diff options
Diffstat (limited to 'wqflask')
20 files changed, 328 insertions, 168 deletions
diff --git a/wqflask/__init__.py b/wqflask/__init__.py index 315b709e..e69de29b 100644 --- a/wqflask/__init__.py +++ b/wqflask/__init__.py @@ -1 +0,0 @@ -from wqflask import app 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/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1ef2bc26..1e66e957 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) +assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py new file mode 100644 index 00000000..14a2d689 --- /dev/null +++ b/wqflask/run_gunicorn.py @@ -0,0 +1,19 @@ +# Run with gunicorn, see ./bin/genenetwork2 for an example +# +# Run standalone with +# +# ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py + +# from flask import Flask +# application = Flask(__name__) + +print "Starting up Gunicorn process" + +from wqflask import app + +@app.route("/gunicorn") +def hello(): + return "<h1 style='color:blue'>Hello There!</h1>" + +if __name__ == "__main__": + app.run(host='0.0.0.0') diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 50805643..a0c76e51 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -1,5 +1,7 @@ # Starts the webserver with the ./bin/genenetwork2 command # +# This uses Werkzeug WSGI, see ./run_gunicorn.py for the alternative +# # Please note, running with host set externally below combined with # debug mode is a security risk unless you have a firewall setup, e.g. # @@ -22,11 +24,19 @@ 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..d3113302 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -16,7 +16,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id,value) - value + return value def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in @@ -51,7 +51,7 @@ def get_setting(command_id,guess=None): return None # ---- Check whether environment exists - logger.debug("Looking for "+command_id+"\n") + # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": command = OVERRIDES.get(command_id) @@ -63,7 +63,7 @@ def get_setting(command_id,guess=None): if command is None or command == "": # print command raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') - logger.debug("Set "+command_id+"="+str(command)) + # print("Set "+command_id+"="+str(command)) return command def get_setting_bool(id): @@ -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)) @@ -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. @@ -239,15 +247,17 @@ 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 = pylmm_command() -GEMMA_COMMAND = gemma_command() +PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +assert(GEMMA_COMMAND is not None) +PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() -PLINK_COMMAND = plink_command() -TEMPDIR = tempdir() # defaults to UNIX TMPDIR +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")) @@ -257,7 +267,7 @@ from six import string_types if os.environ.get('WQFLASK_OVERRIDES'): jsonfn = get_setting('WQFLASK_OVERRIDES') - logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + logger.info("WQFLASK_OVERRIDES: %s" % jsonfn) with open(jsonfn) as data_file: overrides = json.load(data_file) for k in overrides: @@ -267,3 +277,6 @@ if os.environ.get('WQFLASK_OVERRIDES'): else: OVERRIDES[k] = cmd logger.debug(OVERRIDES) + +# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") +assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 24432ad0..3d1c0d17 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -75,6 +75,46 @@ def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss #print("{}: {}".format(stage, mem/1024)) +def is_float(value): + try: + float(value) + return True + except: + return False + +def is_int(value): + try: + int(value) + return True + except: + return False + +def is_str(value): + if value is None: + return False + try: + str(value) + return True + except: + return False + +def get_float(vars,name,default=None): + if name in vars: + if is_float(vars[name]): + return float(vars[name]) + return None + +def get_int(vars,name,default=None): + if name in vars: + if is_int(vars[name]): + return float(vars[name]) + return default + +def get_string(vars,name,default=None): + if name in vars: + if not vars[name] is None: + return str(vars[name]) + return default class AuthException(Exception): pass @@ -96,7 +136,19 @@ class CorrelationResults(object): # get trait list from db (database name) # calculate correlation with Base vector and targets - print("TESTING...") + # Check parameters + assert('corr_type' in start_vars) + assert(is_str(start_vars['corr_type'])) + assert('dataset' in start_vars) + # assert('group' in start_vars) permitted to be empty? + assert('corr_sample_method' in start_vars) + assert('corr_samples_group' in