From e48ec8826ec48bd4ba53f681796a235737ab0d29 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 30 Jan 2015 17:21:19 +0000 Subject: Fixed several bugs Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem --- wqflask/base/data_set.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 15a8c7cc..8965e1d1 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -640,7 +640,7 @@ class PhenotypeDataSet(DataSet): 'Year', 'Max LRS', 'Max LRS Location', - 'Add. Effect'] + 'Add. Effect ?'] self.type = 'Publish' @@ -901,7 +901,7 @@ class MrnaAssayDataSet(DataSet): 'Mean Expr', 'Max LRS', 'Max LRS Location', - 'Add. Effect'] + 'Add. Effect ?'] # Todo: Obsolete or rename this field self.type = 'ProbeSet' -- cgit v1.2.3 From 69e509720d9242972a49635ef0fd8e725a7d9cc6 Mon Sep 17 00:00:00 2001 From: DannyArends Date: Tue, 17 Mar 2015 19:39:39 +0100 Subject: Converting an absolute path to a relative path --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8965e1d1..489bd374 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -79,7 +79,7 @@ class Dataset_Types(object): def __init__(self): self.datasets = {} - file_name = "/home/zas1024/gene/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) -- cgit v1.2.3 From 9a5fe211a846184aea7027aa90fde3fba93697e4 Mon Sep 17 00:00:00 2001 From: DannyArends Date: Mon, 23 Mar 2015 14:59:18 +0000 Subject: Updates to make GN2 work on my version of penguin (ports, and paths) --- wqflask/base/webqtlConfig.py | 2 +- wqflask/runserver.py | 4 ++-- wqflask/secure_server.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 23d32233..019d592b 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -49,7 +49,7 @@ GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mam ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" -GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later +GNROOT = "/home/danny/GeneNetwork/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 8ab88580..9d5686a9 100755 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -20,7 +20,7 @@ from wqflask import app import logging #from themodule import TheHandlerYouWant -file_handler = logging.FileHandler("/tmp/flask_gn_log") +file_handler = logging.FileHandler("/tmp/flask_gn_log_danny_unsecure") file_handler.setLevel(logging.DEBUG) app.logger.addHandler(file_handler) @@ -28,7 +28,7 @@ import logging_tree logging_tree.printout() app.run(host='0.0.0.0', - port=5002, + port=5003, use_debugger=False, threaded=True, use_reloader=True) diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py index 975c97c0..248559f3 100755 --- a/wqflask/secure_server.py +++ b/wqflask/secure_server.py @@ -72,7 +72,7 @@ if __name__ == '__main__': app.run(host='0.0.0.0', - port=5002, + port=5003, use_debugger=True, threaded=True, use_reloader=True) -- cgit v1.2.3 From 5eebf10533e0f03254a89fd886c02fed3a7e188d Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 24 Mar 2015 16:27:58 +0000 Subject: Change back port location and home directory location; this should be in external settings --- wqflask/base/webqtlConfig.py | 4 ++-- wqflask/secure_server.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 019d592b..e74b9ce5 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -49,13 +49,13 @@ GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mam ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" -GNROOT = "/home/danny/GeneNetwork/" # Will remove this and dependent items later +GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' PYLMM_PATH = '/home/zas1024/plink/' SNP_PATH = '/home/zas1024/snps/' -IMGDIR = HTMLPATH +'image/' +IMGDIR = GNROOT + '/wqflask/wqflask/images/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' TMPDIR = '/tmp/' diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py index 248559f3..975c97c0 100755 --- a/wqflask/secure_server.py +++ b/wqflask/secure_server.py @@ -72,7 +72,7 @@ if __name__ == '__main__': app.run(host='0.0.0.0', - port=5003, + port=5002, use_debugger=True, threaded=True, use_reloader=True) -- cgit v1.2.3 From 93dcba89f7e424a759e3177a74b1ce322cdd7c57 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 25 Mar 2015 16:11:56 +0000 Subject: Pair scan image now loads properly --- wqflask/base/webqtlConfig.py | 2 +- .../wqflask/marker_regression/marker_regression.py | 6 +-- wqflask/wqflask/templates/pair_scan_results.html | 55 ++++------------------ wqflask/wqflask/templates/show_image.html | 5 ++ wqflask/wqflask/views.py | 23 ++++++++- 5 files changed, 38 insertions(+), 53 deletions(-) create mode 100644 wqflask/wqflask/templates/show_image.html (limited to 'wqflask/base') diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index e74b9ce5..49a596aa 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -58,7 +58,7 @@ SNP_PATH = '/home/zas1024/snps/' IMGDIR = GNROOT + '/wqflask/wqflask/images/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' -TMPDIR = '/tmp/' +TMPDIR = '/home/zas1024/tmp/' # Will remove this and dependent items later GENODIR = HTMLPATH + 'genotypes/' NEWGENODIR = HTMLPATH + 'new_genotypes/' GENO_ARCHIVE_DIR = GENODIR + 'archive/' diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index af441489..3fb9915b 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -321,9 +321,9 @@ class MarkerRegression(object): print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=self.model, method=self.method, n_cluster = 16) print("Pair scan results:", result_data_frame) - - self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") - png(file=webqtlConfig.IMGDIR+self.pair_scan_filename+".png") + + self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png" + png(file=webqtlConfig.TMPDIR+self.pair_scan_filename) plot(result_data_frame) dev_off() diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index a0041e11..869dabed 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -1,13 +1,13 @@ {% extends "base.html" %} -{% block title %}Interval Mapping{% endblock %} +{% block title %}Pair Scan{% endblock %} {% block css %} - {% endblock %} + {% block content %} {{ header("Mapping", @@ -21,7 +21,12 @@
- + + Embedded Image
@@ -31,30 +36,12 @@
