Fixed an issue that caused global phenotype search to often not work and certain phenotype datasets to not show up in drop-downs

3 files changed, 177 insertions, 103 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 48849c8d..4d1b34a3 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -187,7 +187,6 @@ def get_datasets(types):
     for species, group_dict in types.iteritems():
         datasets[species] = {}
         for group, type_list in group_dict.iteritems():
-            #print("type_list: ", type_list)
             datasets[species][group] = {}
             for type_name in type_list:
                 these_datasets = build_datasets(species, group, type_name[0])
@@ -209,7 +208,7 @@ def build_datasets(species, group, type_name):
                     PublishFreeze.CreateTime asc""" % group)
 
         results = Cursor.fetchall()
-        if results != None:
+        if len(results) > 0:
             for result in results:
                 print(result)
                 dataset_id = str(result[0])
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 2a643d19..56769112 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -139,13 +139,15 @@ class GSearch(object):
                     this_trait['name'] = str(line[4])
                     this_trait['dataset'] = line[2]
                     this_trait['dataset_fullname'] = line[3]
-                    this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[5], line[3]))
+                    this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[2]))
                     this_trait['species'] = line[0]
                     this_trait['group'] = line[1]
-                    if line[9] != None:
+                    if line[9] != None and line[6] != None:
                         this_trait['description'] = line[6]
-                    else:
+                    elif line[5] != None:
                         this_trait['description'] = line[5]
+                    else:
+                        this_trait['description'] = "N/A"
                     this_trait['authors'] = line[7]
                     this_trait['year'] = line[8]
                     if this_trait['year'].isdigit():
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 55858b5a..120174a1 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -117,14 +117,14 @@
                   "Barley1 Leaf MAS 5.0 SCRI (Dec06)"
                ],
                [
-                  "126",
-                  "B30_K_1206_Rn",
-                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
-               ],
-               [
                   "125",
                   "B30_K_1206_R",
                   "Barley1 Leaf gcRMA SCRI (Dec06)"
+               ],
+               [
+                  "126",
+                  "B30_K_1206_Rn",
+                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
                ]
             ],
             "Phenotypes": [
@@ -1436,6 +1436,13 @@
                   "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
                ]
             ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "HSBPublish",
+                  "HSB Phenotypes"
+               ]
+            ],
             "Posterior Inferior Parietal Cortex mRNA": [
                [
                   "338",
@@ -1493,8 +1500,23 @@
                ]
             ]
          },
-         "Islets-Gerling": {},
+         "Islets-Gerling": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "Islets-GerlingPublish",
+                  "Islets-Gerling Phenotypes"
+               ]
+            ]
+         },
          "TIGEM-Retina-RNA-Seq": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "TIGEM-Retina-RNA-SeqPublish",
+                  "TIGEM-Retina-RNA-Seq Phenotypes"
+               ]
+            ],
             "Retina mRNA": [
                [
                   "802",
@@ -1586,14 +1608,14 @@
                   "NCI Mammary LMT miRNA v2 (Apr09) RMA"
                ],
                [
-                  "37",
-                  "MA_M_0704_R",
-                  "NCI Mammary mRNA M430 (July04) RMA"
-               ],
-               [
                   "36",
                   "MA_M_0704_M",
                   "NCI Mammary mRNA M430 (July04) MAS5"
+               ],
+               [
+                  "37",
+                  "MA_M_0704_R",
+                  "NCI Mammary mRNA M430 (July04) RMA"
                ]
             ]
          },
@@ -1661,14 +1683,14 @@
             ],
             "Liver mRNA": [
                [
-                  "39",
-                  "LVF2_M_0704_R",
-                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
-               ],
-               [
                   "38",
                   "LVF2_M_0704_M",
                   "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
+               ],
+               [
+                  "39",
+                  "LVF2_M_0704_R",
+                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
                ]
             ],
             "Phenotypes": [
@@ -1679,15 +1701,18 @@
                ]
             ]
          },
-         "B6D2": {},
+         "B6D2": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "B6D2Publish",
+                  "B6D2 Phenotypes"
+               ]
+            ]
+         },
          "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"
@@ -1698,19 +1723,24 @@
                   "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"
                ],
                [
-                  "32",
-                  "BRF2_M_0304_R",
-                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
-               ],
-               [
                   "31",
                   "BRF2_M_0304_M",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
+               ],
+               [
+                  "32",
+                  "BRF2_M_0304_R",
+                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
                ]
             ],
             "Genotypes": [
@@ -1789,6 +1819,11 @@
             ],
             "Striatum mRNA": [
                [
+                  "83",
+                  "SA_M2_0905_M",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
+               ],
+               [
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
@@ -1797,11 +1832,6 @@
                   "84",
                   "SA_M2_0905_R",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
-               ],
-               [
-                  "83",
-                  "SA_M2_0905_M",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
                ]
             ]
          },
@@ -1863,6 +1893,13 @@
                   "UCLA_BHF2_LIVER_0605",
                   "UCLA BHF2 Liver (June05) mlratio"
                ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "BHF2Publish",
+                  "BHF2 Phenotypes"
+               ]
             ]
          },
          "BHHBF2": {
@@ -2070,21 +2107,26 @@
                   "INIA Brain mRNA M430 (Jun06) RMA"
                ],
                [
-                  "102",
-                  "IBR_M_0106_R",
-                  "INIA Brain mRNA M430 (Jan06) RMA"
-               ],
-               [
                   "101",
                   "IBR_M_0106_P",
                   "INIA Brain mRNA M430 (Jan06) PDNN"
                ],
                [
+                  "102",
+                  "IBR_M_0106_R",
+                  "INIA Brain mRNA M430 (Jan06) RMA"
+               ],
+               [
                   "95",
                   "BR_U_1105_P",
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
                ],
                [
+                  "82",
+                  "BR_U_0805_R",
+                  "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
+               ],
+               [
                   "81",
                   "BR_U_0805_P",
                   "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
@@ -2095,11 +2137,6 @@
                   "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
                ],
                [
-                  "82",
-                  "BR_U_0805_R",
-                  "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
-               ],
-               [
                   "42",
                   "CB_M_0204_P",
                   "INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2196,11 +2233,6 @@
                   "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"
@@ -2211,6 +2243,11 @@
                   "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"
@@ -2494,16 +2531,16 @@
             ],
             "Kidney mRNA": [
                [
-                  "239",
-                  "MA_M2F_0706_R",
-                  "Mouse kidney M430v2 Female (Aug06) RMA"
-               ],
-               [
                   "240",
                   "MA_M2M_0706_R",
                   "Mouse kidney M430v2 Male (Aug06) RMA"
                ],
                [
+                  "239",
+                  "MA_M2F_0706_R",
+                  "Mouse kidney M430v2 Female (Aug06) RMA"
+               ],
+               [
                   "118",
                   "MA_M2_0806_R",
                   "Mouse kidney M430v2 Sex Balanced (Aug06) RMA"
@@ -2514,23 +2551,18 @@
                   "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
                ],
                [
-                  "116",
-                  "MA_M2_0706_P",
-                  "Mouse Kidney M430v2 (Jul06) PDNN"
-               ],
-               [
                   "115",
                   "MA_M2_0706_R",
                   "Mouse Kidney M430v2 (Jul06) RMA"
+               ],
+               [
+                  "116",
+                  "MA_M2_0706_P",
+                  "Mouse Kidney M430v2 (Jul06) PDNN"
                ]
             ],
             "Liver Metabolome": [
                [
-                  "836",
-                  "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817",
-                  "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2"
-               ],
-               [
                   "838",
                   "UTHSC-ETHZ-EPFL_LivPMetExtBHFD0817",
                   "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2"
@@ -2546,6 +2578,11 @@
                   "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2"
                ],
                [
+                  "836",
+                  "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817",
+                  "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2"
+               ],
+               [
                   "473",
                   "EPFL-LISP_LivPMetCDHFD1213",
                   "EPFL/LISP BXD Liver Polar Metabolites CD+HFD (Jun14)"
@@ -2655,6 +2692,11 @@
                   "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
+                  "849",
+                  "EPFLMouseLiverCDEx0413",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
                   "848",
                   "EPFLMouseLiverHFCEx0413",
                   "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2665,11 +2707,6 @@
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
-                  "849",
-                  "EPFLMouseLiverCDEx0413",
-                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
-               ],
-               [
                   "433",
                   "EPFLMouseLiverBothExRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2798,16 +2835,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "375",
-                  "DevNeocortex_ILM6.2P14RInv_1111",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "374",
                   "DevNeocortex_ILM6.2P3RInv_1111",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
                ],
                [
+                  "375",
+                  "DevNeocortex_ILM6.2P14RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -3063,6 +3100,11 @@
             ],
             "Ventral Tegmental Area mRNA": [
                [
+                  "228",
+                  "VCUSal_0609_R",
+                  "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
+               ],
+               [
                   "230",
                   "VCUEtvsSal_0609_R",
                   "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
@@ -3071,11 +3113,6 @@
                   "229",
                   "VCUEtOH_0609_R",
                   "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
-               ],
-               [
-                  "228",
-                  "VCUSal_0609_R",
-                  "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
                ]
             ]
          },
@@ -3135,6 +3172,13 @@
                   "LV_G_0106_F",
                   "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females"
                ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "BXD300Publish",
+                  "BXD300 Phenotypes"
+               ]
             ]
          },
          "BXH": {
@@ -3262,6 +3306,13 @@
                   "INIA_LCMB_1215",
                   "INIA LCM (11 Regions) BASELINE RNA-seq Transcript Level (Dec15)"
                ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "CIE-INIAPublish",
+                  "CIE-INIA Phenotypes"
+               ]
             ]
          },
          "CIE-RMA": {
@@ -3283,9 +3334,24 @@
                   "INIA_UTHSC_Mid_AffyMTA1_Ex_May17",
                   "INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA"
                ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "CIE-RMAPublish",
+                  "CIE-RMA Phenotypes"
+               ]
+            ]
+         },
+         "CMS": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "CMSPublish",
+                  "CMS Phenotypes"
+               ]
             ]
          },
-         "CMS": {},
          "CTB6F2": {
             "Adipose mRNA": [
                [
@@ -3387,14 +3453,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "100",
-                  "HC_M2CB_1205_R",
-                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
-               ],
-               [
                   "99",
                   "HC_M2CB_1205_P",
                   "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
+               ],
+               [
+                  "100",
+                  "HC_M2CB_1205_R",
+                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
                ]
             ],
             "Liver mRNA": [
@@ -3485,16 +3551,6 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "213",
-                  "Illum_LXS_Hipp_NOS_1008",
-                  "Hippocampus Illumina NOS (Oct08) RankInv beta"
-               ],
-               [
-                  "219",
-                  "Illum_LXS_Hipp_NON_1008",
-                  "Hippocampus Illumina NON (Oct08) RankInv beta"
-               ],
-               [
                   "212",
                   "Illum_LXS_Hipp_RSE_1008",
                   "Hippocampus Illumina RSE (Oct08) RankInv beta"
@@ -3510,6 +3566,16 @@
                   "Hippocampus Illumina RSS (Oct08) RankInv beta"
                ],
                [
+                  "213",
+                  "Illum_LXS_Hipp_NOS_1008",
+                  "Hippocampus Illumina NOS (Oct08) RankInv beta"
+               ],
+               [
+                  "219",
+                  "Illum_LXS_Hipp_NON_1008",
+                  "Hippocampus Illumina NON (Oct08) RankInv beta"
+               ],
+               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3600,14 +3666,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "273",
-                  "UMUTAffyExon_0209_RMA_MDP",
-                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
-               ],
-               [
                   "272",
                   "HC_M2_0606_MDP",
                   "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
+               ],
+               [
+                  "273",
+                  "UMUTAffyExon_0209_RMA_MDP",
+                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
                ]
             ],
             "Liver mRNA": [
@@ -3669,6 +3735,13 @@
             ]
          },
          "Retina-RGC-Rheaume": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "Retina-RGC-RheaumePublish",
+                  "Retina-RGC-Rheaume Phenotypes"
+               ]
+            ],
             "Retina Single-cell RNA-Seq": [
                [
                   "865",