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Decommissioning a Pedon Database

This document discusses a procedure for decommissioning a pedon database. By that we mean, saving all of the data in a pedon database, and then dropping that database, permanently.

For the process of decommissioning a pedon database to prepare its data for conversion into NASIS, we are recommending that you save your pedon data in two different export formats. One way is via the export function of the pedon program. The other way is to do a dbexport (an Informix utility) of your pedon database. Some of you may have already decommissioned a pedon database and saved your data by using the pedon program export. If you have, this export will obviously have to suffice.

The first part of this document discusses the procedure for decommissioning a pedon database at length. A cookbook listing of these procedures is provided at the end of this document. If you need any help with the procedures described in this document, please contact either Tammy Cheever or Steve Speidel at the Soils Hotline at (402) 437-5379 and (402) 437-5378 respectively.

Before You Export Your Pedon Data

In our work in testing our pedon to NASIS conversion program, we found that at least one of the databases that provided our test data was corrupted. We didn't find this out until after the dbexport was performed. Fortunately there is an Informix utility (bcheck) to repair corrupted databases. It is safe to run this utility, even if your database is not corrupted. We recommend that you run this utility regardless of whether or not you think that your pedon database might be corrupted.

In order to run the Informix utility to repair a corrupted pedon database, as well as to be able to run the Informix utility dbexport, you must be logged in as “informix”, and your shell environment must be properly configured.

Two things are required to establish your Informix environment. The environmental variable INFORMIXDIR must contain the name of the directory where Informix is installed. This is typically /usr/informix or usr/informix5. The other environmental requirement is that the Informix bin directory must be in your path.

Example: Suppose that Informix was installed to /usr/informix5. The following commands, for Bourne shell, would establish the correct Informix environment.

INFORMIXDIR=/usr/informix5

export INFORMIXDIR

PATH=$INFORMIXDIR/bin:$PATH

export PATH

After you have established the correct Informix environment, you must determine where the pedon program was installed. This could be almost anywhere on your system, but we have often found it in /usr/sdis, /usr/soils/sdis or /soils/sdis.

Steve Speidel suggests that the easiest way to establish your Informix environment is to enter the following command:

. /usr/lbin/pedon (Bourne shell)

This command should establish both your Informix environment and a group of pedon program environmental variables. The environmental variable SDIS points to the root directory where the pedon program was installed.

From the directory where pedon was installed, cd into DBS/sdis.dbs. After you have positioned yourself in DBS/sdis.dbs, issue the following two commands:

bcheck -y *.idx

bcheck -y *.dat

Information will scroll across your screen as this utility runs. The -y option means “answer yes to all questions”, which means “yes, make any needed repairs”. Please remember that you must be logged in as “informix” to be able to run this utility. If you enter a bcheck command and your system responds with something to the effect “command not found”, your Informix environment is not properly configured. If you enter a bcheck command and your system responds with “Error: cannot open C-ISAM file”, you are not logged in as “informix”.

After you have completed this step, you can then do the following exports, in any order.

Naming Your Export Files

Please make sure the both resulting export files have exactly the same name prior to any file name extensions. If you do not do this, both exports might erroneously end up being converted into NASIS resulting in duplicate pedons.

The pedon program export utility restricts the name you select to 10 characters. Given this limitation, here is what we recommend.

As a general guideline, try to assign a file name with the following components:

The first 5 or 2 characters should be the soil survey area ID, for data from a project office, or the state alpha FIPS code for data from a state office.

The next 3 characters should be “pdp”. This will help identify this file as a pedon data export file.

The last character is an optional sequence number to distinguish between multiple export files created by the same office.

Example 1: The name for the pedon program export file from the Lancaster Co. NE project office would be “ne109pdp.arc”. The name for the dbexport export file from the Lancaster Co. NE project office would be “ne109pdp.tar.z”.

Example 2: The name for the pedon program export file from the Montana state office would be “mtpdp.arc”. The name for the dbexport export file from the Montana state office would be “mtdpd.tar.z”.

We will distinguish pedon program exports from dbexports from the same database by whether the file extension is .arc (pedon program) or .tar.z (dbexport process).

Export Process 1 - Using the Pedon Program

Before running this procedure, please make sure that you have completed the procedure described in the section titled “Before You Export Your Pedon Data”. Also, before you start this procedure, please run the utility named “cr_cleanup” in the sdis/bin directory. Steve Speidel of the Soils Hotline tells me that running this utility insures that the data you export will be able to be successfully imported.

  • After running “cr_cleanup”, fire up the pedon program and select “Transfer” from the main menu, and then select “Export Pedon Data”. Do this will bring up a dialog box.
     
