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⇤ ← Revision 1 as of 2019-03-28 16:15:35
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| Interbull Centre is providing a convert program to help member organizations with a smooth transition from the old file formats to the new XML based file format that will be used when uploading performance data to the Interbull Centre from now on: |
Interbull Centre is providing a convert program to help member organizations with a smooth transition from the old file formats to the new XML based file format that will be used when uploading performance data to the Interbull Centre from now on: |
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| The program will be available for download in IDEA and can be run by an overall script if so desired.<<BR>> ''Note that the support provided by the Interbull Centre of the program is time limited and ends at the end of 2019, but it will still be available for download after that, just not with any support.'' |
The program will be available for download in IDEA and can be run by an overall script if so desired.<<BR>> ''Note that the support provided by the Interbull Centre of the program is time limited and ends at the end of 2019, but it will still be available for download after that, just not with any support.'' |
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| (If you have a choice, prefer Python3 over Python2) | . (If you have a choice, prefer Python3 over Python2) |
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| The shown commands assume that the working directory in point b above, is used as current directory, i.e. start by calling `cd <name of directory>` (once) before running the commands shown below. |
The shown commands assume that the working directory in point b above, is used as current directory, i.e. start by calling `cd <name of directory>` (once) before running the commands shown below. |
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| Arguments within square brackets (i.e. `[]`) are optional to specify.<<BR>> Arguments are meant to be specified in the order indicated.<<BR>> All arguments with a name that ends in "file" are supposed to be a filename that may be either relative (i.e. relative to the current directory) or absolute (i.e. it starts with a slash) | |
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| Arguments within square brackets (i.e. `[]`) are optional to specify.<<BR>> Arguments are meant to be specified in the order indicated.<<BR>> All arguments with a name that ends in "file" are supposed to be a filename that may be either relative (i.e. relative to the current directory) or absolute (i.e. it starts with a slash) |
The `-t` argument is used when no output is desired, i.e. only test the input files for correctness. |
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| The `-t` argument is used when no output is desired, i.e. only test the input files for correctness. |
The `-v` argument shows additional information that are sometimes useful, but for normal usage it is recommended to '''not''' use it. |
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| The `-v` argument shows additional information that are sometimes useful, but for normal usage it is recommended to '''not''' use it. |
If neither the `-t` argument nor the `-o` argument has been provided, the generated XML data is put in a file in the current directory named `out.xml` (i.e. it behaves as if `-o out.xml` was specified on the command line). |
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| If neither the `-t` argument nor the `-o` argument has been provided, the generated XML data is put in a file in the current directory named `out.xml` (i.e. it behaves as if `-o out.xml` was specified on the command line). |
The program need to behave differently for traits that are calving or not, so a mechanism (`-C` and `-N` arguments) has been provided to explicitly control which behaviour is needed. If neither of these arguments has been provided, the behaviour is selected based on the name of the trait (that is retrieved from the 603 file). |
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| The program need to behave differently for traits that are calving or not, so a mechanism (`-C` and `-N` arguments) has been provided to explicitly control which behaviour is needed. If neither of these arguments has been provided, the behaviour is selected based on the name of the trait (that is retrieved from the 603 file). |
Running this will show a brief description of how to run the program if you need a reminder: |
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| Running this will show a brief description of how to run the program if you need a reminder: |
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| === Output From the Program === If no problems are discovered in the input files, the following message will be written, for example for aww trait: |
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| === Output From the Program === If no problems are discovered in the input files, you should simply see this (or something very similar): |
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| and an out.xml will be produced, either in the working directory or in the specified target directory. | |
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| If problems are discovered, the above will be followed by one or more messages each trying to describe what the problem is and where it was discovered. If the number of problems discovered is too great, a message to that effect is shown and the program terminates immediately. |
