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| author | zsloan | 2017-11-06 22:10:34 +0000 |
|---|---|---|
| committer | zsloan | 2017-11-06 22:10:34 +0000 |
| commit | b2a3979f055492c0eef11253d669ee35c79c2004 (patch) | |
| tree | 3dce3862172d2328b8640eacaee4aba7165e8d65 /wqflask/base | |
| parent | e6a9a6719e03e2ac0acf328d29188ac00813e150 (diff) | |
| parent | e3b27c18f379e969c06f8e0b79daf8b762d4fc1d (diff) | |
| download | genenetwork2-b2a3979f055492c0eef11253d669ee35c79c2004.tar.gz | |
Merge branch 'testing' of https://github.com/genenetwork/genenetwork2
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 9 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 1 |
2 files changed, 7 insertions, 3 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index dbdbb51c..6649f8af 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -111,7 +111,7 @@ Publish or ProbeSet. E.g. new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type # Set LOG_LEVEL_DEBUG=5 to see the following: - logger.debugf(5,"datasets",self.datasets) + logger.debugf(5, "datasets",self.datasets) def __call__(self, name): return self.datasets[name] @@ -426,13 +426,15 @@ def datasets(group_name, this_group = None): FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and PublishFreeze.public > %s) + and PublishFreeze.public > %s + and PublishFreeze.confidentiality < 1) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and GenoFreeze.public > %s) + and GenoFreeze.public > %s + and GenoFreeze.confidentiality < 1) UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue @@ -441,6 +443,7 @@ def datasets(group_name, this_group = None): and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s and ProbeSetFreeze.public > %s + and ProbeSetFreeze.confidentiality < 1 ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId) ''' % (group_name, webqtlConfig.PUBLICTHRESH, group_name, webqtlConfig.PUBLICTHRESH, diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index c3f1e76a..1ef2bc26 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -49,6 +49,7 @@ PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db= UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' +UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s" ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' |