- - {% endblock %} {% block js %} - - - - - - - - - @@ -62,30 +49,4 @@ - {% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_image.html b/wqflask/wqflask/templates/show_image.html new file mode 100644 index 00000000..521f5414 --- /dev/null +++ b/wqflask/wqflask/templates/show_image.html @@ -0,0 +1,5 @@ +Embedded Image \ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4b7bd639..7fec0456 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1,3 +1,4 @@ +# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function import sys @@ -20,6 +21,8 @@ import redis Redis = redis.StrictRedis() import flask +import base64 +import array import sqlalchemy #import config @@ -83,11 +86,18 @@ def index_page(): return render_template("index_page.html") -@app.route("/tmp") -def tmp_page(): +@app.route("/tmp/") +def tmp_page(img_path): print("In tmp_page") + print("img_path:", img_path) initial_start_vars = request.form print("initial_start_vars:", initial_start_vars) + imgfile = open('/home/zas1024/tmp/' + img_path, 'rb') + imgdata = imgfile.read() + imgB64 = imgdata.encode("base64") + bytesarray = array.array('B', imgB64) + return render_template("show_image.html", + img_base64 = bytesarray ) @app.route("/data_sharing") @@ -344,6 +354,15 @@ def marker_regression_page(): with Bench("Rendering template"): if result['pair_scan'] == True: + img_path = result['pair_scan_filename'] + print("img_path:", img_path) + initial_start_vars = request.form + print("initial_start_vars:", initial_start_vars) + imgfile = open('/home/zas1024/tmp/' + img_path, 'rb') + imgdata = imgfile.read() + imgB64 = imgdata.encode("base64") + bytesarray = array.array('B', imgB64) + result['pair_scan_array'] = bytesarray rendered_template = render_template("pair_scan_results.html", **result) else: rendered_template = render_template("marker_regression.html", **result) -- cgit v1.2.3 From a840ad18e1fe3db98a359a159e9b9b72367a2839 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 26 Mar 2015 21:24:24 +0000 Subject: Removed several unused files from the base folder and their references in other files --- wqflask/base/GeneralObject.py | 68 ----- wqflask/base/JinjaPage.py | 28 -- wqflask/base/admin.py | 86 ------ wqflask/base/cgiData.py | 66 ----- wqflask/base/cookieData.py | 49 ---- wqflask/base/footer.py | 6 - wqflask/base/generate_probesetfreeze_file.py | 31 --- wqflask/base/header.py | 6 - wqflask/base/indexBody.py | 290 --------------------- wqflask/base/myCookie.py | 51 ---- wqflask/base/sessionData.py | 50 ---- wqflask/base/templatePage.py | 222 ---------------- wqflask/base/webqtlFormData.py | 6 - wqflask/wqflask/search_results.py | 2 - .../static/new/javascript/css/bar_chart.css | 15 -- .../wqflask/static/new/javascript/css/box_plot.css | 20 -- .../wqflask/static/new/javascript/css/charts.css | 28 -- .../static/new/javascript/css/corr_matrix.css | 12 - .../new/javascript/css/corr_scatter_plot.css | 13 - .../static/new/javascript/css/d3-tip.min.css | 1 - .../static/new/javascript/css/interval_mapping.css | 32 --- wqflask/wqflask/static/new/javascript/css/main.css | 4 - .../new/javascript/css/marker_regression.css | 38 --- .../static/new/javascript/css/panelutil.css | 91 ------- .../wqflask/static/new/javascript/css/parsley.css | 20 -- .../static/new/javascript/css/scatter-matrix.css | 40 --- .../static/new/javascript/css/show_trait.css | 7 - .../wqflask/static/new/javascript/css/table.css | 36 --- 28 files changed, 1318 deletions(-) delete mode 100755 wqflask/base/GeneralObject.py delete mode 100755 wqflask/base/JinjaPage.py delete mode 100755 wqflask/base/admin.py delete mode 100755 wqflask/base/cgiData.py delete mode 100755 wqflask/base/cookieData.py delete mode 100755 wqflask/base/footer.py delete mode 100755 wqflask/base/generate_probesetfreeze_file.py delete mode 100755 wqflask/base/header.py delete mode 100755 wqflask/base/indexBody.py delete mode 100755 wqflask/base/myCookie.py delete mode 100755 wqflask/base/sessionData.py delete mode 100755 wqflask/base/templatePage.py delete mode 100755 wqflask/wqflask/static/new/javascript/css/bar_chart.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/box_plot.css delete mode 100644 wqflask/wqflask/static/new/javascript/css/charts.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/corr_matrix.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css delete mode 100644 wqflask/wqflask/static/new/javascript/css/d3-tip.min.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/interval_mapping.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/main.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/marker_regression.css delete mode 100644 wqflask/wqflask/static/new/javascript/css/panelutil.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/parsley.css delete mode 100644 wqflask/wqflask/static/new/javascript/css/scatter-matrix.css delete mode 100644 wqflask/wqflask/static/new/javascript/css/show_trait.css delete mode 100755 wqflask/wqflask/static/new/javascript/css/table.css (limited to 'wqflask/base') diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py deleted file mode 100755 index 53d1357b..00000000 --- a/wqflask/base/GeneralObject.py +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -class GeneralObject: - """ - Base class to define an Object. - a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] - a.sort(lambda x, y: cmp(x.eggs, y.eggs)) - """ - - def __init__(self, *args, **kw): - self.contents = list(args) - for name, value in kw.items(): - setattr(self, name, value) - - def __setitem__(self, key, value): - setattr(self, key, value) - - def __getitem__(self, key): - return getattr(self, key) - - def __getattr__(self, key): - if key in self.__dict__.keys(): - return self.__dict__[key] - else: - return eval("self.__dict__.%s" % key) - - def __len__(self): - return len(self.__dict__) - 1 - - def __str__(self): - s = '' - for key in self.__dict__.keys(): - if key != 'contents': - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __repr__(self): - s = '' - for key in self.