If problems are discovered, the above message will be followed by one or more messages each trying to describe what the problem is and where it was discovered. If the number of problems discovered is too great, a message to that effect is shown and the program terminates immediately. No xml file will be created untill all problems are fixed. Here a list of the most common errors found in the data and the actions needed to correct them. |
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| Syntax of the 605 file, 605awwDlim.che(1), do not follow the specification Data: 605 LIMFRAM008795002134 89 CHE. |
Syntax of the 605 file, 605awwDlim.cou(1), do not follow the specification Data: 605 LIMFRAM008795002134 89 COU. |
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This message specifies that the 605awwDlim.che file (on line 1) has data that do not follow the expected format of this type of file (i.e. 605 format files).<<BR>> The "Data" line shows what is there, and the "RX" line shows what is expected to be found.<<BR>> In this case it shows that one column of data is missing in the file. |
This message specifies that the 605awwDlim.cou file (on line 1) has data that do not follow the expected format of this type of file (i.e. 605 format files).<<BR>> The "Data" line shows what is there, and the "RX" line shows what is expected to be found.<<BR>> In this case it shows that one column of data is missing in the file. |
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| Syntax of the 605 file, 605caeDlim.irl(1425), do not follow the specification Data: 605 LIMFRAM001295161096 10010 IRL. |
Syntax of the 605 file, 605caeDlim.cou(1425), do not follow the specification Data: 605 LIMFRAM001295161096 10010 COU. |
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This message specifies that the 605caeDlim.irl file (on line 1425) has data that do not follow the expected format of this type of file (i.e. 605 format files).<<BR>> In this case it shows that one column delimiter is "0" instead of " ". |
This message specifies that the 605caeDlim.cou file (on line 1425) has data that do not follow the expected format of this type of file (i.e. 605 format files).<<BR>> In this case it shows that one column delimiter is "0" instead of " ". |
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| The 602 file, filebwtlim.cze(1720), animal LIMCZEF000000104735 has inconsistent (illegal - discarded) name of calf: 'UUUUUUUUUUUUUUUUUUU' | Syntax of the 602 file, fileawwlim.cou, do not follow the specification Data: 602 AWW LIM COU LIMFRAF008609359309 1 0 COU000360047467 308 27 7992 2 1550 302500 220 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 100 0 0 0 0. RX : tail too short, is 548, expected 567 |
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| This shows that the length of the records in the file fileawwlim.cou are shorter than expected given the overall number of fixed effects reported (total number of fixed effects*21) | |
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| This shows that the file filebwtlim.cze, on line 1720, has the specification of a calf with no useful name of it's own though the name of the dam is provided. This specification has thus been discarded.<<BR>> This message is not really a problem report but rather an informational message and thus will not cause termination due to too many problems found. |
==== Example message 4 ==== {{{ The 602 file, filebwtlim.cou(1720), animal LIMCZEF000000104735 has inconsistent (illegal - discarded) name of calf: 'UUUUUUUUUUUUUUUUUUU' }}} This shows that the file filebwtlim.cou, on line 1720, has the specification of a calf with no useful name of it's own though the name of the dam is provided. This specification has thus been discarded.<<BR>> This message is not really a problem report but rather an informational message and thus will not cause termination due to too many problems found. '''Example message 5''' {{{ Duplicate: 602 CAE BSM COU BSMCZEF000002764617 1 0 CZE003200397411 1 9 1368 BSMDNKM000415240598 1 19990828 BSMCZEM000110893384 1 43 1849 1999 *Duplicate: 602 CAE BSM COU BSMCZEF000002764617 1 0 CZE003200397411 1 9 1368 BSMDNKM000415240598 1 19990828 BSMCZEM000110893384 1 43 1849 1999 1 }}} This shows presence of a duplicate record in a given file (in this case file602). Duplicate records are ignored by the program so they do not really represent a problem per se, but a warning is issued. |
Contents
General information
Interbull Centre is providing a convert program to help member organizations with a smooth transition from the old file formats to the new XML based file format that will be used when uploading performance data to the Interbull Centre from now on:
convert_performance.py ==> converts a set of the old flat file (602, 603, 604 and 605) formats to the corresponding new XML based performance file
The program will be available for download in IDEA and can be run by an overall script if so desired.
Note that the support provided by the Interbull Centre of the program is time limited and ends at the end of 2019, but it will still be available for download after that, just not with any support.
Before Running the Program
a. Install Python (either Python3, version 3.4.8 or later, or Python2, version 2.7.5 or later) if necessary
- (If you have a choice, prefer Python3 over Python2)
- b. Create a working directory/folder
- c. Copy the python program to the new directory
- d. Copy the files you want to convert to the working directory (This is optional. The path to the files can also be written by the prompt as /path/filename)
Executing the Program
The shown commands assume that the working directory in point b above, is used as current directory, i.e. start by calling cd <name of directory> (once) before running the commands shown below.
