. 'Connect to schema') that might also be causing problems. We can look at this better in a webex.

Tim