Changeset 16243

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Timestamp:
16/07/08 15:26:13 (1 month ago)
Author:
julie
Message:

updated acceptance tests with new model

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  • trunk/bio/core/test/resources/flymine_acceptance_test.conf

    r14467 r16243  
    22 
    33assert { 
    4   sql: select count(*) = 15 from organism 
     4  sql: select count(*) = 26 from organism 
    55} 
    66 
    77no-results { 
    8   sql: select * from organism where genus is null or species is null or abbreviation is null or shortname is null or name is null or taxonid is null 
     8  sql: select * from organism where genus is null or species is null or shortname is null or name is null or taxonid is null 
    99  note: all fields of all organisms should be filled in 
    1010} 
    …… 
    2020} 
    2121some-results { 
    22   sql: select cds.id, identifier, length(intermine_sequence.residues), intermine_end - intermine_start + 1 as calc_length from cds, location, intermine_sequence where chromosomelocationid = location.id and length(intermine_sequence.residues) <> intermine_end - intermine_start + 1 limit 10 
     22  sql: select cds.id, primaryidentifier, length(intermine_sequence.residues), intermine_end - intermine_start + 1 as calc_length from cds, location, intermine_sequence where chromosomelocationid = location.id and length(intermine_sequence.residues) <> intermine_end - intermine_start + 1 limit 10 
    2323  note: make sure that there are at least some CDSs with lengths shorter than the end-start+1, which is evidence that the CDS lengths are the (sum of the exon lengths - UTR length) see #621 
    2424} 
    …… 
    2828} 
    2929 
     30# GO Converter doesn't create proteins 
    3031no-results { 
    31   sql: select * from intermineobject where id in (select b.id from bioentity b where organismid is null and not exists (select p.id from proteindomain p where b.id = p.id)) 
    32   note: all BioEntity objects should have an organism (exception if ProteinFeature or ProteinRegion) 
     32  sql: select * from intermineobject where id in (select b.id from bioentity b where organismid is null and not exists (select p.id from proteindomain p where b.id = p.id) and not exists (select r.id from proteininteractionregion r where b.id = r.id)) 
     33  note: all BioEntity objects should have an organism (exception if ProteinFeature) 
    3334} 
     35 
     36 
    3437no-results { 
    35   sql: select * from intermineobject where id in (select b.id from bioentity b where organismid is null and not exists (select p.id from proteindomain p where b.id = p.id) and not exists (select pr.id from proteinregion pr where b.id = pr.id)) limit 1000 
    36   note: all BioEntity objects should have an organism (exception if ProteinFeature or ProteinRegion) 
    37 } 
    38 no-results { 
    39   sql: select gene.id from gene where length > 1000000 
     38  sql: select gene.id from gene where length > 2000000 
    4039  note: no genes should be too long 
    4140} 
     41 
    4242no-results { 
    4343  sql: select l1.id, l1.intermine_start, l2.id, l2.intermine_end from location as l1, location as l2 where l1.subjectid = l2.subjectid and l1.objectid = l2.objectid and l1.intermine_start = l2.intermine_start and l1.intermine_end = l2.intermine_end and l1.id <> l2.id 
    …… 
    4545} 
    4646no-results { 
    47   sql: select rr1.identifier, rr1.id, rr2.identifier, rr2.id from regulatoryregion as rr1, regulatoryregion as rr2 where rr1.identifier = rr2.identifier and rr1.id <> rr2.id 
     47  sql: select rr1.primaryidentifier, rr1.id, rr2.primaryidentifier, rr2.id from regulatoryregion as rr1, regulatoryregion as rr2 where rr1.primaryidentifier = rr2.primaryidentifier and rr1.id <> rr2.id 
    4848  note: no two regulatoryregions should have the same identifier (see #564) 
    4949} 
    5050no-results { 
    51   sql: select gene1.identifier, gene1.id, gene2.identifier, gene2.id from gene as gene1, gene as gene2 where gene1.identifier = gene2.identifier and gene1.id <> gene2.id 
     51  sql: select gene1.primaryidentifier, gene1.id, gene2.primaryidentifier, gene2.id from gene as gene1, gene as gene2 where gene1.primaryidentifier = gene2.primaryidentifier and gene1.id <> gene2.id 
    5252  note: no two genes should have the same identifier 
    5353} 
    5454no-results { 
    55   sql: select translation1.identifier, translation1.id, translation2.identifier, translation2.id from intermine_translation as translation1, intermine_translation as translation2 where translation1.identifier = translation2.identifier and translation1.id <> translation2.id 
