diff options
| -rwxr-xr-x | wqflask/maintenance/gen_select_dataset.py | 45 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 99 |
2 files changed, 100 insertions, 44 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index fda46792..ea0d4a56 100755 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -156,15 +156,6 @@ def build_types(species, group): """ - #print("""select distinct Tissue.Name - # from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species - # where Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and - # InbredSet.Name = '{}' and - # ProbeFreeze.TissueId = Tissue.Id and - # ProbeFreeze.InbredSetId = InbredSet.Id and - # ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - # ProbeSetFreeze.public > 0 - # order by Tissue.Name""".format(species, group)) Cursor.execute("""select distinct Tissue.Name from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and @@ -199,6 +190,19 @@ def build_datasets(species, group, type_name): """Gets dataset names from database""" dataset_text = dataset_value = None if type_name == "Phenotypes": + print("GROUP:", group) + Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 order by + PublishFreeze.CreateTime desc""", (group)) + + results = Cursor.fetchone() + if results != None: + dataset_id = str(results[0]) + else: + dataset_id = "None" dataset_value = "%sPublish" % group if group == 'MDP': dataset_text = "Mouse Phenome Database" @@ -206,20 +210,24 @@ def build_datasets(species, group, type_name): dataset_text = "%s Published Phenotypes" % group elif type_name == "Genotypes": + Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where + InbredSet.Name = %s and + GenoFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = GenoFreeze.ShortName and + GenoFreeze.public > 0 order by + GenoFreeze.CreateTime desc""", (group)) + + results = Cursor.fetchone() + if results != None: + dataset_id = str(results[0]) + else: + dataset_id = "None" dataset_value = "%sGeno" % group dataset_text = "%s Genotypes" % group if dataset_value: - return [(dataset_value, dataset_text)] + return [(dataset_id, dataset_value, dataset_text)] else: - #print("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from - # ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where - # Species.Name = '{}' and Species.Id = InbredSet.SpeciesId and - # InbredSet.Name = '{}' and - # ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{}' - # and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = - # InbredSet.Id and ProbeSetFreeze.public > 0 order by - # ProbeSetFreeze.CreateTime desc""".format(species, group, type_name)) Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and @@ -247,7 +255,6 @@ def main(): species = get_species() groups = get_groups(species) - print("groups:", groups) types = get_types(groups) datasets = get_datasets(types) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index da9beb9b..5194cb96 100755 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -14,12 +14,14 @@ "BayXSha": { "Genotypes": [ [ + "None", "BayXShaGeno", "BayXSha Genotypes" ] ], "Phenotypes": [ [ + "642", "BayXShaPublish", "BayXSha Published Phenotypes" ] @@ -28,12 +30,14 @@ "ColXBur": { "Genotypes": [ [ + "None", "ColXBurGeno", "ColXBur