From 837ce8b9c779b1da6e4390220ccd353b289c1fca Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Dec 2017 09:11:31 -0600 Subject: Bring in some earlier work - mostly documentation and startup handling --- wqflask/base/data_set.py | 2 +- wqflask/runserver.py | 12 ++++++++++-- wqflask/utility/logger.py | 2 +- wqflask/utility/tools.py | 27 +++++++++++++++++++++------ 4 files changed, 33 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6649f8af..a4eaaa2e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -332,7 +332,7 @@ class DatasetGroup(object): if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers if self.genofile: self.markers = marker_class(self.genofile[:-5]) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 50805643..50f134db 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -22,11 +22,19 @@ ENDC = '\033[0m' import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE,get_setting_int +from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool port = get_setting_int("SERVER_PORT") -logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC)) +print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + +if get_setting_bool("USE_GN_SERVER"): + import requests + page = requests.get(get_setting("GN_SERVER_URL")) + if page.status_code != 200: + raise Exception("API server not found!") + +print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) werkzeug_logger = logging.getLogger('werkzeug') diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index bacb0aa4..128706df 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI). def warning(self,*args): """Call logging.warning for multiple args""" self.collect(self.logger.warning,*args) - self.logger.warning(self.collect(*args)) + # self.logger.warning(self.collect(*args)) def error(self,*args): """Call logging.error for multiple args""" diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c5685cdd..63b7149c 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -147,9 +147,14 @@ def assert_writable_dir(dir): fh.close() os.remove(fn) except IOError: - raise Exception('Unable to write test.txt to directory ' + dir ) + raise Exception('Unable to write test.txt to directory ' + dir) return dir +def assert_file(fn): + if not valid_file(fn): + raise Exception('Unable to find file '+fn) + return fn + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) @@ -174,6 +179,9 @@ def locate(name, subdir=None): if subdir: sys.stderr.write(subdir) raise Exception("Can not locate "+name+" in "+base) +def locate_phewas(name, subdir=None): + return locate(name,'/phewas/'+subdir) + def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -243,11 +251,11 @@ JS_GUIX_PATH = get_setting('JS_GUIX_PATH') JS_GN_PATH = get_setting('JS_GN_PATH') # assert_dir(JS_GN_PATH) -PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = gemma_command() -GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() -PLINK_COMMAND = plink_command() -TEMPDIR = tempdir() # defaults to UNIX TMPDIR +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 +assert_dir(TEMPDIR) # ---- Handle specific JS modules JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) @@ -267,3 +275,10 @@ if os.environ.get('WQFLASK_OVERRIDES'): else: OVERRIDES[k] = cmd logger.debug(OVERRIDES) + +assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") +assert_dir(get_setting("JS_BIODALLIANCE")) +assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") +assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") +assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) +assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js") -- cgit v1.2.3 From 8ae775f831c278a3ad97372ad90cba5845e8e6ca Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 20 Dec 2017 10:02:43 -0600 Subject: tools: find path for JS and gemma_wrapper --- wqflask/utility/tools.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 63b7149c..57f97a81 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -105,7 +105,7 @@ def js_path(module=None): 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)" + raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" def pylmm_command(guess=None): return assert_bin(get_setting("PYLMM_COMMAND",guess)) @@ -247,13 +247,14 @@ USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') GENENETWORK_FILES = get_setting('GENENETWORK_FILES') JS_GUIX_PATH = get_setting('JS_GUIX_PATH') -# assert_dir(JS_GUIX_PATH) - don't enforce right now +assert_dir(JS_GUIX_PATH) 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()) +GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) @@ -276,9 +277,9 @@ if os.environ.get('WQFLASK_OVERRIDES'): OVERRIDES[k] = cmd logger.debug(OVERRIDES) -assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -assert_dir(get_setting("JS_BIODALLIANCE")) -assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") -assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") -assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) -assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js") +# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") +# assert_dir(get_setting("JS_BIODALLIANCE")) +# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") +# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") +# assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) +assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") -- cgit v1.2.3 From 623cdd2cfafc3d2dd45bc1adf460c9f3c5120e7a Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 24 Jan 2018 20:11:59 +0000 Subject: Added links for markers in mapping results table when genotypes exist in DB Added more info to trait details for phenotype traits Changed order of mapping methods Fixed layout of mapping loading screen to hopefully be centered on different screen