  • In the dialog box, for “Records to export:”, select “All”.
     
  • For “Export to:”, select “File”.
     
  • For “Path name:”, you can either accept the default or enter the directory of your choice.
     
  • For “File name:”, enter the name you want to assign to the export file. (See the section titled “Naming Your Export Files”.) Do not provide a file extension. The resulting single file will be named “yournamehere.arc”, where “yournamehere” is the name that you provided.

Export Process 2 - Informix dbexport

Before running this procedure, please make sure that you have completed the procedure described in the section titled “BEFORE YOU EXPORT YOUR PEDON DATA”. This dbexport procedure will not work if you have not correctly established your Informix environment. Also, remember that in order to be able to run the Informix utility dbexport, you must be logged in as “informix”.

In order to run this utility, you must know the directory where the pedon program was installed. This could be almost anywhere on your system, but we have often found it in /usr/sdis, /usr/soils/sdis or /soils/sdis.

To run the dbexport utility, position yourself in a directory where you have write access. Make sure that a sub-directory by the name of “sdis.exp” does not already exist in that directory. Once you have done this, issue the following command:

dbexport /pedon_install_directory/DBS/sdis

Example: If the pedon program was installed in /usr/sdis, you would use the following comand:

dbexport /usr/sdis/DBS/sdis

This utility will then create a file by the name of “dbexport.out”, and a sub-directory by the name of “sdis.exp”, in your current working directory. Information will scroll across your screen as this utility is running.

Once the utility has finished, copy “dbexport.out” into “sdis.exp”, and then cd into “sdis.exp”.

Next, in the sdis.exp directory, create a text file named “readme.txt” with the following information:

Export file name prefix (the part of the name before .arc or .tar.z) This prefix should be common to the both the export file generated by the pedon program and the export file created by the dbexport process. (See the section titled “Naming Your Export Files”.)

  • Your name
  • Your phone number
  • Your e-mail address
  • The date that you created the export file
  • The location of the office that created this export
  • A narrative text description of the contents of this export

Now we are going to tar up and compress all of the individual files that dbexport created, and the “readme.txt” text file that you created, into a single compressed file using the following commands:

tar cf yournamehere.tar * (creates a file named “yournamehere.tar”)

pack -f yournamehere.tar (creates a file named “yournamehere.tar.z”)

What to do With Your Export Files

The program to convert your pedon data into NASIS is now operational. The window for converting your pedon data is from August 2000 until NASIS 5.0 is released, which is currently scheduled to be delivered near the end of 2000. Pedon data is being converted at the 17 MLRA offices. After you have prepared your pedon data for conversion, please transfer that data to your MLRA office.

If you have any questions about the procedures described in this document, please contact either Tammy Cheever or Steve Speidel at the Soils Hotline at (402) 437-5379 and (402) 437-5378 respectively.

How to Copy the Export Files to Diskette

Most sites that we have worked with are running a version of UNIX where the system administration utility FACE is available. FACE may be used to format a floppy diskette. In most cases, the address of the 3.5 inch floppy diskette has been /dev/rdsk/f03ht.

After you have formatted a floppy diskette, the files may be cpio'ed to diskette using the following command:

ls yournamehere.arc | cpio -ovcd -O/dev/rdsk/f03ht (for a pedon program export file)

or

ls yournamehere.tar.z | cpio -ovcd -O/dev/rdsk/f03th (for a dbexport export file)

Pedon Database Decommissioning Cookbook

  1. Log in as “informix”.
     
  2. Establish your Informix environment by setting INFORMIXDIR and making sure that $INFORMIXDIR/bin is in your path. The easiest way to do this is to enter the following Bourne shell command: . /usr/lbin/pedon
     
  3. Position yourself in the proper directory and run the two “bcheck” commands.
     
  4. Run the pedon utility “cr_cleanup”.
     
  5. Export all data from your pedon database using the Pedon program's export menu item, into a single file whose name follows our suggested naming conventions.
     
  6. Position yourself in a directory where you have “write” permission and run the Informix utility “dbexport”: dbexport /pedon_install_directory/DBS/sdis
     
  7. Copy “dbexport.out” into the “sdis.exp” directory.
     
  8. Position yourself in the “sdis.exp” directory and create the “readme.txt” file using the guidelines provided in this document.
     
  9. Tar up and pack the individual export files into a single file whose name follows our suggested naming conventions.
     
  10. Transfer your pedon data to your MLRA office for conversion to NASIS.
     
  11. You may optionally want to do something to insure that the pedon database for which you just created exports, is never used again to enter new pedons. The easiest way to insure this would be to delete everything from the directory where the pedon program was installed, including all sub-directories. You may wish to not do this until we have verified that your export files are OK.