|
Size: 7483
Comment:
|
Size: 6447
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| . A Python program called CheckProofsPara.py will check the 300/700 proof file format and the associated 301/701 parameter file for format correctness against the IDEA EBV User Manual Appendix II. The program prepares a zip file,IB-ORGCODE-IG-yyymmddThhmmss.zip for conventional MACE and IB-ORGCODE-GG-yyymmddThhmmss.zip for GMACE,if no errors are found in the file. The zip file contains the input proof and parameter files, renamed to proof.dat and param.dat, respectively. The program requires access to the internet and specifically to few functions/pages in the IDEA web application. Firstly, in order to ensure that the user has the most recent version of the software, the program checks its internal version with the version stored on the Interbull server. If there is a mismatch in versions, a message is printed and the program exits and the program must be re downloaded. Lists of valid orgcode’s and breed-pop-trait combinations for which the user’s organization has EBV upload authority are also obtained from the IDEA web application. If errors occur they are listed to the screen and no zip file is created. The zip file represents your checked data file to upload to the Interbull Centre IDEA database (https://idea.interbull.org/). For technical reason the program rejects files containing more than a million of data. | |
| Line 5: | Line 6: |
| A Python program called CheckProofsPara.py will check the 300/700 proof file format and the associated 301/701 parameter file for format correctness and prepare a zip file for upload if no errors are found in the files. Each record in the proof file has associated information for a single brd-pop-trt combination. One file may contain records for as many or few brd-pop-trt combinations as desired. It may be natural for organizations to include all traits in a trait group in the same file, as they have in the past, but this is not essential. They may also choose to upload evaluations for all breeds, populations and traits in a single file if they find that more convenient. Every proof file must be accompanied by a parameter file!. The records in the parameter file give information about the national evaluations that is common to all records in the proof file for a given brd-pop-trt combination. There must be a record in the parameter file for each brd-pop-trt combination present in the proof file. A proof file may contain only conventional (300) or only GEBV (700) records, not both. CheckProofsPara.py will fail if both record types are found in one file. If no errors are found, a zip file is created with the name IB-ORGCODE-IG-yyymmddThhmmss.zip (for conventional MACE) or IB-ORGCODE-GG-yyymmddThhmmss.zip (for GMACE) containing the input proof and parameter files, renamed to proof.dat and param.dat, respectively. |
When checking the proof file only the first 10 errors of each type are listed. |
| Line 10: | Line 8: |
| CheckProofPara.py will perform a series of checks on your performance and parameter data to insure that the data is all right. If no errors are detected then a zip file will be created. The zip file represents your checked data file to upload to the Interbull Centre IDEA database. For technical reason the program rejects files containing more than a million of data. The checks performed on the parameter file relate to: * Check correct record type (301) and record length (46) * Check correct use of breed abbreviation as reported in the IDEA EBV User Manual, Appendix II * Check correct use of population codes as reported in the IDEA EBV User Manual, Appendix II * Check correct use of trait codes as evaluated at ITBC and reported in the IDEA EBV User Manual, Appendix II * Check that the organization has upload authority for the 'brd;pop;trt' combination, fetched from IDEA * Check that the other information in the file are according to the specification reported in the IDEA EBV User Manual, Appendix II The checks performed on the proof file relate to: * Check correct record type (300) and record length (85) * Check that correct values for type of proofs are used according to what reported in the IDEA EBV User Manual, Appendix I * Check that correct publication codes are used according to what reported in the IDEA EBV User Manual, Appendix I * Check that correct values for bull status are used according to what reported in the IDEA EBV User Manual, Appendix I * Check that the 'brd,pop,trt' combination has also an entry in the parameter file. * Check that the other information in the file are according to the specification reported in the IDEA EBV User Manual, Appendix I === Before Running the Programs: === 1. Install [[http://www.python.org|Python]] (version 2.5 to 2.7) if necessary 1. Create a working directory/folder 1. Download the !CheckProofPara.py program from https://idea.interbull.org/software and copy