sizes Improved layout of some elements in mapping results page --- .../wqflask/marker_regression/marker_regression.py | 10 ++ .../marker_regression/marker_regression_gn1.py | 17 +- .../new/javascript/dataset_menu_structure.json | 24 +++ .../new/javascript/show_trait_mapping_tools.js | 1 + wqflask/wqflask/templates/loading.html | 18 +-- .../wqflask/templates/marker_regression_gn1.html | 22 +-- wqflask/wqflask/templates/show_trait.html | 2 + wqflask/wqflask/templates/show_trait_details.html | 31 +++- .../templates/show_trait_mapping_tools.html | 174 ++++++++++----------- wqflask/wqflask/views.py | 1 + 10 files changed, 184 insertions(+), 116 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index bcb14451..087b95b4 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -79,6 +79,16 @@ class MarkerRegression(object): self.samples.append(sample) self.vals.append(value) + #ZS: Check if genotypes exist in the DB in order to create links for markers + if "geno_db_exists" in start_vars: + self.geno_db_exists = start_vars['geno_db_exists'] + else: + try: + geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno") + self.geno_db_exists = "True" + except: + self.geno_db_exists = "False" + self.mapping_method = start_vars['method'] if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 93bd9d42..211cf187 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -174,6 +174,8 @@ class MarkerRegression(object): if 'genofile_string' in start_vars: self.genofile_string = start_vars['genofile_string'] + self.geno_db_exists = start_vars['geno_db_exists'] + #Needing for form submission when doing single chr mapping or remapping after changing options self.samples = start_vars['samples'] self.vals = start_vars['vals'] @@ -576,7 +578,7 @@ class MarkerRegression(object): self.gifmap = gifmap.__str__() self.filename= webqtlUtil.genRandStr("Itvl_") - intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg') + intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png') intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap') #Scales plot differently for high resolution @@ -616,7 +618,7 @@ class MarkerRegression(object): else: showLocusForm = intImg - if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm: + if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm): self.perm_filename = self.drawPermutationHistogram() #perm_text_file = self.permutationTextFile() @@ -1200,8 +1202,10 @@ class MarkerRegression(object): if self.controlLocus and self.doControl != "false": string2 = 'Using %s as control' % self.controlLocus else: - if self.mapping_method == "gemma": + if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": + string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": string2 = 'Using PLINK mapping method with no control for other QTLs.' else: @@ -1963,6 +1967,8 @@ class MarkerRegression(object): if self.permChecked and self.nperm > 0 and not self.multipleInterval: LRS_LOD_Max = max(self.significant, LRS_LOD_Max) + else: + LRS_LOD_Max = 1.15*LRS_LOD_Max #genotype trait will give infinite LRS LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS) @@ -2164,10 +2170,7 @@ class MarkerRegression(object): # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: - if previous_chr_as_int % 2 == 1: - point_color = pid.grey - else: - point_color = pid.black + point_color = pid.black canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 8de85a86..b7ebb9ed 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -2974,6 +2974,20 @@ ] ] }, + "BXD-Harvested": { + "Liver mRNA": [ + [ + "843", + "UTHSC-BXD-Harv_Liv-0118", + "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **" + ] + ] + }, "BXD300": { "Genotypes": [ [ @@ -3863,6 +3877,10 @@ "BXD-Bone", "BXD Bone" ], + [ + "BXD-Harvested", + "BXD NIA Longevity Study" + ], [ "BXD300", "BXD300" @@ -5007,6 +5025,12 @@ "Phenotypes" ] ], + "BXD-Harvested": [ + [ + "Liver mRNA", + "Liver mRNA" + ] + ], "BXD300": [ [ "Phenotypes", diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 2f1d836a..4d98f5d8 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -245,6 +245,7 @@ //$("#static_progress_bar_container").modal(); url = "/loading"; $('input[name=method]').val("gemma_bimbam"); + $('input[name=num_perm]').val(0); $('input[name=genofile]').val($('#genofile_gemma').val()); $('input[name=maf]').val($('input[name=maf_gemma]').val()); form_data = $('#trait_data_form').serialize(); diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index cede0e86..46136ddb 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -1,20 +1,20 @@ Loading Mapping Results - - - -
{% for key, value in start_vars.iteritems() %} {% endfor %}
-
-
-

Loading Mapping Results...

+
+
+
+

Loading Mapping Results...

+
-
-
+
+
+
+
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index d13c68cd..08a934a6 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -15,6 +15,7 @@ + {% for sample in samples %} @@ -154,7 +155,7 @@
{{ gifmap|safe }} - + {% if additiveChecked|upper == "ON" %}
A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values. @@ -180,10 +181,10 @@ {% if selectedChr == -1 %} -
-

Results

-
- +
+

Mapping Statistics

+
+
@@ -194,7 +195,7 @@ {% if plotScale != "physic" %} {% else %} - + {% endif %} {% if 'additive' in trimmed_markers[0] %} @@ -209,11 +210,11 @@ - + {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} {% if 'lod_score' in marker %} @@ -294,6 +295,7 @@ {% endif %} + {% if mapping_method != "gemma" and mapping_method != "plink" %} @@ -304,7 +306,7 @@
cMMbMbAdd Eff
+ class="checkbox trait_checkbox" + value="{{ marker.name }}"> {{ loop.index }}{{ marker.name }}{% if geno_db_exists == "True" %}{{ marker.name }}{% else %}{{ marker.name }}{% endif %}{{ '%0.2f' | format(marker.lod_score|float) }}