diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 40 | ||||
| -rw-r--r-- | wqflask/wqflask/database.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/corr_scatter_plot2.css | 39 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 284 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js | 122 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/corr_scatterplot.html | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/error.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_statistics.html | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 7 |
17 files changed, 399 insertions, 182 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1e47e183..e5f10edf 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp # want to reach this base dir assert_writable_dir(TEMPDIR) -TMPDIR = mk_dir(TEMPDIR+'gn2') +TMPDIR = mk_dir(TEMPDIR+'/gn2/') assert_writable_dir(TMPDIR) CACHEDIR = mk_dir(TMPDIR+'/cache/') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index e5726656..a5fd86e2 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -57,7 +57,7 @@ import urlparse from pprint import pformat as pf -#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI) +#Engine = sa.create_engine(zach_settings.SQL_URI) # build MySql database connection diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c28c617a..393ff2df 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -13,6 +13,11 @@ logger = logging.getLogger(__name__ ) OVERRIDES = {} +def app_set(command_id, value): + """Set application wide value""" + app.config.setdefault(command_id,value) + value + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -40,6 +45,7 @@ def get_setting(command_id,guess=None): def value(command): if command: # sys.stderr.write("Found "+command+"\n") + app_set(command_id,command) return command else: return None @@ -89,6 +95,18 @@ def valid_path(dir): return dir return None +def js_path(module=None): + """ + Find the JS module in the two paths + """ + try_gn = get_setting("JS_GN_PATH")+"/"+module + if valid_path(try_gn): + return try_gn + try_guix = get_setting("JS_GUIX_PATH")+"/"+module + if valid_path(try_guix): + return try_guix + raise "No JS path found for "+module+" (check JS_GN_PATH)" + def pylmm_command(guess=None): return valid_bin(get_setting("PYLMM_COMMAND",guess)) @@ -205,21 +223,27 @@ SQL_URI = get_setting('SQL_URI') LOG_LEVEL = get_setting('LOG_LEVEL') LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') LOG_SQL = get_setting_bool('LOG_SQL') -LOG_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY') +LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') LOG_BENCH = get_setting_bool('LOG_BENCH') LOG_FORMAT = "%(message)s" # not yet in use USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') GENENETWORK_FILES = get_setting('GENENETWORK_FILES') -TEMP_TRAITS = get_setting('TEMP_TRAITS') - -PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = gemma_command() -GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH') -PLINK_COMMAND = plink_command() +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +# assert_dir(JS_GUIX_PATH) - don't enforce right now +JS_GN_PATH = get_setting('JS_GN_PATH') +# assert_dir(JS_GN_PATH) + +PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) TEMPDIR = tempdir() # defaults to UNIX TMPDIR +# ---- Handle specific JS modules +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) +assert_dir(JS_TWITTER_POST_FETCHER_PATH) + from six import string_types if os.environ.get('WQFLASK_OVERRIDES'): @@ -234,5 +258,3 @@ if os.environ.get('WQFLASK_OVERRIDES'): else: OVERRIDES[k] = cmd logger.debug(OVERRIDES) - -assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH")) diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index 4df872ad..96c2c301 100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -22,8 +22,8 @@ def init_db(): # they will be registered properly on the metadata. Otherwise # you will have to import them first before calling init_db() #import yourapplication.models + logger.info("Initializing database connection") import wqflask.model - logger.debug("Creating all model metadata") Base.metadata.create_all(bind=engine) logger.info("Done creating all model metadata") diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 87532445..8882c515 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -37,7 +37,7 @@ from utility import temp_data from utility.benchmark import Bench from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping -from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, GEMMA_RESULTS_PATH, PLINK_COMMAND, TEMPDIR +from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR from utility.external import shell from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 49959a74..82a44796 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1018,7 +1018,7 @@ class MarkerRegression(object): else: if self.selectedChr > -1: for i, qtlresult in enumerate(self.qtlresults): - if qtlresult['Chr'] != self.selectedChr: + if qtlresult['chr'] != self.selectedChr: continue if i==0 and qtlresult['Mb'] >= Mb: @@ -1027,7 +1027,7 @@ class MarkerRegression(object): #the trait's position is between two traits if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: - locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])) + locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])) break #the trait's position is on the right of the last genotype @@ -1036,11 +1036,12 @@ class MarkerRegression(object): else: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList): - if _chr != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale - else: - locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale - break + if i < (len(self.ChrList)-1): + if _chr != Chr: + locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale + else: + locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale + break if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12)) canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot2.css b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css index 92e777c2..5aa9b9bf 100644 --- a/wqflask/wqflask/static/new/css/corr_scatter_plot2.css +++ b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css @@ -1,19 +1,40 @@ .nvd3 .nv-axis.nv-x text { - font-size: 16px; - font-weight: normal; - fill: black; + font-size: 16px; + font-weight: normal; + fill: black; } .nvd3 .nv-axis.nv-y text { - font-size: 16px; - font-weight: normal; - fill: black; + font-size: 16px; + font-weight: normal; + fill:black; } -.nv-y .tick.zero line { - stroke: black; +.nv-x .nv-axis g path.domain { + stroke: black; + stroke-width: 2; } .nv-y .nv-axis g path.domain { - stroke: black; + stroke: black; + stroke-width: 2; +} + +.nvd3 .nv-axis.nv-x path.domain { + stroke-opacity: 1; +} + +.nvd3 .nv-axis.nv-y path.domain { + stroke-opacity: 1; +} + +line.nv-regLine { + stroke: red !important; +} + +.nv-axisMin-x, +.nv-axisMax-x, +.nv-axisMin-y, +.nv-axisMax-y { + display: none; } diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 861af3d6..f3712b5d 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1340,14 +1340,14 @@ "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], [ - "384", - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ], - [ "383", "HLCM_0311", "GSE9588 Human Liver Normal (Mar11) Males" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" ] ], "Phenotypes": [ @@ -1493,6 +1493,15 @@ ] ] }, + "Islets-Gerling": { + "Phenotypes": [ + [ + "None", + "Islets-GerlingPublish", + "Islets-Gerling Published Phenotypes" + ] + ] + }, "TIGEM-Retina-RNA-Seq": { "Phenotypes": [ [ @@ -1561,6 +1570,11 @@ ], "Heart mRNA": [ [ + "820", + "UCLA_AXB_BXA_Aor_Jan16", + "UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA" + ], + [ "421", "IRCM_AXBXA_HRI0213", "IRCM AXB/BXA Mouse Heart ILM MouseRef-8 v2.0 (Feb13) RankInv" @@ -1568,6 +1582,11 @@ ], "Liver mRNA": [ [ + "822", + "UCLA_AXB_BXA_Liv_Jan16", + "UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA" + ], + [ "352", "GSE16780AB_UCLA_ML0911", "GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA" @@ -1727,11 +1746,6 @@ ], "Striatum mRNA": [ [ - "85", - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ "84", "SA_M2_0905_R", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" @@ -1740,22 +1754,27 @@ "83", "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" + ], + [ + "85", + "SA_M2_0905_P", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" ] ] }, "BHF2": { "Adipose mRNA": [ [ - "197", - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ "196", "UCLA_BHF2_ADIPOSE_MALE", "UCLA BHF2 Adipose Male mlratio" ], [ + "197", + "UCLA_BHF2_ADIPOSE_FEMALE", + "UCLA BHF2 Adipose Female mlratio" + ], + [ "165", "UCLA_BHF2_ADIPOSE_0605", "UCLA BHF2 Adipose (June05) mlratio" @@ -1763,16 +1782,16 @@ ], "Brain mRNA": [ [ - "199", - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ "198", "UCLA_BHF2_BRAIN_MALE", "UCLA BHF2 Brain Male mlratio" ], [ + "199", + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], + [ "166", "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" @@ -1787,16 +1806,16 @@ ], "Liver mRNA": [ [ - "201", - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ "200", "UCLA_BHF2_LIVER_MALE", "UCLA BHF2 Liver Male mlratio" ], [ + "201", + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ "167", "UCLA_BHF2_LIVER_0605", "UCLA BHF2 Liver (June05) mlratio" @@ -2000,11 +2019,6 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ "80", "BR_U_0805_M", "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" @@ -2015,6 +2029,11 @@ "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], + [ "42", "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" @@ -2142,6 +2161,13 @@ "BXD Genotypes" ] ], + "Heart mRNA": [ + [ + "819", + "UCLA_BXD_Aor_Jan16", + "UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA" + ] + ], "Hematopoietic Cells mRNA": [ [ "149", @@ -2218,6 +2244,26 @@ "UMUTAffy Hippocampus Exon (Feb09) RMA" ], [ + "814", + "UTHSC_ILM_BXD_hipp_NOSb_0217", + "UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) RankInv" + ], + [ + "815", + "UTHSC_ILM_BXD_hipp_NOEb_0217", + "UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) RankInv" + ], + [ + "816", + "UTHSC_ILM_BXD_hipp_RSSb_0217", + "UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv" + ], + [ + "817", + "UTHSC_ILM_BXD_hipp_RSEb_0217", + "UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) RankInv" + ], + [ "780", "UTHSC_ILM_BXD_hipp_NOEb_0216", "UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) RankInv" @@ -2391,14 +2437,24 @@ ], "Liver Proteome": [ [ + "540", + "EPFLETHZBXDprotCD0514", + "EPFL/ETHZ BXD Liver, Chow Diet (Jun16) Top100 SWATH" + ], + [ + "541", + "EPFLETHZBXDprotHFD0514", + "EPFL/ETHZ BXD Liver, High Fat Diet (Jun16) Top100 SWATH" + ], + [ "704", "EPFLETHZBXDprotCD_LS1114", - "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Light SWATH" + "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Top10 SWATH" ], [ "705", "EPFLETHZBXDprotHF_LS1114", - "EPFL/ETHZ BXD Liver, High Fat Diet (Oct14) Light SWATH" + "EPFL/ETHZ BXD Liver, High Fat Diet Diet (Oct14) Top10 SWATH" ], [ "703", @@ -2414,20 +2470,15 @@ "489", "EPFLBXDprotHFDRPN0214", "EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM" - ], - [ - "540", - "EPFLETHZBXDprotCD0514", - "EPFL/ETHZ BXD Liver, Soluble Proteins CD (Jun14) SWATH" - ], - [ - "541", - "EPFLETHZBXDprotHFD0514", - "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (Jun14) SWATH" ] ], "Liver mRNA": [ [ + "818", + "UCLA_BXD_Liv_Jan16", + "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA" + ], + [ "430", "EPFLMouseLiverRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" @@ -2443,6 +2494,11 @@ "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], [ + "433", + "EPFLMouseLiverBothExRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], + [ "700", "UTHSC-VGX_MmBXDHepatocytesRMA1014", "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA" @@ -2466,6 +2522,51 @@ "702", "SUH_Liv_RMAEx_0611", "SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA" + ], + [ + "256", + "GenEx_BXD_liverEt_M5_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes" + ], + [ + "257", + "GenEx_BXD_liverEt_M5M_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males" + ], + [ + "258", + "GenEx_BXD_liverEt_M5F_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females" + ], + [ + "307", + "GenEx_BXD_liverEt_RMA_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes" + ], + [ + "308", + "GenEx_BXD_liverEt_RMA_M_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males" + ], + [ + "309", + "GenEx_BXD_liverEt_RMA_F_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females" + ], + [ + "310", + "GenEx_BXD_liverSal_RMA_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes" + ], + [ + "311", + "GenEx_BXD_liverSal_RMA_M_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males" + ], + [ + "312", + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females" ] ], "Lung mRNA": [ @@ -2546,14 +2647,14 @@ "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], [ - "275", - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" - ], - [ "274", "DevNeocortex_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" + ], + [ + "275", + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -2761,11 +2862,6 @@ ], "Ventral Tegmental Area mRNA": [ [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" - ], - [ "229", "VCUEtOH_0609_R", "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" @@ -2774,6 +2870,11 @@ "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" ] ] }, @@ -2920,6 +3021,27 @@ ] ] }, + "CIE-RMA": { + "Midbrain mRNA": [ + [ + "830", + "INIA_UTHSC_Mid_AffyMTA1_Apr17", + "INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) RMA" + ], + [ + "834", + "INIA_UTHSC_Mid_AffyMTA1_Ex_May17", + "INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA" + ] + ], + "Phenotypes": [ + [ + "None", + "CIE-RMAPublish", + "CIE-RMA Published Phenotypes" + ] + ] + }, "CMS": { "Phenotypes": [ [ @@ -3021,6 +3143,13 @@ "CXB Genotypes" ] ], + "Heart mRNA": [ + [ + "821", + "UCLA_CXB_Aor_Jan16", + "UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA" + ] + ], "Hippocampus mRNA": [ [ "100", @@ -3033,6 +3162,13 @@ "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], + "Liver mRNA": [ + [ + "823", + "UCLA_CXB_Liv_Jan16", + "UCLA CXB Liver Affy M430 2.0 (Jan16) RMA" + ] + ], "Phenotypes": [ [ "628", @@ -3048,6 +3184,7 @@ ] ] }, + "EMSR": {}, "HS": { "Hippocampus mRNA": [ [ @@ -3545,6 +3682,10 @@ "Brain, Development: Normal Gene Expression (Yale/Sestan)" ], [ + "Islets-Gerling", + "Pancreatic: Islets (UTHSC/Gerling)" + ], + [ "TIGEM-Retina-RNA-Seq", "Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)" ] @@ -3616,7 +3757,11 @@ ], [ "CIE-INIA", - "Chronic Intermittent Ethanol" + "Chronic Intermittent Ethanol Phase 1" + ], + [ + "CIE-RMA", + "Chronic Intermittent Ethanol Phase 2" ], [ "CMS", @@ -3631,6 +3776,10 @@ "CXB" ], [ + "EMSR", + "Ethanol-Medicated Stress Reduction" + ], + [ "HS", "Heterogeneous Stock" ], @@ -4414,6 +4563,12 @@ "Ventrolateral Prefrontal Cortex mRNA" ] ], + "Islets-Gerling": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "TIGEM-Retina-RNA-Seq": [ [ "Phenotypes", @@ -4630,6 +4785,10 @@ "Gastrointestinal mRNA" ], [ + "Heart mRNA", + "Heart mRNA" + ], + [ "Hematopoietic Cells mRNA", "Hematopoietic Cells mRNA" ], @@ -4780,6 +4939,16 @@ "LCM Brain Regions mRNA" ] ], + "CIE-RMA": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Midbrain mRNA", + "Midbrain mRNA" + ] + ], "CMS": [ [ "Phenotypes", @@ -4822,14 +4991,23 @@ "Genotypes" ], [ + "Heart mRNA", + "Heart mRNA" + ], + [ "Hippocampus mRNA", "Hippocampus mRNA" ], [ + "Liver mRNA", + "Liver mRNA" + ], + [ "Spleen mRNA", "Spleen mRNA" ] ], + "EMSR": [], "HS": [ [ "Phenotypes", diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js index 7a5a86bd..96763aca 100644 --- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js +++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js @@ -1,74 +1,64 @@ var chart; nv.addGraph(function() { - // - chart = nv.models.scatterChart(); - // - chart.showLegend(false); - chart.duration(300); - chart.color(d3.scale.category10().range()); - chart.pointRange([200,0]); - // - // chart.showDistX(true); - // chart.showDistY(true); - chart.xAxis.tickFormat(d3.format('.02f')); - chart.yAxis.tickFormat(d3.format('.02f')); - // chart.showXAxis(false); - // chart.showYAxis(false); - chart.xAxis.axisLabel(js_data.trait_1); - chart.yAxis.axisLabel(js_data.trait_2); - // - xmin = d3.min(js_data.data[0]); - xmax = d3.max(js_data.data[0]); - xrange = xmax - xmin; - ymin = d3.min(js_data.data[1]); - ymax = d3.max(js_data.data[1]); - yrange = ymax - ymin; - chart.xDomain([xmin - xrange/10, xmax + xrange/10]); - chart.yDomain([ymin - yrange/10, ymax + yrange/10]); - // - d3.select('#scatterplot2 svg').datum(nv.log(getdata())).call(chart); - nv.utils.windowResize(chart.update); - return chart; + // + chart = nv.models.scatterChart(); + // + chart.showLegend(false); + chart.duration(300); + chart.color(d3.scale.category10().range()); + chart.pointRange([200,0]); + // + chart.xAxis.axisLabel(js_data.trait_1); + chart.xAxis.axisLabelDistance(11); + chart.yAxis.axisLabel(js_data.trait_2); + chart.yAxis.axisLabelDistance(11); + // + xmin = d3.min(js_data.data[0]); + xmax = d3.max(js_data.data[0]); + xrange = xmax - xmin; + ymin = d3.min(js_data.data[1]); + ymax = d3.max(js_data.data[1]); + yrange = ymax - ymin; + chart.xDomain([xmin - xrange/10, xmax + xrange/10]); + chart.yDomain([ymin - yrange/10, ymax + yrange/10]); + chart.xAxis.tickFormat(d3.format(checkformat(xrange))); + chart.yAxis.tickFormat(d3.format(checkformat(yrange))); + // + chart.tooltip.contentGenerator(function (obj) { + return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>'; + }); + // + d3.select('#scatterplot2 svg').datum(nv.log(getdata())).call(chart); + nv.utils.windowResize(chart.update); + return chart; }); function getdata () { - var data = []; - data.push({ - values: [], - slope: js_data.slope, - intercept: js_data.intercept - }); - for (j = 0; j < js_data.data[0].length; j++) { - data[0].values.push({ - x: js_data.data[0][j], - y: js_data.data[1][j], - size: 10, - shape: 'circle' - }); - } - return data; + var data = []; + data.push({ + values: [], + slope: js_data.slope, + intercept: js_data.intercept + }); + for (j = 0; j < js_data.data[0].length; j++) { + data[0].values.push({ + x: js_data.data[0][j], + y: js_data.data[1][j], + size: 10, + shape: 'circle' + }); + } + return data; } - -function randomData(groups, points) { - var data = [], - shapes = ['circle'], - random = d3.random.normal(); - for (i = 0; i < groups; i++) { - data.push({ - key: 'Group ' + i, - values: [], - slope: Math.random() - .01, - intercept: Math.random() - .5 - }); - for (j = 0; j < points; j++) { - data[i].values.push({ - x: random(), - y: random(), - size: Math.random(), - shape: shapes[j % shapes.length] - }); - } - } - return data; + +function checkformat (range) { + cell = range / 10.0; + if (cell >= 1) { + return ",r"; + } else { + cell = -Math.log(cell); + n = cell.toString().split(".")[0].length; + return ",.0" + n + "f"; + } } diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index ec55ebeb..9ca3d63a 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -144,7 +144,7 @@ <p> Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel). {% if version: %} - <p><small>GeneNetwork v{{ version }}</small></p> + <p><small>GeneNetwork {{ version }}</small></p> {% endif %} </div> diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index 4464025e..05891c95 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -53,16 +53,6 @@ <h2>Correlation Scatterplot</h2> -<table class="table"> - <tbody> - <tr><th class="text-right">num overlap</th> <td>{{jsdata.num_overlap}}</td></tr> - <tr><th class="text-right">slope</th> <td>{{jsdata.slope}}</td></tr> - <tr><th class="text-right">intercept</th> <td>{{jsdata.intercept}}</td></tr> - <tr><th class="text-right">r value</th> <td>{{jsdata.r_value}}</td></tr> - <tr><th class="text-right">p value</th> <td>{{jsdata.p_value}}</td></tr> - </tbody> -</table> - <!-- <table class="table"> <tr> @@ -85,12 +75,12 @@ --> <div id="scatterplot2"> - <svg style="width: 1000px; height: 800px;"></svg> + <svg style="width: 1000px; height: 800px; margin-left: 10px;"></svg> </div> <br> -<div style="margin-left: 75px;"> +<div style="margin-left: 80px;"> {% if trait_1.dataset.type == "ProbeSet" %} <div> @@ -144,6 +134,18 @@ </div> +<br> + +<table class="table table-hover table-striped table-bordered" style="width: 250px; margin-left: 80px;"> + <tbody> + <tr><th>Number</th> <td>{{jsdata.num_overlap}}</td></tr> + <tr><th>Slope</th> <td>{{'%0.3f' % jsdata.slope}}</td></tr> + <tr><th>Intercept</th> <td>{{'%0.3f' % jsdata.intercept}}</td></tr> + <tr><th>R value</th> <td>{{'%0.3f' % jsdata.r_value}}</td></tr> + <tr><th>P value</th> <td>{{'%0.3e' % jsdata.p_value}}</td></tr> + </tbody> +</table> + {% endblock %} {% block js %} diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html index c707a4fc..2f1e06fa 100644 --- a/wqflask/wqflask/templates/error.html +++ b/wqflask/wqflask/templates/error.html @@ -35,7 +35,7 @@ </p> <pre> - GeneNetwork v{{ version }} {{ stack[0] }} + GeneNetwork {{ version }} {{ stack[0] }} {{ message }} (error) {{ stack[-3] }} {{ stack[-2] }} @@ -50,7 +50,7 @@ <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a> <div id="Stack" class="collapse"> <pre> - GeneNetwork v{{ version }} {% for line in stack %} {{ line }} + GeneNetwork {{ version }} {% for line in stack %} {{ line }} {% endfor %} </pre> </div> diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 4cea51b2..65debd10 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -14,7 +14,7 @@ <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}"> <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> <input type="hidden" name="dataset" value="{{ dataset.name }}"> - {% if mapping_method == "reaper" %} + {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %} <input type="hidden" name="genofile" value="{{ dataset.group.genofile }}"> {% endif %} <input type="hidden" name="method" value="{{ mapping_method }}"> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 56b6cc62..5a880647 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -129,6 +129,7 @@ <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script> <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script> <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script> + <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script> <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script> <script type="text/javascript" src="/static/new/javascript/stats.js"></script> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 0a0e9990..ac44b656 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -94,12 +94,15 @@ <div class="tab-pane" id="probability_plot"> <div style="padding: 20px" class="form-horizontal"> {% if sample_groups|length != 1 %} + Select Group: <select class="prob_plot_samples_group"> {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}">{{ pretty_group }}</option> {% endfor %} </select> - <br><br> + <button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button> + <br> + <br> {% endif %} <div id="prob_plot_container"> diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 1e831896..f7fcd2d0 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -46,7 +46,7 @@ from wqflask.database import db_session from wqflask import model from utility import Bunch, Struct, after -from utility.tools import LOG_SQL, LOG_SQLALCHEMY +from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY import logging from utility.logger import getLogger @@ -69,7 +69,7 @@ class AnonUser(object): if self.cookie: logger.debug("already is cookie") self.anon_id = verify_cookie(self.cookie) - + else: logger.debug("creating new cookie") self.anon_id, self.cookie = create_signed_cookie() @@ -78,17 +78,17 @@ class AnonUser(object): @after.after_this_request def set_cookie(response): response.set_cookie(self.cookie_name, self.cookie) - + def add_collection(self, new_collection): collection_dict = dict(name = new_collection.name, created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), num_members = new_collection.num_members, members = new_collection.get_members()) - + Redis.set(self.key, json.dumps(collection_dict)) Redis.expire(self.key, 60 * 60 * 24 * 5) - + def delete_collection(self, collection_name): existing_collections = self.get_collections() updated_collections = [] @@ -106,7 +106,7 @@ class AnonUser(object): updated_collections.append(this_collection) Redis.set(self.key, json.dumps(updated_collections)) - + def get_collections(self): json_collections = Redis.get(self.key) if json_collections == None or json_collections == "None": @@ -117,7 +117,7 @@ class AnonUser(object): collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p') collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p') return collections - + def import_traits_to_user(self): collections_list = json.loads(Redis.get(self.key)) for collection in collections_list: @@ -131,7 +131,7 @@ class AnonUser(object): uc.members = json.dumps(collection['members']) db_session.add(uc) db_session.commit() - + def display_num_collections(self): """ Returns the number of collections or a blank string if there are zero. @@ -217,7 +217,7 @@ class UserSession(object): """Actual sqlalchemy record""" # Only look it up once if needed, then store it try: - if LOG_SQLALCHEMY: + if LOG_SQL_ALCHEMY: logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG) # Already did this before @@ -237,7 +237,7 @@ class UserSession(object): def before_request(): g.user_session = UserSession() g.cookie_session = AnonUser() - + class UsersManager(object): def __init__(self): self.users = model.User.query.all() @@ -541,9 +541,9 @@ class LoginUser(object): import_col = "true" else: import_col = "false" - - #g.cookie_session.import_traits_to_user() - + + #g.cookie_session.import_traits_to_user() + return self.actual_login(user, import_collections=import_col) else: diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 39f4a686..07151425 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -53,7 +53,7 @@ from wqflask.ctl import ctl_analysis #from wqflask.trait_submission import submit_trait from utility import temp_data -from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION +from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH from utility.helper_functions import get_species_groups from base import webqtlFormData @@ -147,9 +147,8 @@ def tmp_page(img_path): img_base64 = bytesarray ) @app.route("/twitter/<path:filename>") -def bd_files(filename): - bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH'] - return send_from_directory(bd_path, filename) +def twitter(filename): + return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) #@app.route("/data_sharing") #def data_sharing_page(): |