it to your new directory 1. Copy your proof and parameter file to the working directory === Running the Program: === * Ensure there is a working network connection Execute: python26 CheckProofsPara.py -m <ORGCODE> –f <prooffile> –g <paramfile> [-o <outpath>] • Use your uppercase ORGCODE (DFSNAV, CAN CDN, DEUVIT). • <prooffile> is the filename of the format 300 or 700 national (G)EBV file to be checked. • <paramfile> is the filename of the associated format 301 or 701 evaluation parameter file. • <outpath> is an optional path for creation of the zipfile for uploading. Example on how to run the program: For MACE write: python26 CheckProofsPara.py -m CDN -f file300.GUE.CAN.prod -g file301.GUE.CAN.prod For GMACE write: python26 CheckProofsPara.py -m CDN -f file700.GUE.CAN.prod -g file701.GUE.CAN.prod Output screen: Eventual errors are displayed on the screen (which can redirect to a log file if desired). If no errors are found in the file If no errors are detected, the data files will be written into a zip file called IB-ORGCODE-IG-yyyymmddThhmmss.zip for mace and IB-ORGCODE-GG-yyyymmddThhmmss.zip for gmace (an example of output in case of no errors below). Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre Organization code :: CDN Parameter file :: file301.GUE.CAN.prod Proof file :: file300.GUE.CAN.prod 0 errors in 3 lines from paramfile 0 errors in 309 lines from prooffile Record counts by breed_population_trait combination GUE CAN fat 103 GUE CAN mil 103 GUE CAN pro 103 Everything OK. Zip file is ready for upload. IB-CDN-IG-20131021T152303.zip If errors are found in the file In case of errors, no zip file will be created. Correct the data and re-run the program until the data successfully pass all required checks. (an example of output in case of errors below. Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre Organization code :: CDN Parameter file :: file701.HOL.CAN.work Proof file :: file700.HOL.CAN.work 2 errors in 2 lines from paramfile Parameter line 1. Base definition error: <BB12345>. See file format (eg. H00BB95) Parameter line 2. Base definition error: <BB12345>. See file format (eg. H00BB95) Error(s) in parameter file. Skipping proof file. |
CheckProofsPara.py will fail if both record types are found in one file. |
| Line 88: | Line 12: |
| * Use the command: '''python !CheckProofPara.py -m <ORGCODE> -f <prooffile> -g <paramfile> [-o outpath]''' where: | . Every proof file must be accompanied by a parameter file and each record in the proof file must have associated information for a single brd-pop-trt combination in the parameterfile. One zip file may contain records for as many or few brd-pop-trt combinations as desired. All traits in a trait group can be put in the same file, as they have in the past, but this is not essential. There is also an option to upload evaluations for all breeds, populations and traits in a single file if that is more convenient. A proof/parameter file may contain only conventional (300/301) or only GEBV (700/701) records, not both.If problems are found with some specific combinations, only those combinations need to be re-loaded. It is essential that proof records for all bulls are included in the same file for any one brd-pop-trt combination whether the dataset is a first submission for the IGE run in question, or a re-submission with some problem corrected. When new data are uploaded for any combination, all records present in IDEA for that combination are deleted prior to loading the new records. Thus, it is not acceptable to submit a partial dataset in order to correct the evaluations of some subset of bulls. Extra records present in the parameter file will simply be ignored. This allows users to maintain a single parameter file to be submitted with several proof files, if desired. The user instructions and file formats (see Appendix I and II) give details on how to run the program and on the checks performed. If no errors are found, a zip file is created with the name IB-ORGCODE-IG-yyymmddThhmmss.zip containing the input proof and parameter files. |
| Line 90: | Line 14: |
| * '''<ORGCODE>''' is an assigned member organization code (upper case) | |
| Line 92: | Line 15: |
| * '''<prooffile>''' is /path/to/filename of the format 300 national EBV file | . If you need assistance, please do not hesitate to contact us at [[mailto:interbull-hgen@slu.se|interbull@slu.se]] . |
| Line 94: | Line 17: |
| * '''<paramfile>''' is /path/to/filename of the format 301 evaluation parameter file | <<span(style="color: #FF0000;")>>Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again inside IDEA to double-check the data file uploaded in the zip file.<<span>> |
| Line 96: | Line 19: |
| * '''<outpath>''' is an optional path for creation of the zipfile for uploading | |
| Line 98: | Line 20: |
| * Use your uppercase ORGCODE as shown on the upper right hand side of the IDEA page.Your organization code is reported within brackets beside the "'''Logged in as'''" information. | === Before Running the Programs === |