__dict__.keys(): - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __cmp__(self,other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) diff --git a/wqflask/base/JinjaPage.py b/wqflask/base/JinjaPage.py deleted file mode 100755 index 07e485b1..00000000 --- a/wqflask/base/JinjaPage.py +++ /dev/null @@ -1,28 +0,0 @@ -import logging -logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO) -_log = logging.getLogger("search") - -from pprint import pformat as pf - -import templatePage - -from utility import formatting - -import jinja2 -JinjaEnv = jinja2.Environment(loader=jinja2.FileSystemLoader('/gnshare/gn/web/webqtl/templates')) -JinjaEnv.globals['numify'] = formatting.numify - - -class JinjaPage(templatePage.templatePage): - """Class derived from our regular templatePage, but uses Jinja2 instead. - - When converting pages from Python generated templates, change the base class from templatePage - to JinjaPage - - """ - - - def write(self): - """We override the base template write so we can use Jinja2.""" - _log.info(pf(self.__dict__)) - return self.jtemplate.render(**self.__dict__) diff --git a/wqflask/base/admin.py b/wqflask/base/admin.py deleted file mode 100755 index 1ba75117..00000000 --- a/wqflask/base/admin.py +++ /dev/null @@ -1,86 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - - - - - -#XZ, 04/02/2009: we should put this into database. - - -###LIST of databases used into gene name query - - -ADMIN_search_dbs = { - 'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'], - 'KIDNEY': ['KI_2A_0405_Rz'], - 'ADRENAL GLAND': ['HXB_Adrenal_1208'], - 'HEART': ['HXB_Heart_1208'] - }, - 'mouse': {'CEREBELLUM': ['CB_M_0305_R'], - 'STRIATUM': ['SA_M2_0905_R', 'SA_M2_0405_RC', 'UTHSC_1107_RankInv', 'Striatum_Exon_0209'], - 'HIPPOCAMPUS': ['HC_M2_0606_R', 'UMUTAffyExon_0209_RMA'], - 'WHOLE BRAIN': ['BR_M2_1106_R', 'IBR_M_0106_R', 'BRF2_M_0805_R', 'UCLA_BHF2_BRAIN_0605'], - 'LIVER': ['LV_G_0106_B', 'UCLA_BHF2_LIVER_0605'], - 'EYE': ['Eye_M2_0908_R'], - 'HEMATOPOIETIC STEM CELLS': ['HC_U_0304_R'], - 'KIDNEY': ['MA_M2_0806_R'], - 'MAMMARY TUMORS': ['MA_M_0704_R', 'NCI_Agil_Mam_Tum_RMA_0409'], - 'PREFRONTAL CORTEX': ['VCUSal_1206_R'], - 'SPLEEN': ['IoP_SPL_RMA_0509'], - 'NUCLEUS ACCUMBENS': ['VCUSalo_1007_R'], - 'NEOCORTEX': ['HQFNeoc_0208_RankInv'], - 'ADIPOSE': ['UCLA_BHF2_ADIPOSE_0605'], - 'RETINA': ['Illum_Retina_BXD_RankInv0410'] - }, - 'human': { - 'LYMPHOBLAST B CELL': ['Human_1008', 'UT_CEPH_RankInv0909'], - 'WHOLE BRAIN': ['GSE5281_F_RMA0709', 'GSE15222_F_RI_0409'] - } - } - - -###LIST of tissue alias - -ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'], - 'STRIATUM': ['Str'], - 'HIPPOCAMPUS': ['Hip'], - 'WHOLE BRAIN': ['Brn'], - 'LIVER': ['Liv'], - 'EYE': ['Eye'], - 'PERITONEAL FAT': ['Fat'], - 'HEMATOPOIETIC STEM CELLS': ['Hsc'], - 'KIDNEY': ['Kid'], - 'ADRENAL GLAND': ['Adr'], - 'HEART': ['Hea'], - 'MAMMARY TUMORS': ['Mam'], - 'PREFRONTAL CORTEX': ['Pfc'], - 'SPLEEN': ['Spl'], - 'NUCLEUS ACCUMBENS': ['Nac'], - 'NEOCORTEX': ['Ctx'], - 'ADIPOSE': ['Wfat'], - 'RETINA': ['Ret'] - } diff --git a/wqflask/base/cgiData.py b/wqflask/base/cgiData.py deleted file mode 100755 index 155b3ec3..00000000 --- a/wqflask/base/cgiData.py +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -######################################### -#convert Field storage object to Dict object -#in order to be able to saved into a session file -######################################### - -class cgiData(dict): - '''convert Field storage object to Dict object - Filed storage object cannot be properly dumped - ''' - - def __init__(self, field_storage=None): - - if not field_storage: - field_storage={} - - for key in field_storage.keys(): - temp = field_storage.getlist(key) - if len(temp) > 1: - temp = map(self.toValue, temp) - elif len(temp) == 1: - temp = self.toValue(temp[0]) - else: - temp = None - self[key]= temp - - def toValue(self, obj): - '''fieldstorge returns different type of objects, \ - need to convert to string or None''' - try: - return obj.value - except: - return "" - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default - - getfirst = getvalue diff --git a/wqflask/base/cookieData.py b/wqflask/base/cookieData.py deleted file mode 100755 index eeb7c0cf..00000000 --- a/wqflask/base/cookieData.py +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -######################################### -#convert mod_python object to Dict object -#in order to be able to be pickled -######################################### - -class cookieData(dict): - 'convert mod python Cookie object to Dict object' - - def __init__(self, cookies=None): - - if not cookies: - cookies={} - - for key in cookies.keys(): - self[key.lower()]= cookies[key].value - - def getvalue(self, k, default= None): - try: - return self[k.lower()] - except: - return default - - getfirst = getvalue diff --git a/wqflask/base/footer.py b/wqflask/base/footer.py deleted file mode 100755 index 6f92fdf8..00000000 --- a/wqflask/base/footer.py +++ /dev/null @@ -1,6 +0,0 @@ -import webqtlConfig - -footer_html = open(webqtlConfig.HTMLPATH + 'footer.html', 'r').read() -footer = footer_html.replace('%"','%%"') - -footer_string = footer.replace('', '%s') diff --git a/wqflask/base/generate_probesetfreeze_file.py b/wqflask/base/generate_probesetfreeze_file.py deleted file mode 100755 index a0ff804b..00000000 --- a/wqflask/base/generate_probesetfreeze_file.py +++ /dev/null @@ -1,31 +0,0 @@ -from __future__ import absolute_import, print_function, division -import os -import math - -import json -import itertools - -from flask import Flask, g - -from base import webqtlConfig -from dbFunction import webqtlDatabaseFunction -from utility import webqtlUtil - -from MySQLdb import escape_string as escape -from pprint import pformat as pf - - -query = """ select ProbeSet.Name - from ProbeSetXRef, - ProbeSetFreeze, - ProbeSet - where ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and - ProbeSetFreeze.Name = "EPFLMouseMuscleCDRMA1211" and - ProbeSetXRef.ProbeSetId = ProbeSet.Id; - """ - -markers = g.db.execute(query).fetchall() -print("markers: ", pf(markers)) - -if __name__ == '__main__': - main() \ No newline at end of file diff --git a/wqflask/base/header.py b/wqflask/base/header.py deleted file mode 100755 index ec15e174..00000000 --- a/wqflask/base/header.py +++ /dev/null @@ -1,6 +0,0 @@ -import webqtlConfig - -header_string = open(webqtlConfig.HTMLPATH + 'header.html', 'r').read() -header_string = header_string.replace("\\'", "'") -header_string = header_string.replace('%"','%%"') -header_string = header_string.replace('', '%s') diff --git a/wqflask/base/indexBody.py b/wqflask/base/indexBody.py deleted file mode 100755 index a5bc4c17..00000000 --- a/wqflask/base/indexBody.py +++ /dev/null @@ -1,290 +0,0 @@ -index_body_string = """ - -

