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.ace dumper scripts overview
Eight .ace files need to be dumped for each upload:
- transgene.ace ->transgene objects curated through the Transgene OA
- var_phene.ace ->variation, rearrangements, transgenes, strains annotated with phenotypes curated through the Phenotype OA
- mol_phene.ace ->molecules associated with phenotypes curated during object-phenotype curation through the Phenotype OA
- alle_paper.ace ->object-paper connections curated through object-phenotype curation through the Phenotype OA, for viewing on gene pages in page reference section
- Molecule.ace ->molecule objects curated through the Molecule OA
- database.ace ->database objects used in molecule curation, this is a manually-generated file. All modifications to the file need to be done manually to this flat file.
- process.ace ->process terms created through the process OA
- process_curation.ace ->entities associated with processes curated through the process curation OA
five .ace files are now dumped on tazendra and picked up by spica on a weekly basis: files are created Wednesday mornings at 4 am and picked up Thursday morning at 8 am.
Four cronjobs on the acedb account on tazendra :
0 4 * * wed /home/acedb/karen/Molecule/dump_molecule_ace.pl creates Molecule.ace
0 4 * * wed /home/acedb/karen/phenote/paper_object/get_paper_object.pl creates alle_paper.ace
0 4 * * wed cd /home/acedb/karen/transgene ./use_package.pl creates transgene.ace
0 4 * * wed cd /home/acedb/work/allele_phenotype/; ./use_package.pl creates var_phene.ace and mol_phene.ace
All files are placed in the directory : /home/acedb/public_html/karen/ which is symlinked to original folders on tazendra :
alle_paper.ace -> /home/acedb/karen/phenote/paper_object/alle_paper.ace
Molecule.ace -> /home/acedb/karen/Molecule/Molecule.ace
mol_phene.ace -> /home/acedb/work/allele_phenotype/mol_phene.ace
transgene.ace -> /home/acedb/karen/transgene/transgene.ace
var_phen.ace -> /home/acedb/work/allele_phenotype/var_phen.ace
database.ace -> /home/acedb/karen/Molecule/database.ace (manually generated and placed file)
One cronjob on spica:
0 8 * * thu /home/citace/cronjobs/getPhenoteTransgene.pl
puts 6 files at /home/citace/Data_for_citace/Data_from_Karen for upload
dump_molecule_ace.pl writes to /home/acedb/karen/Molecule/Molecule.ace
get_paper_object.pl writes to /home/acedb/karen/phenote/paper_object/alle_paper.ace
(transgene) use_package.pl writes to /home/postgres/work/citace_upload/transgene/transgene.ace and transgene.ace<date>
(allele_phenotype) use_package.pl writes to /home/postgres/work/citace_upload/allele_phenotype/allele_phenotype.ace.<date>, var_phene.ace, mol_phene.ace<date> and mol_phene.ace
alle_paper.ace is just a symlink to /home/acedb/karen/phenote/paper_object/alle_paper.ace