Synopsis of how to run the program:
python3 convert_performance.py [-t] [-v] [-o destfile] [-C | -N] 602file 603file [604file [D605file [M605file]]]
Arguments within square brackets (i.e. []) are optional to specify.
Arguments are meant to be specified in the order indicated.
All arguments with a name that ends in "file" are supposed to be a filename that may be either relative (i.e. relative to the current directory) or absolute (i.e. it starts with a slash)
The -t argument is used when no output is desired, i.e. only test the input files for correctness.
The -v argument shows additional information that are sometimes useful, but for normal usage it is recommended to not use it.
If neither the -t argument nor the -o argument has been provided, the generated XML data is put in a file in the current directory named out.xml (i.e. it behaves as if -o out.xml was specified on the command line).
The program need to behave differently for traits that are calving or not, so a mechanism (-C and -N arguments) has been provided to explicitly control which behaviour is needed. If neither of these arguments has been provided, the behaviour is selected based on the name of the trait (that is retrieved from the 603 file).
Running this will show a brief description of how to run the program if you need a reminder:
python3 convert_performance.py -h
Output From the Program
If no problems are discovered in the input files, the following message will be written, for example for aww trait:
Running convert_performance.py version 2019-03-26 v1.17 Trait aww is not calving.
and an out.xml will be produced, either in the working directory or in the specified target directory.
If problems are discovered, the above message will be followed by one or more messages each trying to describe what the problem is and where it was discovered. If the number of problems discovered is too great, a message to that effect is shown and the program terminates immediately. No xml file will be created untill all problems are fixed.
Here a list of the most common errors found in the data and the actions needed to correct them.
Example message 1
Syntax of the 605 file, 605awwDlim.cou(1), do not follow the specification Data: 605 LIMFRAM008795002134 89 COU. RX : 605 ................... .. .. ...
This message specifies that the 605awwDlim.cou file (on line 1) has data that do not follow the expected format of this type of file (i.e. 605 format files).
The "Data" line shows what is there, and the "RX" line shows what is expected to be found.
In this case it shows that one column of data is missing in the file.
Example message 2
Syntax of the 605 file, 605caeDlim.cou(1425), do not follow the specification Data: 605 LIMFRAM001295161096 10010 COU. RX : 605 ................... .. .. ...
This message specifies that the 605caeDlim.cou file (on line 1425) has data that do not follow the expected format of this type of file (i.e. 605 format files).
In this case it shows that one column delimiter is "0" instead of " ".
Example message 3
Syntax of the 602 file, fileawwlim.cou, do not follow the specification Data: 602 AWW LIM COU LIMFRAF008609359309 1 0 COU000360047467 308 27 7992 2 1550 302500 220 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 100 0 0 0 0. RX : tail too short, is 548, expected 567
This shows that the length of the records in the file fileawwlim.cou are shorter than expected given the overall number of fixed effects reported (total number of fixed effects*21)
Example message 4
The 602 file, filebwtlim.cou(1720), animal LIMCZEF000000104735 has inconsistent (illegal - discarded) name of calf: 'UUUUUUUUUUUUUUUUUUU'
This shows that the file filebwtlim.cou, on line 1720, has the specification of a calf with no useful name of it's own though the name of the dam is provided. This specification has thus been discarded.
This message is not really a problem report but rather an informational message and thus will not cause termination due to too many problems found.
Example message 5
Duplicate: 602 CAE BSM COU BSMCZEF000002764617 1 0 CZE003200397411 1 9 1368 BSMDNKM000415240598 1 19990828 BSMCZEM000110893384 1
43 1849 1999
*Duplicate: 602 CAE BSM COU BSMCZEF000002764617 1 0 CZE003200397411 1 9 1368 BSMDNKM000415240598 1 19990828 BSMCZEM000110893384 1
43 1849 1999
1This shows presence of a duplicate record in a given file (in this case file602). Duplicate records are ignored by the program so they do not really represent a problem per se, but a warning is issued.