Select and Search -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Species: - - - -
- Group: - - - -
- Type: - - - -
- Database: - - - - -
- - -

    Databases marked with ** suffix are not public yet. -
    Access requires user login.

-
- Get Any: - - - - -
- - - -

    Enter terms, genes, ID numbers in the Get Any field. -
    Use * or ? wildcards (Cyp*a?, synap*). -
    Use Combined for terms such as tyrosine kinase.

- -
- Combined: - - - - -
- - -      -      - - -
- - - -
- - - - - - - - -

 ______________________________________________________ - -

  - -Quick HELP Examples and - - User's Guide

- - -  You can also use advanced commands. Copy these simple examples -
  into the Get Any or Combined search fields: - - - - - - - - -

Websites Affiliated with GeneNetwork

-

-

-

-

____________________________ - -

Getting Started   

-
    -
  1. Select Species (or select All) -
  2. Select Group (a specific sample) -
  3. Select Type of data: -
      -
    • Phenotype (traits) -
    • Genotype (markers) -
    • Expression (mRNAs) -
    -
  4. Select a Database -
  5. Enter search terms in the Get Any or Combined field: words, genes, ID numbers, probes, advanced search commands -
  6. Click on the Search button -
  7. Optional: Use the Make Default button to save your preferences -
- -

____________________________ - -

How to Use GeneNetwork - -

-

Take a 20-40 minute GeneNetwork Tour that includes screen shots and typical steps in the analysis.

-
-
-

For information about resources and methods, select the INFO buttons.

- - - -

Try the Workstation site to explore data and features that are being implemented.

- - -

Review the Conditions and Contacts pages for information on the status of data sets and advice on their use and citation.

- - -
- - - -

Mirror and Development Sites

- - - - -

History and Archive - -

-

GeneNetwork's Time Machine links to earlier versions that correspond to specific publication dates.

- -
- - -

- -""" diff --git a/wqflask/base/myCookie.py b/wqflask/base/myCookie.py deleted file mode 100755 index add7e6ea..00000000 --- a/wqflask/base/myCookie.py +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -######################################### -## python cookie and mod python cookie are -## not compatible -######################################### - -class myCookie(dict): - 'define my own cookie' - - def __init__(self, name="", value="", expire = None, path="/"): - self['name']= name - self['value']= value - self['expire']= expire - self['path']= path - - def __getattr__(self, key): - if key in self.keys(): - return self[key] - else: - return None - - def __nonzero__ (self): - if self['name']: - return 1 - else: - return 0 diff --git a/wqflask/base/sessionData.py b/wqflask/base/sessionData.py deleted file mode 100755 index 4b23060f..00000000 --- a/wqflask/base/sessionData.py +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -######################################### -#convert mod_python object to Dict object -#in order to be able to be pickled -######################################### - -class sessionData(dict): - 'convert mod python Session object to Dict object' - - def __init__(self, mod_python_session=None): - - if not mod_python_session: - mod_python_session = {} - - for key in mod_python_session.keys(): - self[key]= mod_python_session[key] - - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default - - getfirst = getvalue diff --git a/wqflask/base/templatePage.py b/wqflask/base/templatePage.py deleted file mode 100755 index a94d5153..00000000 --- a/wqflask/base/templatePage.py +++ /dev/null @@ -1,222 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -#templatePage.py -# -#--Genenetwork generates a lot of pages; this file is the generic version of them, defining routines they all use. -# -#Classes: -#templatePage -# -#Functions (of templatePage): -#__init__(...) -- class constructor, allows a more specific template to be used in addition to templatePage -#__str__(self) -- returns the object's elements as a tuple -#__del__(self) -- closes the current connection to MySQL, if there is one -#write -- explained below -#writefile -- explained below -#openMysql(self) -- opens a MySQL connection and stores the resulting cursor in the object's cursor variable -#updMysql(self) -- same as openMysql -#error -- explained below -#session -- explained below - - -import socket -import time -import shutil -import MySQLdb -import os - -from htmlgen import HTMLgen2 as HT - -import template -import webqtlConfig -import header -import footer -from utility import webqtlUtil - - - -class templatePage: - - contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer'] - - # you can pass in another template here if you want - def __init__(self, fd=None, template=template.template): - - # initiate dictionary - self.starttime = time.time() - self.dict = {} - self.template = template - - for item in self.contents: - self.dict[item] = "" - - self.dict['basehref'] = "" #webqtlConfig.BASEHREF - self.cursor = None - - self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed - self.content_type = 'text/html' - self.content_disposition = '' - self.redirection = '' - self.debug = '' - self.attachment = '' - - #XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!! - self.session_data_changed = {} - - self.userName = 'Guest' - self.privilege = 'guest' - - # Commenting this out for flask - we'll have to reimplement later - Sam - #if fd.input_session_data.has_key('user'): - # self.userName = fd.input_session_data['user'] - #if fd.input_session_data.has_key('privilege'): - # self.privilege = fd.input_session_data['privilege'] - - def __str__(self): - - #XZ: default setting - thisUserName = self.userName - thisPrivilege = self.privilege - #XZ: user may just go through login or logoff page - if self.session_data_changed.has_key('user'): - thisUserName = self.session_data_changed['user'] - if self.session_data_changed.has_key('privilege'): - thisPrivilege = self.session_data_changed['privilege'] - - if thisUserName == 'Guest': - userInfo = 'Welcome! Login' - else: - userInfo = 'Hi, %s! Logout' % thisUserName - - reload(header) - self.dict['header'] = header.header_string % userInfo - - serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn()) - reload(footer) - self.dict['footer'] = footer.footer_string % serverInfo - - slist = [] - for item in self.contents: - slist.append(self.dict[item]) - return self.template % tuple(slist) - - - def __del__(self): - if self.cursor: - self.cursor.close() - - def write(self): - 'return string representation of this object' - - if self.cursor: - self.cursor.close() - - return str(self) - - def writeFile(self, filename): - 'save string representation of this object into a file' - if self.cursor: - self.cursor.close() - - try: - 'it could take a long time to generate the file, save to .tmp first' - fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb') - fp.write(str(self)) - fp.close() - path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp') - path_html = os.path.join(webqtlConfig.TMPDIR, filename) - shutil.move(path_tmp,path_html) - except: - pass - - def openMysql(self): - try: - self.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \ - user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) - self.cursor = self.db_conn.cursor() - return True - except Exception: - heading = "Connect MySQL Server" - detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \ - The server may be down at this time"] - self.error(heading=heading,detail=detail,error="Error 2003") - return False - - def updMysql(self): - try: - self.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \ - user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD) - self.cursor = self.db_conn.cursor() - return True - except Exception: - heading = "Connect MySQL Server" - detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \ - The server may be down at this time "] - self.error(heading=heading,detail=detail,error="Error 2003") - return False - - def error(self,heading="",intro=[],detail=[],title="Error",error="Error"): - 'generating a WebQTL style error page' - Heading = HT.Paragraph(heading) - Heading.__setattr__("class","title") - - Intro = HT.Blockquote() - if intro: - for item in intro: - Intro.append(item) - else: - Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\ - your request.', HT.P(),'The nature of the error generated is as\ - follows:') - - Detail = HT.Blockquote() - Detail.append(HT.Span("%s : " % error,Class="fwb cr")) - if detail: - Detail2 = HT.Blockquote() - for item in detail: - Detail2.append(item) - Detail.append(HT.Italic(Detail2)) - - #Detail.__setattr__("class","subtitle") - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top") - TD_LR.append(Heading,Intro,Detail) - self.dict['body'] = str(TD_LR) - self.dict['title'] = title - - def session(self,mytitle="",myHeading=""): - 'generate a auto-refreshing temporary html file(waiting page)' - self.filename = webqtlUtil.generate_session() - self.dict['title'] = mytitle - self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF - - TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee') - Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr") - # NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py; - TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR) - self.dict['body'] = TD_LR - self.writeFile(self.filename + '.html') - return self.filename diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index a3537c87..44fdcc3f 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -35,15 +35,9 @@ import os import reaper import webqtlConfig -import cookieData -import sessionData -from cgiData import cgiData from webqtlCaseData import webqtlCaseData from utility import webqtlUtil - - - class webqtlFormData(object): 'Represents data from a WebQTL form page, needed to generate the next page' diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index a2958108..df1edb13 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -37,8 +37,6 @@ from dbFunction import webqtlDatabaseFunction from utility import formatting -#from base.JinjaPage import JinjaEnv, JinjaPage - #class QuickSearchResult(object): #def __init__(self, key, result_fields): # self.key = key diff --git a/wqflask/wqflask/static/new/javascript/css/bar_chart.css b/wqflask/wqflask/static/new/javascript/css/bar_chart.css deleted file mode 100755 index 78d31eee..00000000 --- a/wqflask/wqflask/static/new/javascript/css/bar_chart.css +++ /dev/null @@ -1,15 +0,0 @@ -.barchart .axis path, -.barchart .axis line { - fill: none; - stroke: #000; - shape-rendering: crispEdges; -} - -.bar { - fill: steelblue; - shape-rendering: crispEdges; -} -/* -.x.axis path { - display: none; -}*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/box_plot.css b/wqflask/wqflask/static/new/javascript/css/box_plot.css deleted file mode 100755 index 4c743b33..00000000 --- a/wqflask/wqflask/static/new/javascript/css/box_plot.css +++ /dev/null @@ -1,20 +0,0 @@ -.box { - font: 10px sans-serif; -} - -.box line, -.box rect, -.box circle { - fill: #fff; - stroke: #000; - stroke-width: 1.5px; -} - -.box .center { - stroke-dasharray: 3,3; -} - -.box .outlier { - fill: none; - stroke: #ccc; -} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/charts.css b/wqflask/wqflask/static/new/javascript/css/charts.css deleted file mode 100644 index 5f2d4d23..00000000 --- a/wqflask/wqflask/static/new/javascript/css/charts.css +++ /dev/null @@ -1,28 +0,0 @@ -body { - font-family: sans-serif; -} - -svg { - margin-top: 10px; - margin-left: 50px; -} - -.line { - stroke-width: 1; - fill: none; -} - -text { - font-family: sans-serif; - font-size: 11pt; -} - -p { - font-family: sans-serif; - font-size: 12pt; -} - -p#caption { - margin-left: 100px; - width: 500px; -} diff --git a/wqflask/wqflask/static/new/javascript/css/corr_matrix.css b/wqflask/wqflask/static/new/javascript/css/corr_matrix.css deleted file mode 100755 index f4838f77..00000000 --- a/wqflask/wqflask/static/new/javascript/css/corr_matrix.css +++ /dev/null @@ -1,12 +0,0 @@ -.vertical_label { - -webkit-transform: rotate(-90deg); - -moz-transform: rotate(-90deg); - -ms-transform: rotate(-90deg); - -o-transform: rotate(-90deg); - trasnform: rotate(-90deg); - color: #000 - font-size: 22px; - height: 50px; - width: 100px; - float: left; -} diff --git a/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css b/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css deleted file mode 100755 index c62d4c9a..00000000 --- a/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css +++ /dev/null @@ -1,13 +0,0 @@ -.chart { - -} - -.main text { - font: 10px sans-serif; -} - -.axis line, .axis path { - shape-rendering: crispEdges; - stroke: black; - fill: none; -} diff --git