From 5813a1a3006dc67278eb094513c455b9cb2fa91f Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 4 Dec 2017 17:50:14 +0000 Subject: Fixed drop-down scripts to more appropriately deal with BXD300 groups (though there's still a minor issue with a few datasets) Added some header data to mapping output file Fixed links in Network Group nodes/edges --- wqflask/maintenance/gen_select_dataset.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 6553f090..1123f997 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -96,13 +96,14 @@ def get_groups(species): Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = '%s' - and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and + and InbredSet.SpeciesId = Species.Id and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) group by InbredSet.Name order by InbredSet.Name""" % species_name) - groups[species_name] = list(Cursor.fetchall()) + results = Cursor.fetchall() + groups[species_name] = list(results) return groups -- cgit v1.2.3 From d692e4f79f61691ecac7a14d0d7c7e93ead919e4 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 6 Dec 2017 16:40:19 +0000 Subject: Fixed drop-down group order --- wqflask/maintenance/gen_select_dataset.py | 2 +- .../new/javascript/dataset_menu_structure.json | 98 +++++++++++++--------- 2 files changed, 60 insertions(+), 40 deletions(-) (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 1123f997..f62d0cc1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -101,7 +101,7 @@ def get_groups(species): or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) group by InbredSet.Name - order by InbredSet.Name""" % species_name) + order by InbredSet.FullName""" % species_name) results = Cursor.fetchall() groups[species_name] = list(results) return groups diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 8bdd91db..eabddbc4 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -2218,6 +2218,26 @@ "819", "UCLA_BXD_Aor_Jan16", "UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA" + ], + [ + "485", + "EPFL-LISPBXDHeCD0114", + "EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA" + ], + [ + "486", + "EPFL-LISPBXDHeHFD0114", + "EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA" + ], + [ + "487", + "EPFL-LISPBXDHeCDEx0114", + "EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA" + ], + [ + "488", + "EPFL-LISPBXDHeHFDEx0114", + "EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA" ] ], "Hematopoietic Cells mRNA": [ @@ -3729,6 +3749,10 @@ ] ], "human": [ + [ + "HB", + "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)" + ], [ "AD-cases-controls", "Brain, Aging: AD, Normal Gene Expression (Liang)" @@ -3741,6 +3765,14 @@ "Aging-Brain-UCI", "Brain, Aging: Normal Gene Expression (UCI/Cotman)" ], + [ + "HCP", + "Brain, Cognition, Human Connectome Project" + ], + [ + "HSB", + "Brain, Development: Normal Gene Expression (Yale/Sestan)" + ], [ "Brain-Normal-NIH-Gibbs", "Brain: Normal Gene Expression (NIH/Gibbs)" @@ -3749,10 +3781,6 @@ "CANDLE", "Child Development: CANDLE Cohort with Genotypes (TUCI/UTHSC)" ], - [ - "CEPH-2004", - "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" - ], [ "GTEx", "GTEx v3 All Tissues, RNA-Seq with Genotypes" @@ -3761,14 +3789,6 @@ "GTEx_v5", "GTEx v5 All Tissues, RNA-Seq with Genotypes" ], - [ - "HB", - "Brain, Aging: AD, HD, Normal Gene Expression (Harvard/Merck)" - ], - [ - "HCP", - "Brain, Cognition, Human Connectome Project" - ], [ "HLC", "Liver: Normal Gene Expression with Genotypes (Merck)" @@ -3778,8 +3798,8 @@ "Lung: Normal Gene Expression (Merck)" ], [ - "HSB", - "Brain, Development: Normal Gene Expression (Yale/Sestan)" + "CEPH-2004", + "Lymphoblastoid Cells: Gene Expression (CEPH, Williams)" ], [ "Islets-Gerling", @@ -3804,8 +3824,8 @@ "B6BTBRF2" ], [ - "B6D2", - "Glaucoma and Aged Retina, UTHSC" + "Linsenbardt-Boehm", + "B6D2 EtOH Selected Advanced Intercross" ], [ "B6D2F2", @@ -3815,10 +3835,6 @@ "B6D2F2-PSU", "B6D2F2 PSU" ], - [ - "B6D2RI", - "BXD Aged" - ], [ "BDF2-1999", "BDF2 UCLA" @@ -3827,18 +3843,22 @@ "BDF2-2005", "BDF2-2005" ], - [ - "BHF2", - "BHF2 (Apoe Null) UCLA" - ], [ "BHHBF2", "BH/HB F2 UCLA" ], + [ + "BHF2", + "BHF2 (Apoe Null) UCLA" + ], [ "BXD", "BXD" ], + [ + "B6D2RI", + "BXD Aged" + ], [ "BXD-Bone", "BXD Bone" @@ -3852,8 +3872,8 @@ "BXH" ], [ - "C57BL-6JxC57BL-6NJF2", - "Reduced Complexity Cross (B6JxB6N F2)" + "CTB6F2", + "CastB6/B6Cast F2 UCLA" ], [ "CFW", @@ -3871,10 +3891,6 @@ "CMS", "Chronic Mild Stress" ], - [ - "CTB6F2", - "CastB6/B6Cast F2 UCLA" - ], [ "CXB", "CXB" @@ -3883,6 +3899,10 @@ "EMSR", "Ethanol-Medicated Stress Reduction" ], + [ + "B6D2", + "Glaucoma and Aged Retina, UTHSC" + ], [ "HS", "Heterogeneous Stock" @@ -3891,10 +3911,6 @@ "HS-CC", "Heterogeneous Stock Collaborative Cross" ], - [ - "Linsenbardt-Boehm", - "B6D2 EtOH Selected Advanced Intercross" - ], [ "LXS", "LXS" @@ -3907,6 +3923,10 @@ "NZBXFVB-N2", "NZB/FVB N2 NCI" ], + [ + "C57BL-6JxC57BL-6NJF2", + "Reduced Complexity Cross (B6JxB6N F2)" + ], [ "Scripps-2013", "Scripps C57BL/6J" @@ -3923,6 +3943,10 @@ ] ], "rat": [ + [ + "HXBBXH", + "HXB/BXH" + ], [ "HSNIH-Palmer", "NIH Heterogeneous Stock (Palmer)" @@ -3931,10 +3955,6 @@ "HSNIH-RGSMC", "NIH Heterogeneous Stock (RGSMC 2013)" ], - [ - "HXBBXH", - "HXB/BXH" - ], [ "SRxSHRSPF2", "UIOWA SRxSHRSP F2" @@ -3968,7 +3988,7 @@ ], [ "rat", - "Rat (rn3)" + "Rat (rn6)" ], [ "drosophila", -- cgit v1.2.3