| Line 100: | Line 22: |
| * The program checks its internal version with the value stored on the Interbull server. You will have to download the most recent version if there is a mismatch. | . a. Ensure there is a working network connection . b. Install [[http://www.python.org|Python]] (version 2.6 to 2.7) if necessary . b. Create a working directory/folder . d. Download the CheckProofPara.py program from https://idea.interbull.org/software and copy it to your new directory . e. Copy your proof and parameter file to the working directory |
| Line 102: | Line 28: |
| === After Running the Program: === If no errors are detected, the pedigree file will be written into a zip file called '''IB-ORGCODE-IG-yyyymmddThhmmss.zip'''. Upload the zip file to IDEA: https://idea.interbull.org/. |
=== The Program === |
| Line 105: | Line 30: |
| In case of errors, no zip file will be created. Please correct your data and re-run the program until the data successfully pass all required checks.The first 10 errors of each kind will be printed on the screen. | . '''Execute''': <<span(style="background-color: #00FF00;")>> python26 CheckProofsPara.py -m <ORGCODE> –f <prooffile> –g <paramfile> [-o <outpath>] <<span>> .where: . <ORGCODE>=the assigned member organization code (upper case) as shown on the upper right hand side of the IDEA page. Your organization code is reported within brackets beside the "'''Logged in as'''" information . <prooffile>= /path/to/filename of the format 300/700 national EBV/GEBV file . <paramfile>= /path/to/filename of the format 301/701 evaluation parameter file . <outpath>= optional path for creation of the zipfile for uploading |
| Line 107: | Line 37: |
| === Note === Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again inside IDEA to double-check the data file uploaded in the zip file. |
. '''''Example on how to run the program:''''' .For MACE write: python26 CheckProofsPara.py -m CDN -f file300.GUE.CAN.prod -g file301.GUE.CAN.prod .For GMACE write: python26 CheckProofsPara.py -m CDN -f file700.GUE.CAN.prod -g file701.GUE.CAN.prod |
| Line 110: | Line 41: |
| ---- If you need assistance, please do not hesitate to contact us at [[mailto:interbull-hgen@slu.se|interbull@slu.se]] . |
.''' Output''': Eventual errors are displayed on the screen and can redirect to alog file if desired. . Example of output on the screen in case of no errors: . Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre . Organization code : CDN . Parameter file : file301.GUE.CAN.prod . Proof file : file300.GUE.CAN.prod . 0 errors in 3 lines from paramfile . 0 errors in 309 lines from prooffile . Record counts by breed_population_trait combination . GUE CAN fat 103 GUE CAN mil 103 GUE CAN pro 103 .Everything OK. Zip file is ready for upload. IB-CDN-IG-20131021T152303.zip . In case of errors, no zip file will be created. Correct the data and re-run the program until the data successfully pass all required checks.The first 10 errors of each kind will be printed on the screen. . Example of output in case of errors. . Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre . Organization code : CDN . Parameter file : file701.HOL.CAN.work . Proof file : file700.HOL.CAN.work . 2 errors in 2 lines from paramfile . Parameter line 1. Base definition error: <BB12345>. See file format (eg. H00BB95) . Parameter line 2. Base definition error: <BB12345>. See file format (eg. H00BB95) . Error(s) in parameter file. Skipping proof file. |
General information
A Python program called CheckProofsPara.py will check the 300/700 proof file format and the associated 301/701 parameter file for format correctness against the IDEA EBV User Manual Appendix II. The program prepares a zip file,IB-ORGCODE-IG-yyymmddThhmmss.zip for conventional MACE and IB-ORGCODE-GG-yyymmddThhmmss.zip for GMACE,if no errors are found in the file. The zip file contains the input proof and parameter files, renamed to proof.dat and param.dat, respectively. The program requires access to the internet and specifically to few functions/pages in the IDEA web application. Firstly, in order to ensure that the user has the most recent version of the software, the program checks its internal version with the version stored on the Interbull server. If there is a mismatch in versions, a message is printed and the program exits and the program must be re downloaded. Lists of valid orgcode’s and breed-pop-trait combinations for which the user’s organization has EBV upload authority are also obtained from the IDEA web application. If errors occur they are listed to the screen and no zip file is created. The zip file represents your checked data file to upload to the Interbull Centre IDEA database (https://idea.interbull.org/). For technical reason the program rejects files containing more than a million of data.