a/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css b/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css deleted file mode 100644 index 3d253caf..00000000 --- a/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css +++ /dev/null @@ -1 +0,0 @@ -.d3-tip{line-height:1;font-weight:bold;padding:12px;background:rgba(0,0,0,0.8);color:#fff;border-radius:2px;pointer-events:none}.d3-tip:after{box-sizing:border-box;display:inline;font-size:10px;width:100%;line-height:1;color:rgba(0,0,0,0.8);position:absolute;pointer-events:none}.d3-tip.n:after{content:"\25BC";margin:-1px 0 0 0;top:100%;left:0;text-align:center}.d3-tip.e:after{content:"\25C0";margin:-4px 0 0 0;top:50%;left:-8px}.d3-tip.s:after{content:"\25B2";margin:0 0 1px 0;top:-8px;left:0;text-align:center}.d3-tip.w:after{content:"\25B6";margin:-4px 0 0 -1px;top:50%;left:100%} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/interval_mapping.css b/wqflask/wqflask/static/new/javascript/css/interval_mapping.css deleted file mode 100755 index 4a55d2e3..00000000 --- a/wqflask/wqflask/static/new/javascript/css/interval_mapping.css +++ /dev/null @@ -1,32 +0,0 @@ -.chr_interval_map .y_axis path, -.chr_interval_map .y_axis line { - fill: none; - stroke: black; - shape-rendering: crispEdges; -} -.chr_interval_map .y_axis text { - font-family: sans-serif; - font-size: 14px; -} - -.chr_interval_map .x_axis path, -.chr_interval_map .x_axis line { - fill: none; - stroke: black; - shape-rendering: crispEdges; -} -.chr_interval_map .x_axis text { - text-anchor: end; - font-family: sans-serif; - font-size: 8px; -} -/* -interval_map rect { - stroke: WhiteSmoke; - fill: white; -} - -interval_map path { - stroke: steelblue; - stroke-width: 1; -}*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/main.css b/wqflask/wqflask/static/new/javascript/css/main.css deleted file mode 100755 index 017bbdb8..00000000 --- a/wqflask/wqflask/static/new/javascript/css/main.css +++ /dev/null @@ -1,4 +0,0 @@ -.security_box { - padding-left: 30px; - padding-right: 30px; -} diff --git a/wqflask/wqflask/static/new/javascript/css/marker_regression.css b/wqflask/wqflask/static/new/javascript/css/marker_regression.css deleted file mode 100755 index d81b5021..00000000 --- a/wqflask/wqflask/static/new/javascript/css/marker_regression.css +++ /dev/null @@ -1,38 +0,0 @@ -.chr_manhattan_plot .y_axis path, -.chr_manhattan_plot .y_axis line { - fill: none; - stroke: black; - shape-rendering: crispEdges; -} -.chr_manhattan_plot .y_axis text { - font-family: sans-serif; - font-size: 14px; -} - -.chr_manhattan_plot .x_axis path, -.chr_manhattan_plot .x_axis line { - fill: none; - stroke: black; - shape-rendering: crispEdges; -} - -.chr_manhattan_plot .x_axis text { - text-anchor: end; - font-family: sans-serif; - font-size: 10px; -} - -rect.pane { - cursor: move; - fill: none; - pointer-events: all; -} - -/*rect { - stroke: WhiteSmoke; - fill: lightgrey; -}*/ -/*rect { - stroke: WhiteSmoke; - fill: Azure; -}*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/panelutil.css b/wqflask/wqflask/static/new/javascript/css/panelutil.css deleted file mode 100644 index ccd7eb01..00000000 --- a/wqflask/wqflask/static/new/javascript/css/panelutil.css +++ /dev/null @@ -1,91 +0,0 @@ - -/* figures will always be within a div with class="qtlcharts" */ -div.qtlcharts { - font-family: sans-serif; - font-size: 11pt; -} - -div.qtlcharts .title text { - dominant-baseline: middle; - fill: blue; - text-anchor: middle; -} - -div.qtlcharts .y.axis text { - dominant-baseline: middle; - text-anchor: end; -} - -div.qtlcharts .y.axis text.title { - text-anchor: middle; - fill: slateblue; -} - -div.qtlcharts .x.axis text { - dominant-baseline: hanging; - text-anchor: middle; -} - -div.qtlcharts .x.axis text.title { - fill: slateblue; -} - -/*div.qtlcharts line.axis.grid { - fill: none; - stroke-width: 1; - pointer-events: none; -} - -div.qtlcharts line.x.axis.grid { - stroke: rgb(200, 200, 200); - stroke-width: 3; -} - -div.qtlcharts line.y.axis.grid { - stroke: white; -}*/ - -div.qtlcharts .extent { - fill: #cac; - opacity: 0.3; -} - -div.qtlcharts circle.selected { - fill: hotpink; - opacity: 1; -} - -div.qtlcharts a { - color: #08c; - text-decoration: none; -} - -div.qtlcharts a:hover { - color: #333; - text-decoration: underline; -} - - -/* figure captions */ -.caption { - font-family: Sans-serif; - font-size: 11pt; - margin-left: 60px; - width: 600px; -} - - -/* d3 tip for tool tips */ -.d3-tip { - background: darkslateblue; - color: #fff; - stroke: none; - font-weight: bold; - font-size: 16px; - font-family: sans-serif; - padding: 5px; -} - -.d3-tip.e:after { - color: darkslateblue; -} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/parsley.css b/wqflask/wqflask/static/new/javascript/css/parsley.css deleted file mode 100755 index 7d244579..00000000 --- a/wqflask/wqflask/static/new/javascript/css/parsley.css +++ /dev/null @@ -1,20 +0,0 @@ -/* Adapted from parsleyjs.org/documentation.html#parsleyclasses */ - -input.parsley-success, textarea.parsley-success { - color: #468847 !important; - background-color: #DFF0D8 !important; - border: 1px solid #D6E9C6 !important; -} -input.parsley-error, textarea.parsley-error { - color: #B94A48 !important; - background-color: #F2DEDE !important; - border: 1px solid #EED3D7 !important; -} -ul.parsley-error-list { - font-size: 11px; - margin: 2px; - list-style-type:none; -} -ul.parsley-error-list li { - line-height: 