start_vars) + assert('corr_dataset' in start_vars) + assert('min_expr' in start_vars) + assert('corr_return_results' in start_vars) + if 'loc_chr' in start_vars: + assert('min_loc_mb' in start_vars) + assert('max_loc_mb' in start_vars) with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": @@ -115,27 +167,17 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] - if 'min_expr' in start_vars: - if start_vars['min_expr'] != "": - self.min_expr = float(start_vars['min_expr']) - else: - self.min_expr = None - self.p_range_lower = float(start_vars['p_range_lower']) - self.p_range_upper = float(start_vars['p_range_upper']) + self.min_expr = get_float(start_vars,'min_expr') + self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0) + self.p_range_upper = get_float(start_vars,'p_range_upper',1.0) if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars and 'max_loc_mb' in start_vars): - self.location_chr = start_vars['loc_chr'] - if start_vars['min_loc_mb'].isdigit(): - self.min_location_mb = start_vars['min_loc_mb'] - else: - self.min_location_mb = None - if start_vars['max_loc_mb'].isdigit(): - self.max_location_mb = start_vars['max_loc_mb'] - else: - self.max_location_mb = None + self.location_chr = get_string(start_vars,'loc_chr') + self.min_location_mb = get_int(start_vars,'min_loc_mb') + self.max_location_mb = get_int(start_vars,'max_loc_mb') self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -183,7 +225,7 @@ class CorrelationResults(object): else: for trait, values in self.target_dataset.trait_data.iteritems(): self.get_sample_r_and_p_values(trait, values) - + elif self.corr_type == "lit": self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") lit_corr_data = self.do_lit_correlation_for_all_traits() @@ -564,7 +606,7 @@ class CorrelationResults(object): self.this_trait_vals.append(sample_value) target_vals.append(target_sample_value) - self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) + self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ if self.corr_method == 'pearson': @@ -574,8 +616,8 @@ class CorrelationResults(object): if num_overlap > 5: self.correlation_data[trait] = [sample_r, sample_p, num_overlap] - - + + """ correlations = [] @@ -673,8 +715,8 @@ class CorrelationResults(object): method=self.method) return trait_list - """ - + """ + def do_tissue_corr_for_all_traits_2(self): """Comments Possibly Out of Date!!!!! @@ -1089,7 +1131,7 @@ class CorrelationResults(object): totalTraits = len(traits) #XZ, 09/18/2008: total trait number return traits - + def calculate_corr_for_all_tissues(self, tissue_dataset_id=None): symbol_corr_dict = {} @@ -1129,7 +1171,7 @@ class CorrelationResults(object): values_2.append(target_value) correlation = calCorrelation(values_1, values_2) self.correlation_data[trait] = correlation - + def getFileName(self, target_db_name): ### dcrowell August 2008 """Returns the name of the reference database file with which correlations are calculated. Takes argument cursor which is a cursor object of any instance of a subclass of templatePage @@ -1144,7 +1186,7 @@ class CorrelationResults(object): return FileName def do_parallel_correlation(self, db_filename, num_overlap): - + #XZ, 01/14/2009: This method is for parallel computing only. #XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1) #XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected @@ -1313,7 +1355,7 @@ class CorrelationResults(object): z_value = z_value*math.sqrt(nOverlap-3) sample_p = 2.0*(1.0 - reaper.normp(abs(z_value))) - correlation_data[traitdataName] = [sample_r, sample_p, nOverlap] + correlation_data[traitdataName] = [sample_r, sample_p, nOverlap] # traitinfo = [traitdataName, sample_r, nOverlap] # allcorrelations.append(traitinfo) @@ -1321,7 +1363,7 @@ class CorrelationResults(object): return correlation_data # return allcorrelations - + datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') print("Invoking parallel computing") @@ -1378,5 +1420,3 @@ class CorrelationResults(object): # for one_result in results: # for one_traitinfo in one_result: # allcorrelations.append( one_traitinfo ) - - diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index a24e43d4..68920130 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,6 +11,7 @@ logger = utility.logger.getLogger(__name__ ) def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" + assert_bin(GEMMA_COMMAND); if this_dataset.group.genofile != None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -27,7 +28,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): if i < (len(this_chromosomes) - 1): chr_list_string += this_chromosomes[i+1].name + "," else: - chr_list_string += this_chromosomes[i+1].name + chr_list_string += this_chromosomes[i+1].name if covariates != "": gen_covariates_file(this_dataset, covariates) @@ -209,8 +210,13 @@ def parse_gemma_output(genofile_name): def parse_loco_output(this_dataset, gwa_output_filename): output_filelist = [] - with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file: - data = json.load(data_file) + jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json" + assert_file(jsonfn) + try: + with open(jsonfn) as data_file: + data = json.load(data_file) + except: + logger.error("Can not parse "+jsonfn) files = data['files'] for file in files: @@ -247,4 +253,4 @@ def parse_loco_output(this_dataset, gwa_output_filename): included_markers.append(line.split("\t")[1]) p_values.append(float(line.split("\t")[10])) - return marker_obs \ No newline at end of file + return marker_obs 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": [ [ @@ -3864,6 +3878,10 @@ "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 @@ <title>Loading Mapping Results</title> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" /> -<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" /> -<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" /> -<link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" /> -<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" /> <form method="post" action="/marker_regression" name="loading_form" id="loading_form" class="form-horizontal"> {% for key, value in start_vars.iteritems() %} <input type="hidden" name="{{ key }}" value="{{ value }}"> {% endfor %} <div class="container"> - <div class="row"> - <div style="margin-left: 46%; margin-right: 50%; min-height: 100vh; display: flex; align-items: center;"> - <h1>Loading Mapping Results...</h1> + <div> + <div style="min-height: 80vh; display: flex; align-items: center;"> + <div class="center-block" style="margin-left: 38%; margin-right: 38%; position: absolute; height:50px; width:24%; top:40%;"> + <h1>Loading Mapping Results...</h1> + </div> </div> - <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;"> - <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div> + <div style="min-height: 80vh; display: flex; align-items: center;"> + <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;"> + <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div> + </div> </div> </div> </div> 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 @@ <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> <input type="hidden" name="dataset" value="{{ dataset.name }}"> <input type="hidden" name="genofile" value="{{ genofile_string }}"> + <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}"> <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> {% for sample in samples %} @@ -154,7 +155,7 @@ <div class="tab-pane active" id="gn1_map"> <div class="qtlcharts"> {{ gifmap|safe }} - <img src="/generated/{{ filename }}.jpeg" usemap="#WebQTLImageMap"> + <img src="/generated/{{ filename }}.png" usemap="#WebQTLImageMap"> {% if additiveChecked|upper == "ON" %} <br> <span style="white-space: nowrap;">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.</span> @@ -180,10 +181,10 @@ </form> {% if selectedChr == -1 %} - <div style="width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> - <h2>Results</h2> - <div id="table_container"> - <table id="qtl_results" class="table table-hover table-striped nowrap"> + <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> + <h2>Mapping Statistics</h2> + <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;"> + <table id="trait_table" class="table table-hover table-striped nowrap"> <thead> <tr> <th></th> @@ -194,7 +195,7 @@ {% if plotScale != "physic" %} <th>cM</th> {% else %} - <th>Mb</th> + <th align="right">Mb</th> {% endif %} {% if 'additive' in trimmed_markers[0] %} <th>Add Eff</th> @@ -209,11 +210,11 @@ <tr> <td align="center" style="padding-right: 0px;"> <input type="checkbox" name="selectCheck" - class="checkbox edit_sample_checkbox" - value="{{ marker.name }}" checked="checked"> + class="checkbox trait_checkbox" + value="{{ marker.name }}"> </td> <td align="right">{{ loop.index }}</td> - <td>{{ marker.name }}</td> + <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} {% if 'lod_score' in marker %} <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> @@ -294,6 +295,7 @@ </script> {% endif %} + <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> {% if mapping_method != "gemma" and mapping_method != "plink" %} <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> @@ -304,7 +306,7 @@ <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); - $('#qtl_results').DataTable( { + $('#trait_table').DataTable( { {% if mapping_method != "reaper" %} "columns": [ { "type": "natural", "width": "5%" }, diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index a291baf3..dd4325e7 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -28,7 +28,9 @@ --> <div class="container"> <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2> + {% if this_trait.dataset.type != 'Publish' %} <h3>{{ this_trait.description_fmt }}</h3> + {% endif %} </div> <form method="post" action="/corr_compute" target="_blank" name="trait_page" id="trait_data_form" diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 2a62733e..1e6d41c2 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -8,6 +8,22 @@ <td>Tissue</td> <td>{{ this_trait.dataset.tissue }}</td> </tr> + <tr> + <td>Phenotype</td> + <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td> + </tr> + <tr> + <td>Authors</td> + <td><div style="width:40%;">{{ this_trait.authors }}</div></td> + </tr> + <tr> + <td>Title</td> + <td><div style="width:40%;">{{ this_trait.title }}</div></td> + </tr> + <tr> + <td>Journal</td> + <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td> + </tr> {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} {% if this_trait.symbol != None %} @@ -50,22 +66,29 @@ </td> </tr> {% endif %} + {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %} + {% if this_trait.dataset.type != 'Publish' %} <tr> <td>Resource Links</td> <td> - {% if this_trait.geneid != None %} + {% if this_trait.pubmed_id %} + <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed"> + PubMed + </a> + {% endif %} + {% if this_trait.geneid %} <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" title="Info from NCBI Entrez Gene"> NCBI </a> {% endif %} - {% if this_trait.omim != None %} + {% if this_trait.omim %} <a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" title="Summary from On Mendelion Inheritance in Man"> OMIM </a> {% endif %} - {% if this_trait.symbol != None %} + {% if this_trait.symbol %} <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> Genotation </a> @@ -77,6 +100,8 @@ {% endif %} </td> </tr> + {% endif %} + {% endif %} </table> <div style="margin-bottom:15px;" class="btn-toolbar"> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 77f78415..dcec2b9e 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -6,16 +6,16 @@ <ul class="nav nav-pills"> {% if dataset.group.mapping_id == "1" %} <li class="active"> - <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> + <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <li> - <a href="#pylmm" data-toggle="tab">pyLMM</a> + <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> </li> <li> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> <li> - <a href="#gemma" data-toggle="tab">GEMMA</a> + <a href="#pylmm" data-toggle="tab">pyLMM</a> </li> {% endif %} {% for mapping_method in dataset.group.mapping_names %} @@ -37,7 +37,60 @@ <div class="tab-content"> {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #} {% if dataset.group.mapping_id == "1" %} - <div class="tab-pane active" id="interval_mapping"> + <div class="tab-pane active" id="gemma"> + <div style="padding-top: 10px;" class="form-horizontal"> + {% if genofiles and genofiles|length>0 %} + <div class="mapping_method_fields form-group"> + <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left: 20px;" class="col-xs-8 controls"> + <select id="genofile_gemma" class="form-control"> + {% for item in genofiles %} + <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> + {% endfor %} + </select> + </div> + </div> + {% endif %} + <div class="mapping_method_fields form-group"> + <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> + <div style="margin-left: 20px;" class="col-xs-3 controls"> + <input name="maf_gemma" value="0.01" type="text" class="form-control"> + </div> + </div> + <div class="mapping_method_fields form-group"> + <label class="col-xs-4 control-label">Use LOCO</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label class="radio-inline"> + <input type="radio" name="use_loco" value="True"> + Yes + </label> + <label class="radio-inline"> + <input type="radio" name="use_loco" value="False" checked=""> + No + </label> + </div> + </div> + </div> + <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> + <div class="mapping_method_fields form-group"> + <button type="button" id="select_covariates" class="btn btn-default"> + Select Covariates + </button> + <button type="button" id="remove_covariates" class="btn btn-default"> + Remove Covariates + </button> + </div> + </div> + + <div class="form-group"> + <div class="col-xs-4 controls"> + <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> + Compute + </button> + </div> + </div> + </div> + <div class="tab-pane" id="interval_mapping"> <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> @@ -131,62 +184,6 @@ <!