Applied Biosystems SQL*LIMS Technical Support Technical Note Document Number: LIMS013 Last Revised: 7/22/2003 Software Versions: SQL*LIMS v4.0.16 and v4.1 Platform: Sun Solaris and HP-UX Author: Deborah Man Subject: How to configure the SQL*LIMS slbfile directory to store attachments externally on a Unix server. Introduction The SQL*LIMS application allows attachments to be created and attached to various template and instance records. The file types of these attachments can be text, Microsoft Excel tabdelimited, Microsoft Word, HTML, PDF, and JPG files, as well as videos and other file types. These documents are stored internally in the SQL*LIMS database in the datafiles of the Multimedia tablespace. Documents can also be stored externally in a particular slbfile directory. The slbfile directory usually resides on the SQL*LIMS server, but it can be on the application server or database server of a three-tier environment. You configure the location during SQL*LIMS installation. Common Error Message If you try to attach a document externally in SQL*LIMS, you might get the following error message: "PEN-11006: The file specified cannot be copied"
This error message might be caused by incorrect setup of the slbfile directory, network logon authentication problems, or file sharing problems across various operating system platforms. The problem is even more complicated to troubleshoot and resolve if a Unix server is involved, because the documents attached and viewed on a Windows client machine have to be shared across different OS platforms transparently. File Sharing Software Many file-sharing software applications are available to exchange files across OS platforms. SAMBA is an open source, free software suite installed on a Unix or Linux server to provide seamless file and print services to Windows-based clients. The HP-UX 11i operating system is bundled with an optional product CIFS/9000 software that runs on top of SAMBA. PC NetLink comes bundled with the Sun Solaris 8 operating system and provides functions similar to those of SAMBA to allow Windows users to access certain directories on Solaris server. To determine the appropriate file sharing utility to use on a Unix server, consult your System Administrator or visit the related websites for more information. Focus of this Technical Note This technical note outlines the proper process to configure the slbfile directory on a Unix server so that external documents can be attached, viewed, edited and deleted where appropriate. The whole process is explained step-by-step so that you can troubleshoot if necessary. In the following example, MINYA is a v4.016 SQL*LIMS server on a two-tier server-client environment and is a Sun Solaris server loaded with the SAMBA file-sharing utility. Procedure 1. The slbfile directory was configured during SQL*LIMS installation. Run the following SQL*Plus queries to verify that this directory has been set up correctly on the SQL*LIMS server: a. Log into the SQL*LIMS database as the LIMS owner: SQL> select * from all_tab_privs where table_name = 'SLBFILE'; An example output might look like this: GRANTEE GRANTOR TABLE_SCHEMA TABLE_NAME PRIVILEGE GRANTABLE SYS SYS SLBFILE READ YES PUBLIC SYS SLBFILE READ YES LIMSUSERA LIMSUSERB LIMSUSERC LIMSUSERD LIMSUSERE LIMSUSERF LIMSUSERG LIMSUSERH LIMSUSERI
The LIMS owner, all SQL*LIMS users (in terms of LIMSUSERX), and the 'PUBLIC' account should have the READ privilege to the SLBFILE table. b. To find any SQL*LIMS users with restricted access to the slbfile directory: SQL> select * from nai_users where accessid not in (select grantee from all_tab_privs where table_name = 'SLBFILE'); The expected output of this query should be 'no rows selected', but if a particular SQL*LIMS user appears in the output, investigate and, where appropriate, grant this user the 'READ' privilege to the SLBFILE directory. c. To find the exact location of the slbfile directory on the SQL*LIMS server: SQL> select * from dba_directories; OWNER DIRECTORY_NAME DIRECTORY_PATH SYS SLBFILE /minya/sqllimssvr/lims4016/slbfile Note: For multiple instances, several slbfile directories co-exist, such as slbfile for the primary instance, slbfile2 for the secondary instance, and slbfile3 for a third instance. Be sure to look at the instance-specific slbfile directory. 2. Install SAMBA on the Solaris server, MINYA. Consult the System Administrator or follow the correct instructions to install the appropriate file-sharing utility on the server. 3. Verify that both the smbd and nmbd daemons for SAMBA are running: minya% ps -ef grep samba root 731 1 0 07:30:42? 0:00 /usr/local/samba/bin/smbd-d-/usr/local/samba/lib/smb.conf root 733 1 0 07:30:43? 0:00 /usr/local/samba/bin/nmbd-d-/usr/local/samba/lib/smb.conf. 4. Set up the SAMBA configuration file (smb.conf) correctly. The suggested smb.conf file below requires no authentication of network logon, so every workstation and user can connect to the SAMBA share directory directly.
A correctly configured smb.conf file looks like this: # Global parameters [global] workgroup = abisj netbios name = minya server string = Samba Server security = share password server = encrypt passwords = no socket options = tcp_nodelay log file = /usr/local/samba/var/log.%m domain logons = no preferred master = no local master = yes domain master = no dns proxy = no wins support = no wins server = 164.113.90.15 wins proxy = no [homes] comment = Home Directories path = /opt/samba.files/homes guest account = guest ok = Yes [public] comment = Public Stuff path = /opt/samba.files/public read only = No [slbfile] comment = SQLLIMD SLB SHARE DIRECTORY path = /minya/sqllimssvr/lims4016/slbfile public = yes browseable = yes writeable = yes read only = no guest ok = yes 5. Log into a Windows client machine as a SQL*LIMS user and, at Command Prompt, use the "ping" command to verify the connection between the client and the Unix server: C:> ping minya The output should confirm the network connection with the IP address assigned to the server MINYA.