     55  sql: select translation1.primaryidentifier, translation1.id, translation2.primaryidentifier, translation2.id from intermine_translation as translation1, intermine_translation as translation2 where translation1.primaryidentifier = translation2.primaryidentifier and translation1.id <> translation2.id 
    5656  note: no two Translation objects should have the same identifier 
    5757} 
    5858no-results { 
    59   sql: select transcript1.identifier, transcript1.id, transcript2.identifier, transcript2.id from transcript as transcript1, transcript as transcript2 where transcript1.identifier = transcript2.identifier and transcript1.id <> transcript2.id 
     59  sql: select transcript1.primaryidentifier, transcript1.id, transcript2.primaryidentifier, transcript2.id from transcript as transcript1, transcript as transcript2 where transcript1.primaryidentifier = transcript2.primaryidentifier and transcript1.id <> transcript2.id 
    6060  note: no two Transcript objects should have the same identifier 
    6161} 
    …… 
    6565} 
    6666no-results { 
    67   sql: select * from chromosomeband where identifier = '-' 
     67  sql: select * from chromosomeband where primaryidentifier = '-' 
    6868  note: see #567 
    6969} 
    …… 
    7373} 
    7474no-results { 
    75   sql: select lsf.id, lsf.identifier, intermine_sequence.id from locatedsequencefeature as lsf, intermine_sequence where intermine_sequence.id = sequenceid and length(intermine_sequence.residues) <> lsf.length 
     75  sql: select lsf.id, lsf.primaryidentifier, intermine_sequence.id from locatedsequencefeature as lsf, intermine_sequence where intermine_sequence.id = sequenceid and length(intermine_sequence.residues) <> lsf.length 
    7676  note: LocatedSequenceFeature.length should equal the length of the Sequence.residues (see #669) 
    7777} 
    78 no-results { 
    79   sql: select lsf.id, lsf.identifier, lsf.length, seq.id, seq.length from locatedsequencefeature as lsf, intermine_sequence as seq where lsf.sequenceid = seq.id and lsf.length != seq.length 
    80   note: LocatedSequenceFeature.length should equal the length of the Sequence.length (see #669) 
    81 } 
     78 
     79# not anymore.  one length is the distance on the chromosome from start to end, the other is the length of the sequence.  for MRNAs, this won't be the same. 
     80#no-results { 
     81#  sql: select lsf.id, lsf.primaryidentifier, lsf.length, seq.id, seq.length from locatedsequencefeature as lsf, intermine_sequence as seq where lsf.sequenceid = seq.id and lsf.length != seq.length 
     82#  note: LocatedSequenceFeature.length should equal the length of the Sequence.length (see #669) 
     83#} 
    8284no-results { 
    8385  sql: select id, length from intermine_sequence where length <= 0; 
    …… 
    8991} 
    9092no-results { 
    91   sql: select * from intermineobject where id in (select b.id from bioentity b where b.identifier is not null and not exists (select * from synonym s where s.intermine_value = b.identifier and s.subjectid = b.id)) limit 100 
     93  sql: select * from intermineobject where id in (select b.id from bioentity b where b.primaryidentifier is not null and not exists (select * from synonym s where s.intermine_value = b.primaryidentifier and s.subjectid = b.id)) limit 100 
    9294  note: all BioEntities should have their identifier as a synonm 
    9395} 
    …… 
    105107} 
    106108no-results { 
    107   sql: select t1.id, t1.identifier, t2.id, t2.identifier from intermine_translation as t1, intermine_translation as t2 where t1.id != t2.id and t1.identifier = t2.identifier 
     109  sql: select t1.id, t1.primaryidentifier, t2.id, t2.primaryidentifier from intermine_translation as t1, intermine_translation as t2 where t1.id != t2.id and t1.primaryidentifier = t2.primaryidentifier 
    108110  note: no two Translations should have the same identifier 
    109111} 
    …… 
    117119} 
    118120no-results { 
    119   sql: select distinct a1_.id, a1_.identifier, a1_.name, a2_.id, a2_.identifier from gene as a1_, intergenicregion as a2_, locatedsequencefeatureoverlappingfeatures as indirect0 where a1_.id = indirect0.overlappingfeatures and indirect0.locatedsequencefeature = a2_.id 
     121  sql: select distinct a1_.id, a1_.primaryidentifier, a1_.name, a2_.id, a2_.primaryidentifier from gene as a1_, intergenicregion as a2_, locatedsequencefeatureoverlappingfeatures as indirect0 where a1_.id = indirect0.overlappingfeatures and indirect0.locatedsequencefeature = a2_.id 
    120122  note: No genes should overlap IntergenicRegions 
    121123} 
    …… 
    129131  max-results: 1000 
    130132} 
    131 results-report { 
    132   sql: select * from organism 
    133 }