--<div id="alert_placeholder"></div>--> </div> </div> - <div class="tab-pane" id="pylmm"> - <div style="margin-top: 20px" class="form-horizontal"> - {% if genofiles and genofiles|length>0 %} - <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> - <select id="genofile_pylmm" class="form-control"> - {% for item in genofiles %} - <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> - {% endfor %} - </select> - </div> - </div> - {% endif %} -<!-- - <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - <input name="control_pylmm" value="{{ nearest_marker }}" type="text" /> - {% else %} - <input name="control_pylmm" value="" type="text" /> - {% endif %} - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="true"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="false" checked=""> - No - </label> - </div> - </div> - <div class="mapping_method_fields form-group"> - <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> - <div class="col-xs-12 controls"> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="True"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> - No - </label> - </div> - </div> ---> - <div class="form-group"> - <div style="padding-left:15px;" class="controls"> - <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression"> - <i class="icon-ok-circle icon-white"></i> Compute - </button> - </div> - </div> - </div> - </div> <div class="tab-pane" id="rqtl_geno"> <div style="margin-top: 20px" class="form-horizontal"> @@ -294,13 +291,13 @@ </div> </div> </div> - <div class="tab-pane" id="gemma"> - <div style="padding-top: 10px;" class="form-horizontal"> + <div class="tab-pane" id="pylmm"> + <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> <div style="margin-left: 20px;" class="col-xs-8 controls"> - <select id="genofile_gemma" class="form-control"> + <select id="genofile_pylmm" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> {% endfor %} @@ -308,42 +305,45 @@ </div> </div> {% endif %} +<!-- <div class="mapping_method_fields form-group"> - <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> - <div style="margin-left: 20px;" class="col-xs-3 controls"> - <input name="maf_gemma" value="0.01" type="text" class="form-control"> + <label for="control_for" class="col-xs-3 control-label">Control for</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> + {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} + <input name="control_pylmm" value="{{ nearest_marker }}" type="text" /> + {% else %} + <input name="control_pylmm" value="" type="text" /> + {% endif %} + <label class="radio-inline"> + <input type="radio" name="do_control_pylmm" value="true"> + Yes + </label> + <label class="radio-inline"> + <input type="radio" name="do_control_pylmm" value="false" checked=""> + No + </label> </div> </div> <div class="mapping_method_fields form-group"> - <label class="col-xs-4 control-label">Use LOCO</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> + <div class="col-xs-12 controls"> <label class="radio-inline"> - <input type="radio" name="use_loco" value="True"> + <input type="radio" name="manhattan_plot_pylmm" value="True"> Yes </label> <label class="radio-inline"> - <input type="radio" name="use_loco" value="False" checked=""> + <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> No </label> </div> </div> - </div> - <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> - <div class="mapping_method_fields form-group"> - <button type="button" id="select_covariates" class="btn btn-default"> - Select Covariates - </button> - <button type="button" id="remove_covariates" class="btn btn-default"> - Remove Covariates - </button> - </div> - </div> - - <div class="form-group"> - <div class="col-xs-4 controls"> - <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> - Compute - </button> +--> + <div class="form-group"> + <div style="padding-left:15px;" class="controls"> + <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression"> + <i class="icon-ok-circle icon-white"></i> Compute + </button> + </div> </div> </div> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 68e779a1..4e81c29c 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -557,6 +557,7 @@ def marker_regression_page(): wanted = ( 'trait_id', 'dataset', + 'geno_db_exists', 'method', 'mapping_results_path', 'trimmed_markers', @@ -765,7 +766,7 @@ def corr_scatter_plot_page(): def submit_bnw(): logger.error(request.url) template_vars = get_bnw_input(request.form) - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) # Todo: Can we simplify this? -Sam def sharing_info_page(): diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py new file mode 100644 index 00000000..be9c7b37 --- /dev/null +++ b/wqflask/wsgi.py @@ -0,0 +1,4 @@ +from run_gunicorn import app as application # expect application as a name + +if __name__ == "__main__": + application.run() |