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-rw-r--r--wqflask/maintenance/gen_select_dataset.py3
-rw-r--r--wqflask/wqflask/gsearch.py8
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json269
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",
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 12:17:29 +0000