When checking the proof file only the first 10 errors of each type are listed.
CheckProofsPara.py will fail if both record types are found in one file.
- Every proof file must be accompanied by a parameter file and each record in the proof file must have associated information for a single brd-pop-trt combination in the parameterfile. One zip file may contain records for as many or few brd-pop-trt combinations as desired. All traits in a trait group can be put in the same file, as they have in the past, but this is not essential. There is also an option to upload evaluations for all breeds, populations and traits in a single file if that is more convenient. A proof/parameter file may contain only conventional (300/301) or only GEBV (700/701) records, not both.If problems are found with some specific combinations, only those combinations need to be re-loaded. It is essential that proof records for all bulls are included in the same file for any one brd-pop-trt combination whether the dataset is a first submission for the IGE run in question, or a re-submission with some problem corrected. When new data are uploaded for any combination, all records present in IDEA for that combination are deleted prior to loading the new records. Thus, it is not acceptable to submit a partial dataset in order to correct the evaluations of some subset of bulls. Extra records present in the parameter file will simply be ignored. This allows users to maintain a single parameter file to be submitted with several proof files, if desired. The user instructions and file formats (see Appendix I and II) give details on how to run the program and on the checks performed. If no errors are found, a zip file is created with the name IB-ORGCODE-IG-yyymmddThhmmss.zip containing the input proof and parameter files.
If you need assistance, please do not hesitate to contact us at interbull@slu.se .
Please do not modify the program to circumvent any checks. Doing so would be pointless because the same checking routine is used again inside IDEA to double-check the data file uploaded in the zip file.
Before Running the Programs
- a. Ensure there is a working network connection
b. Install Python (version 2.6 to 2.7) if necessary
- b. Create a working directory/folder
d. Download the CheckProofPara.py program from https://idea.interbull.org/software and copy it to your new directory
- e. Copy your proof and parameter file to the working directory
The Program
Execute: python26 CheckProofsPara.py -m <ORGCODE> –f <prooffile> –g <paramfile> [-o <outpath>]
- where:
<ORGCODE>=the assigned member organization code (upper case) as shown on the upper right hand side of the IDEA page. Your organization code is reported within brackets beside the "Logged in as" information
<prooffile>= /path/to/filename of the format 300/700 national EBV/GEBV file
<paramfile>= /path/to/filename of the format 301/701 evaluation parameter file
<outpath>= optional path for creation of the zipfile for uploading
Example on how to run the program:
For MACE write: python26 CheckProofsPara.py -m CDN -f file300.GUE.CAN.prod -g file301.GUE.CAN.prod
For GMACE write: python26 CheckProofsPara.py -m CDN -f file700.GUE.CAN.prod -g file701.GUE.CAN.prod
Output: Eventual errors are displayed on the screen and can redirect to alog file if desired.
- Example of output on the screen in case of no errors:
Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre
- Organization code : CDN
- Parameter file : file301.GUE.CAN.prod
- Proof file : file300.GUE.CAN.prod
- 0 errors in 3 lines from paramfile
- 0 errors in 309 lines from prooffile
- Record counts by breed_population_trait combination
- GUE CAN fat 103 GUE CAN mil 103 GUE CAN pro 103
- Everything OK. Zip file is ready for upload. IB-CDN-IG-20131021T152303.zip
- In case of errors, no zip file will be created. Correct the data and re-run the program until the data successfully pass all required checks.The first 10 errors of each kind will be printed on the screen.
- Example of output in case of errors.
Running CheckProofsPara.py version 2013-06-04 v0.6, provided by the Interbull Centre
- Organization code : CDN
- Parameter file : file701.HOL.CAN.work
- Proof file : file700.HOL.CAN.work
- 2 errors in 2 lines from paramfile
Parameter line 1. Base definition error: <BB12345>. See file format (eg. H00BB95)
Parameter line 2. Base definition error: <BB12345>. See file format (eg. H00BB95)
- Error(s) in parameter file. Skipping proof file.
- Example of output on the screen in case of no errors: