From f374b4c75a4cba7361261aaba0e6550104795ee4 Mon Sep 17 00:00:00 2001 From: Glenn Proctor <gp1@sanger.ac.uk> Date: Thu, 22 Sep 2005 08:57:04 +0000 Subject: [PATCH] Changed local sources to have new LOCAL: convention so they can be dealt with more elegantly by BaseParser --- .../xref_mapping/sql/populate_metadata.sql | 26 ++++++++----------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/misc-scripts/xref_mapping/sql/populate_metadata.sql b/misc-scripts/xref_mapping/sql/populate_metadata.sql index 0371e7756d..5a9971eb8e 100644 --- a/misc-scripts/xref_mapping/sql/populate_metadata.sql +++ b/misc-scripts/xref_mapping/sql/populate_metadata.sql @@ -250,12 +250,12 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (5, 9606,'ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.fasta.gz', '', now(), now(), "IPIParser"); ## CCDS -INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2000, 9606,'/dummy/CCDS.txt', '', now(), now(), "CCDSParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2000, 9606,'LOCAL:CCDS/CCDS.txt', '', now(), now(), "CCDSParser"); ## Agilent -INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 9606,'./Agilent/HumanExpression.fasta', '', now(), now(), "AgilentParser"); -INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2701, 9606,'./Agilent/HumanCGH.fasta', '', now(), now(), "AgilentParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 9606,'LOCAL:AgilentProbe/HumanExpression.fasta', '', now(), now(), "AgilentParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2701, 9606,'LOCAL:AgilentCGH/HumanCGH.fasta', '', now(), now(), "AgilentParser"); ## UniGene INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 9606,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz', '', now(), now(), "UniGeneParser"); @@ -291,7 +291,7 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 10090,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz', '', now(), now(), "UniGeneParser"); ## Agilent -INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10090,'./Agilent/MouseExpression.fasta', '', now(), now(), "AgilentParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10090,'LOCAL:AgilentProbe/MouseExpression.fasta', '', now(), now(), "AgilentParser"); # -------------------------------------------------------------------------------- ### RAT @@ -324,7 +324,7 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 10116,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz', '', now(), now(), "UniGeneParser"); ## Agilent -INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10116,'./Agilent/RatExpression.fasta', '', now(), now(), "AgilentParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10116,'LOCAL:AgilentProbe/RatExpression.fasta', '', now(), now(), "AgilentParser"); # -------------------------------------------------------------------------------- @@ -560,11 +560,11 @@ INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_d INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (6,7165,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Anopheles_gambiae/Aga.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Anopheles_gambiae/Aga.data.gz',now(),now(),'UniGeneParser'); # Celera -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2852, 7165,'/Celera_Pep/consensus-proteins_xref.fasta', now(), now(), "CeleraProteinParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2852, 7165,'LOCAL:Celera_Pep/consensus-proteins_xref.fasta', now(), now(), "CeleraProteinParser"); -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2854, 7165,'/Celera_trans/consensus-transcripts_xref.fasta', now(), now(), "CeleraTranscriptParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2854, 7165,'LOCAL:Celera_trans/consensus-transcripts_xref.fasta', now(), now(), "CeleraTranscriptParser"); -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2856, 7165,'/Anopheles_symbol/GeneName_translation_UniqID.txt', now(), now(), "AnophelesSymbolParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (2856, 7165,'LOCAL:Anopheles_symbol/GeneName_translation_UniqID.txt', now(), now(), "AnophelesSymbolParser"); # -------------------------------------------------------------------------------- @@ -583,17 +583,13 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (4, 9913,'ftp://ftp.ncbi.nih.gov/genomes/Bos_taurus/RNA/rna.gbk.gz', '', now(), now(), "RefSeqGPFFParser"); ## GO -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ -(1070, 9913,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9913,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); ## Interpro -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ -(1300, 9913,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9913,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); ## UniGene -INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ -(6, 9913,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Bt.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Bt.data.gz', now(), now(), "UniGeneParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (6, 9913,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Bt.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Bt.data.gz', now(), now(), "UniGeneParser"); ################################################################################ - -- GitLab