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| − | == Upload Phenote data to Citace ==
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| − | === Dumping Phenote into .ace file ===
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| − | Connect to tazendra
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| − | : ssh acedb@tazendra.caltech.edu
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| − | Pswd
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| − | : cd /home/acedb/work/allele_phenotype
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| − | : ls //will see previous .ace files ‘allele_phenotype.ace.<date> and err.out.<date> along with dump script - use_package.pl* -> .ace file program// run script
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| − | : ./use_package.pl //dump info into .ace file command//
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| − | New allele_phenotype.ace and err.out files will be created as noted by date at the end of each. Send them to Allele_Phene_Dump on scoobydoo:
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| − | : scp err.out.20080130 yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest
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| − | : scp allele_phenotype.ace.2008XX yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest
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| − | Open err.out to see if any errors were generated during the dump process.
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| − | Errors in .ace file generated form should be indicated by "ERROR" in the .ace output, or as comments at the top of the form.
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| − | <left over from CGI .ace dump instructions> Is this still necessary?
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| − | Make sure that there are no obsolete phenotype annotations:
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| − | - Script for finding obsolete terms is find_obsolete.pl at path listed below on tazendra:
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| − | /home/Postgres/work/citace_upload/allele_phenotype/
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| − | NOTE: Over time these dump files will add up, so please clean it up from time to time.
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| − | === Testing Phenote .ace for upload ===
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| − | Evaluate how the uploaded data impacts WB by comparing object numbers before and after data upload. This means that you need access to the latest WS and have the means to edit the WS to read the .ace dump.
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| − | ==== Test file on altair or spika ====
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| − | Send new allele_phenotype.ace to kyook on altair:
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| − | : scp <.ace dump files> kyook@altair.caltech.edu:/home3/kyook/alle_phen.ace.latest
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| − | ==== Test file locally on Acedb ====
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| − | This step is to test two things:
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| − | First, that the file is readable.
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| − | Second, that the file does not alter any objects it shouldn’t.
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| − | Launch local acedb:
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| − | $ cd Desktop/acedb
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| − | $ ./xace /Users/Yook/WS_latest/WS188
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| − | Comparing data builds:
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| − | From the latest build, record
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| − | #Number '''strain objects'''
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| − | #Number '''life stage objects'''
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| − | #Number '''anatomy terms'''
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| − | #Number '''alleles linked to phenotype terms:'''
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| − | use either AQL query
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| − | select all class variation where exists_tag ->phenotype
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| − | select a, a-> variation from a in class phenotype where exists_tag a ->variation
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| − | Number '''variations that are alleles:'''
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| − | use WQL
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| − | find variation variation_type=allele
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| − | Checking that the .ace dump file is readable:
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| − | Load in .ace dump
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| − | Hit ‘Edit..‘ button
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| − | Choose ‘Read .ace file’
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| − | Accept change in write priviledges
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| − | Select ‘Open ace file’
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| − | Find and select file to open
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| − | Select ‘Read all’
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| − | If the .ace file is okay, then 100% of the lines will have been read in. This will be noted in the second line called ‘Line:’. If the dump produced a bad file, the read in will stop at the point where the problem occurred. You can go to that line in the .ace file and check it out.
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| − | Checking that the file does not alter any objects it shouldn’t:
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| − | Once .ace dump loaded in redo counts for all objects as above.
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| − | Compare object numbers between latest database and new .ace file to make sure data in the dump looks reasonable, i.e., no lost data or inflated numbers.
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| − | === Uploading .ace for Wen into Citace ===
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| − | Deposit .ace for Wen in citace:
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| − | scp XXXXX citace@altair:~/Data_for_citace/Data_from_<YOU> /home/citace/Data_for_citace/Data_from_<YOU>/ <allele_phenotype_dump_WSxxx.ace>
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