6. On the client machine, at Command Prompt, run \\<server name> to view all shared directories: C:> run \\minya 7. On the client, map a network drive to the server slbfile directory: Please note that the folder name, slbfile, should match with the SAMBA share directory and also the name assigned to the slbfile directory in SQL*LIMS.
If slbfile2 is the directory set up for the secondary SQL*LIMS instance on the same server, map the drive to folder: \\Minya\slbfile2. At the same time, verify the same share name in samb.conf (and in SQL*LIMS), like this: [slbfile2] comment = SLB SHARE DIRECTORY for Secondary instance path = /minya/sqllimssvr/lims4016/slbfile2 public = yes browseable = yes writeable = yes read only = no guest ok = yes In SQL*Plus, log into the secondary instance and enter the following command: SQL> select * from dba_directories; OWNER DIRECTORY_NAME DIRECTORY_PATH SYS SLBFILE2 /minya/sqllimssvr/lims4016/slbfile2 8. Launch the SQL*LIMS client and attach an external attachment as 'Copy Document' or 'Reference Document'. In this example, attach a document to the Define Sample Plans form. a. Select Template > Plans > Sample Plans, then enter (or query for) a Sample Plan. b. Click the icon on the toolbar to bring up the 'Edit Attachments' sub-menu. c. Check radio button 'Attachment'.
d. Check either 'Copy Document' or 'Reference Document'. e. Check radio button 'External Storage'. f. Select the correct 'SLBFILE' directory name in the 'Change Default' field. In a multiple instances server, make sure the name selected in this field matches the slbfile directory name for the connecting instance and is the SAMBA share name. g. Click the yellow browse icon to search for the file on the client machine to attach. h. Click the 'Open' button to launch the document on another screen for confirmation. i. Close the document window. The file path for this document is pasted in the File Name field.
j. Click OK. The document is saved in the slbfile directory on the server. 9. Log onto the SQL*LIMS server as the root account and verify that the external document can be found in the slbfile directory, for example: minya% cd /minya/sqllimssvr/lims4016/slbfile minya% ls -al -rwxr--r-- 1 nobody nobody 21 Jun 11 07:11 100010295_1.TXT -rwxr--r-- 1 nobody nobody 21504 Jun 12 14:41 100010313_1.DOC -rwxr--r-- 1 nobody nobody 26 Jun 11 07:11 100010314_1.TXT -rwxr--r-- 1 nobody nobody 21 Jun 11 07:11 100010333_1.DOC -rwxr--r-- 1 nobody nobody 13824 Jun 13 08:05 100010336_1.XLS -rwxr--r-- 1 nobody nobody 211496 May 5 12:32 100010337_1.JPG -rwxr--r-- 1 nobody nobody 75594 May 1 15:37 100010338_1.PDF -rwxr--r-- 1 nobody nobody 65439 Jun 13 08:22 100010340_1.HTM -rwxr--r-- 1 nobody nobody 23 Jul 15 10:25 100010863_1.TXT In the above example, the documents are saved by 'nobody' since logon authentication is not enforced. The file names are displayed in the format of <document_id>_version.filetype, instead of the original filename seen on the client machine.
10. External attachments can be viewed and edited in the Template menu, but a reference document cannot be modified or updated in instance records. In order to view an external attachment, follow the steps below: a. Go to the proper menu form on the client machine, e.g., Define Materials Form. b. Click the paper clip or the Browse Attachments icon on the top toolbar. c. Select the document to view on the 'Attachments' field by clicking the 'Down' button. d. Click the 'View' button. The document appears in another window. e. After viewing, close the document and close the 'Browse Attachment' menu. In v4.016, it is common for the client machine to get the following error messages when viewing:
The problem is that the TEMP or TMP path environment variable on the client machine exceeds 26 characters as specified in the form design for that release. When the document is pulled from the server, a copy of the document is put on the TEMP or TMP path of the client machine before it can be shown on the screen. By default, on Windows 2000, the TEMP and TMP path are set using the environment variable %USERPROFILE%. The file path and the document_id added together can exceed 26 characters, for example: TEMP = %USERPROFILE%\Local Settings\Temp\100010822.doc TMP = C:\Document Settings\PENLIMS\Local Settings\TMP\100010822.doc In order for SQL*LIMS v4.016 attachments to be viewed and edited correctly, change the TEMP or TMP environment variable to a shorter length and reboot the client machine to take effect. TEMP = C:\TEMP TMP = C:\TMP 11. To edit an external attachment, follow these steps: a. Go to the proper menu form on the client machine, e.g., Define Sample Plan Form. b. Click the icon to bring up the 'Existing Attachments' sub-menu. c. Highlight the document you would like to edit and then click the 'New' button.
d. The 'Edit Attachments' sub-menu appears. e. Check the correct radio buttons as mentioned in step 8 above to select another document: f. Close the document. The document path is pasted in the File Name field.
g. Click OK to save. h. The 'Existing Attachments' sub-menu appears. Highlight the modified attachment and click the 'Edit' button. i. The modified document appears in another window with document_id assigned instead of its original file name. j. Close this document. The 'Edit Binary Attachment' prompts to confirm:
k. Click Yes. The document version changes to 2 on the 'Existing Attachments' sub-menu. l. Commit the changes and then close the 'Existing Attachments' sub-menu. Exit the form. 12. To delete an external attachment in Template Menu, follow these steps: a. Select Template > Plans > Sample Plans, enter (or query for) a Sample Plan. b. Click the icon on the toolbar to bring up the 'Edit Attachments' sub-menu. c. Highlight the document to delete.
d. Click the toolbar 'Record' button and then the 'Delete' option. The document is removed from the 'Existing Attachments' sub-menu. A confirmation appears at the bottom of the window verifying the changes. 'FRM-40400: Transaction complete: 2 records applied and saved.'