check javacod in mrgridservlet - in_recoord should be empty or 'recoord'

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The first step here is for me to figure out how to display the three columns: 
bmrb_id, in_recoord, 
and in_dress.

Original issue reported on code.google.com by schulte....@gmail.com on 1 Oct 2009 at 8:01

Attachments:

• [Picture 1.png](https://storage.googleapis.com/google-code-attachments/nmrrestrntsgrid/issue-229/comment-0/Picture 1.png)

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I see. These are shown by default on tang if you choose all converted entries 
and then click on the STAR link. I 
will see what's up with this.

Original comment by schulte....@gmail.com on 1 Oct 2009 at 8:04

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Thanks Chris!

Original comment by jurge...@gmail.com on 2 Oct 2009 at 7:33

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There are no appreciable differences in the code between tang and grunt. I'm 
looking at the databases.

It doesn't look like the fields bmrb_id, in_recoord, and in_dress are being set 
on grunt.

e.g.
| entry_id | bmrb_id | pdb_id | in_recoord | in_dress |
tang:
|     1196 |    4430 | 1a03   |       NULL |     NULL |
...
|     7145 |    NULL | 108d   |          0 |        0 |   << has the word 
'false' where it shouldn't
grunt:
|     1006 |    NULL | 1a03   |          0 |        0 |
|     1001 |    NULL | 108d   |          0 |        0 |

any pointers?

Original comment by schulte....@gmail.com on 2 Oct 2009 at 5:35

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Consider fixing the issue by either extending the java code to map more cases 
to an empty string or by manually 
changing the db fields.

Original comment by jurge...@gmail.com on 3 Oct 2009 at 8:59

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I think I made a couple of small changes that should fix this, but the setup on 
tang is different than grunt. Do 
you know where I need to place the .war file to get the changes to show up?

Original comment by schulte....@gmail.com on 5 Oct 2009 at 5:09

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The webapp location is given in the doc:
http://code.google.com/p/nmrrestrntsgrid/source/browse/trunk/nmrrestrntsgrid/Doc
umentation/tomcat_setup
_instructions.txt

Can you or D. write one for grunt?

Original comment by jurge...@gmail.com on 6 Oct 2009 at 7:48

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It seems to be fixed now.

http://tang/NRG/MRGridServlet?block_text_type=3-converted-DOCR&db_username=watto
s1&file_detail=3-
converted-DOCR&program=STAR&request_type=block_set

Is it possible to edit the instructions without doing a full checkout? It's not 
a wiki.

One thing I found is that the command '/etc/init.d/tomcat5 restart' had to be 
changed to 
'/etc/init.d/tomcat5 stop' followed by '/etc/init.d/tomcat5 start'.

Original comment by schulte....@gmail.com on 6 Oct 2009 at 2:53

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>Is it possible to edit the instructions without doing a full checkout? 
>It's not a wiki.

Good idea to move it to a wiki.

In comparison to the comment 1 image. It looks like now the information is no 
longer shown at all!
The attached is from:
http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet?block_text_type=3-converte
d-
DOCR&db_username=wattos1&file_detail=3-converted-
DOCR&format=n%2Fa&program=STAR&request_type=block_set&subtype=full&type=entry&pa
ge_id=1

Can you fix this or was it only done on tang yet?

Original comment by jurge...@gmail.com on 7 Oct 2009 at 9:54

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Attachments:

• [Picture 1.png](https://storage.googleapis.com/google-code-attachments/nmrrestrntsgrid/issue-229/comment-8/Picture 1.png)

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I saw this before and noted it in comment #3:
"It doesn't look like the fields bmrb_id, in_recoord, and in_dress are being 
set on grunt."

The differences in the code on tang and grunt were negligible and I don't know 
what the issue was. 

It turned out that my fix yesterday on tang broke something so that data could 
not be retrieved. The variable 
dbfs_root was sometimes accessing /big/jurgen/DB/mrgrid, and sometimes 
/Users/jd/Clonewars/mrgrid. I 
fixed that. Images are not showing up on tang, but the logfiles aren't saying 
what is wrong. I'll look into it.

Should I commit the changes I made on tang and update grunt from there? 

Original comment by schulte....@gmail.com on 7 Oct 2009 at 6:11

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There must be some code in Wattos that sets the info. Can you grep for it in 
the java code and see if you can 
run it?

Original comment by jurge...@gmail.com on 7 Oct 2009 at 8:50

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> There must be some code in Wattos that sets the info.

That's not particularly helpful, Jurgen. I have been grepping and will continue 
to do so. 

The images on tang have been fixed. Is it OK to go ahead and commit the 
changes? I have to get going, but will 
start up on this first thing tomorrow.

Original comment by schulte....@gmail.com on 7 Oct 2009 at 9:14

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Grep for in_recoord and the first program that comes up in Eclipse is 
MRUpdateLinksToExternalDBs.java

I'm not sure what you want to commit but go ahead and I'll check if you like.

Original comment by jurge...@gmail.com on 8 Oct 2009 at 9:05

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I just ran MRUpdateLinksToExternalDBs and described it in the wiki: 
http://code.google.com/p/nmrrestrntsgrid/wiki/UpdatingLinksToBMRB_Etc

Original comment by jurge...@gmail.com on 2 Nov 2009 at 11:33

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Dimitri, can you check if the info on Grunt get's mirrored out to swordfish.
When is the mirroring done exactly?

There should be a link visible in NRG for PDB entry 1brv to RECOORD and BMRB id 
4020.

Original comment by jurge...@gmail.com on 2 Nov 2009 at 11:38

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> When is the mirroring done exactly?

It's a 2-step process. Whatever's in /website is mirrored to public servers 
every
night. Stuff is exported to /website whenever Chris does it.

Original comment by dmitri.m...@gmail.com on 2 Nov 2009 at 5:11

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Go ahead and update the servlet code so in_recoord etc. shows up too.

Original comment by jurge...@gmail.com on 12 Nov 2009 at 2:58

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done and D. also optimized mysql settings with caching enabled.
It's much faster now.

Original comment by jurge...@gmail.com on 19 Nov 2009 at 9:06

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