Genotypes" ] ], "Phenotypes": [ [ + "623", "ColXBurPublish", "ColXBur Published Phenotypes" ] @@ -42,12 +46,14 @@ "ColXCvi": { "Genotypes": [ [ + "None", "ColXCviGeno", "ColXCvi Genotypes" ] ], "Phenotypes": [ [ + "640", "ColXCviPublish", "ColXCvi Published Phenotypes" ] @@ -99,6 +105,7 @@ ], "Genotypes": [ [ + "615", "SXMGeno", "SXM Genotypes" ] @@ -122,6 +129,7 @@ ], "Phenotypes": [ [ + "608", "SXMPublish", "SXM Published Phenotypes" ] @@ -198,6 +206,7 @@ ], "Genotypes": [ [ + "None", "AD-cases-controls-MyersGeno", "AD-cases-controls-Myers Genotypes" ] @@ -285,6 +294,7 @@ ], "Phenotypes": [ [ + "634", "CANDLEPublish", "CANDLE Published Phenotypes" ] @@ -941,6 +951,7 @@ "HCP": { "Phenotypes": [ [ + "None", "HCPPublish", "HCP Published Phenotypes" ] @@ -966,6 +977,7 @@ ], "Phenotypes": [ [ + "635", "HLCPublish", "HLC Published Phenotypes" ] @@ -1153,6 +1165,7 @@ "AKXD": { "Genotypes": [ [ + "611", "AKXDGeno", "AKXD Genotypes" ] @@ -1192,6 +1205,7 @@ ], "Genotypes": [ [ + "636", "AXBXAGeno", "AXBXA Genotypes" ] @@ -1212,6 +1226,7 @@ ], "Phenotypes": [ [ + "629", "AXBXAPublish", "AXBXA Published Phenotypes" ] @@ -1220,6 +1235,7 @@ "B6BTBRF2": { "Genotypes": [ [ + "618", "B6BTBRF2Geno", "B6BTBRF2 Genotypes" ] @@ -1238,6 +1254,7 @@ ], "Phenotypes": [ [ + "603", "B6BTBRF2Publish", "B6BTBRF2 Published Phenotypes" ] @@ -1246,6 +1263,11 @@ "B6D2F2": { "Brain mRNA": [ [ + "77", + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], + [ "76", "BRF2_M_0805_M", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" @@ -1256,11 +1278,6 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], [ - "77", - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ "33", "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" @@ -1278,6 +1295,7 @@ ], "Genotypes": [ [ + "637", "B6D2F2Geno", "B6D2F2 Genotypes" ] @@ -1286,6 +1304,7 @@ "B6D2F2-PSU": { "Genotypes": [ [ + "617", "B6D2F2-PSUGeno", "B6D2F2-PSU Genotypes" ] @@ -1325,6 +1344,7 @@ "BDF2-1999": { "Genotypes": [ [ + "None", "BDF2-1999Geno", "BDF2-1999 Genotypes" ] @@ -1340,6 +1360,7 @@ "BDF2-2005": { "Genotypes": [ [ + "None", "BDF2-2005Geno", "BDF2-2005 Genotypes" ] @@ -1399,6 +1420,7 @@ ], "Genotypes": [ [ + "None", "BHF2Geno", "BHF2 Genotypes" ] @@ -1475,6 +1497,7 @@ ], "Genotypes": [ [ + "None", "BHHBF2Geno", "BHHBF2 Genotypes" ] @@ -1791,6 +1814,11 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], [ + "279", + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA **" + ], + [ "278", "Eye_M2_0908_R_MT", "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" @@ -1801,11 +1829,6 @@ "Eye M430v2 WT WT (Sep08) RMA **" ], [ - "279", - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ "400", "DBA2J-ONH-1212", "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA" @@ -1825,6 +1848,7 @@ ], "Genotypes": [ [ + "600", "BXDGeno", "BXD Genotypes" ] @@ -1940,16 +1964,16 @@ "UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv" ], [ - "206", - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ "296", "UT_ILM_BXD_hipp_RSE_1112", "UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv" ], [ + "206", + "UMUTAffyExon_0209_RMA", + "UMUTAffy Hippocampus Exon (Feb09) RMA" + ], + [ "242", "UT_ILM_BXD_hipp_NON_0909", "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" @@ -2036,16 +2060,16 @@ ], "Kidney mRNA": [ [ - "240", - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], - [ "239", "MA_M2F_0706_R", "Mouse kidney M430v2 Female (Aug06) RMA" ], [ + "240", + "MA_M2M_0706_R", + "Mouse kidney M430v2 Male (Aug06) RMA" + ], + [ "118", "MA_M2_0806_R", "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" @@ -2333,6 +2357,7 @@ ], "Phenotypes": [ [ + "602", "BXDPublish", "BXD Published Phenotypes" ] @@ -2640,6 +2665,7 @@ ], "Genotypes": [ [ + "638", "BXHGeno", "BXH Genotypes" ] @@ -2653,6 +2679,7 @@ ], "Phenotypes": [ [ + "627", "BXHPublish", "BXH Published Phenotypes" ] @@ -2661,12 +2688,14 @@ "C57BL-6JxC57BL-6NJF2": { "Genotypes": [ [ + "622", "C57BL-6JxC57BL-6NJF2Geno", "C57BL-6JxC57BL-6NJF2 Genotypes" ] ], "Phenotypes": [ [ + "620", "C57BL-6JxC57BL-6NJF2Publish", "C57BL-6JxC57BL-6NJF2 Published Phenotypes" ] @@ -2709,6 +2738,7 @@ ], "Genotypes": [ [ + "None", "CTB6F2Geno", "CTB6F2 Genotypes" ] @@ -2749,6 +2779,7 @@ ], "Phenotypes": [ [ + "630", "CTB6F2Publish", "CTB6F2 Published Phenotypes" ] @@ -2757,6 +2788,7 @@ "CXB": { "Genotypes": [ [ + "614", "CXBGeno", "CXB Genotypes" ] @@ -2775,6 +2807,7 @@ ], "Phenotypes": [ [ + "628", "CXBPublish", "CXB Published Phenotypes" ] @@ -2811,6 +2844,7 @@ ], "Phenotypes": [ [ + "624", "HSPublish", "HS Published Phenotypes" ] @@ -2828,6 +2862,7 @@ "LXS": { "Genotypes": [ [ + "601", "LXSGeno", "LXS Genotypes" ] @@ -2869,6 +2904,11 @@ "Hippocampus Illumina (May07) RankInv" ], [ + "219", + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" + ], + [ "212", "Illum_LXS_Hipp_RSE_1008", "Hippocampus Illumina RSE (Oct08) RankInv beta" @@ -2887,15 +2927,11 @@ "213", "Illum_LXS_Hipp_NOS_1008", "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "219", - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" ] ], "Phenotypes": [ [ + "606", "LXSPublish", "LXS Published Phenotypes" ] @@ -2921,12 +2957,14 @@ "Linsenbardt-Boehm": { "Genotypes": [ [ + "None", "Linsenbardt-BoehmGeno", "Linsenbardt-Boehm Genotypes" ] ], "Phenotypes": [ [ + "645", "Linsenbardt-BoehmPublish", "Linsenbardt-Boehm Published Phenotypes" ] @@ -2949,6 +2987,7 @@ ], "Genotypes": [ [ + "609", "MDPGeno", "MDP Genotypes" ] @@ -2994,6 +3033,7 @@ ], "Phenotypes": [ [ + "605", "MDPPublish", "Mouse Phenome Database" ] @@ -3009,6 +3049,7 @@ ], "Phenotypes": [ [ + "607", "NZBXFVB-N2Publish", "NZBXFVB-N2 Published Phenotypes" ] @@ -3017,6 +3058,7 @@ "SOTNOT-OHSU": { "Genotypes": [ [ + "613", "SOTNOT-OHSUGeno", "SOTNOT-OHSU Genotypes" ] @@ -3041,6 +3083,7 @@ "HSNIH": { "Phenotypes": [ [ + "619", "HSNIHPublish", "HSNIH Published Phenotypes" ] @@ -3056,6 +3099,7 @@ ], "Genotypes": [ [ + "None", "HXBBXHGeno", "HXBBXH Genotypes" ] @@ -3112,6 +3156,7 @@ ], "Phenotypes": [ [ + "632", "HXBBXHPublish", "HXBBXH Published Phenotypes" ] @@ -3131,12 +3176,14 @@ "J12XJ58F11": { "Genotypes": [ [ + "None", "J12XJ58F11Geno", "J12XJ58F11 Genotypes" ] ], "Phenotypes": [ [ + "647", "J12XJ58F11Publish", "J12XJ58F11 Published Phenotypes" ] @@ -3145,6 +3192,7 @@ "J12XJ58F2": { "Phenotypes": [ [ + "616", "J12XJ58F2Publish", "J12XJ58F2 Published Phenotypes" ] @@ -3155,6 +3203,7 @@ "LXP": { "Phenotypes": [ [ + "621", "LXPPublish", "LXP Published Phenotypes" ] |