11px; -} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css b/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css deleted file mode 100644 index 147903be..00000000 --- a/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css +++ /dev/null @@ -1,40 +0,0 @@ -#scatter-matrix { font-size: 14px; } - -.axis { shape-rendering: crispEdges; } -.axis line { stroke: #ddd; stroke-width: 1px; } -.axis path { display: none; } -.axis text { font-size: 0.8em; } - -rect.extent { fill: #000; fill-opacity: .125; stroke: #fff; } -rect.frame { fill: #fff; fill-opacity: .7; stroke: #aaa; } - -circle { fill: #ccc; fill-opacity: .5; } - -.legend circle { fill-opacity: 1; } -.legend text { font-size: 18px; font-style: oblique; } - -.cell text { pointer-events: none; } - -.color-0 { fill: #800; } -.color-1 { fill: #080; } -.color-2 { fill: #008; } -.color-3 { fill: #440; } -.color-4 { fill: #044; } -.color-5 { fill: #404; } -.color-6 { fill: #400; } -.color-7 { fill: #040; } -.color-8 { fill: #004; } -.color-9 { fill: #cc0; } -.color-10 { fill: #0cc; } -.color-11 { fill: #c0c; } -.color-12 { fill: #880; } -.color-13 { fill: #088; } -.color-14 { fill: #808; } -.color-15 { fill: #c00; } -.color-16 { fill: #0c0; } -.color-17 { fill: #00c; } - -.scatter-matrix-filter-control ul { list-style: none; padding-left: 10px; } -.scatter-matrix-variable-control ul { list-style: none; padding-left: 10px; } -.scatter-matrix-drill-control ul { list-style: none; padding-left: 10px; } - diff --git a/wqflask/wqflask/static/new/javascript/css/show_trait.css b/wqflask/wqflask/static/new/javascript/css/show_trait.css deleted file mode 100644 index 9fc82a85..00000000 --- a/wqflask/wqflask/static/new/javascript/css/show_trait.css +++ /dev/null @@ -1,7 +0,0 @@ -tr .outlier { - background-color: #ffff99; -} - -#bar_chart_container { - overflow-x:scroll; -} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/css/table.css b/wqflask/wqflask/static/new/javascript/css/table.css deleted file mode 100755 index 1910ef88..00000000 --- a/wqflask/wqflask/static/new/javascript/css/table.css +++ /dev/null @@ -1,36 +0,0 @@ -/* Adapted from http://coding.smashingmagazine.com/2008/08/13/top-10-css-table-designs/ */ - -.one-column-emphasis -{ - font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif; - font-size: 12px; - line-height: 1.6em; - margin: 45px; - width: 480px; - text-align: left; - border-collapse: collapse; -} -.one-column-emphasis th -{ - font-size: 14px; - font-weight: normal; - padding: 12px 15px; - color: #039; -} -.one-column-emphasis td -{ - padding: 10px 15px; - color: #669; - border-top: 1px solid #e8edff; -} -.oce-first -{ - background: #d0dafd; - border-right: 10px solid transparent; - border-left: 10px solid transparent; -} -.one-column-emphasis tr:hover td -{ - color: #339; - background: #eff2ff; -} -- cgit v1.2.3 From 1dd2981a25cdb33ab575206020490c7cf799e2da Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:32:47 +0000 Subject: Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so. --- wqflask/base/webqtlConfig.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base') diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 49a596aa..48d8cd0a 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -52,7 +52,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' -HTMLPATH = GNROOT + 'web/' +HTMLPATH = GNROOT + 'genotype_files/' PYLMM_PATH = '/home/zas1024/plink/' SNP_PATH = '/home/zas1024/snps/' IMGDIR = GNROOT + '/wqflask/wqflask/images/' -- cgit v1.2.3 From 64526b27922053d608147b2ce896b42ee9e5c2dc Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 10 Apr 2015 19:08:18 +0000 Subject: Added git large file system (the .gitattributes files) and fixed an issue where rat trait pages wouldn't work --- genotype_files/genotypes/.gitattributes | 1 + genotype_files/new_genotypes/.gitattributes | 1 + web/images/edit.png | Bin 4322 -> 0 bytes wqflask/base/trait.py | 3 ++ wqflask/wqflask/show_trait/show_trait.py | 41 +++++----------------------- 5 files changed, 12 insertions(+), 34 deletions(-) create mode 100644 genotype_files/genotypes/.gitattributes create mode 100644 genotype_files/new_genotypes/.gitattributes delete mode 100644 web/images/edit.png (limited to 'wqflask/base') diff --git a/genotype_files/genotypes/.gitattributes b/genotype_files/genotypes/.gitattributes new file mode 100644 index 00000000..c311ac85 --- /dev/null +++ b/genotype_files/genotypes/.gitattributes @@ -0,0 +1 @@ +*.geno filter=lfs -crlf diff --git a/genotype_files/new_genotypes/.gitattributes b/genotype_files/new_genotypes/.gitattributes new file mode 100644 index 00000000..912ed80c --- /dev/null +++ b/genotype_files/new_genotypes/.gitattributes @@ -0,0 +1 @@ +*.json filter=lfs -crlf diff --git a/web/images/edit.png b/web/images/edit.png deleted file mode 100644 index dda50521..00000000 Binary files a/web/images/edit.png and /dev/null differ diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 58bed865..f3648b80 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -549,6 +549,9 @@ class GeneralTrait(object): if self.alias: alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") + else: + alias = 'Not available' + return alias diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 929f5abb..836a0be5 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -283,13 +283,13 @@ class ShowTrait(object): # else: # pass - g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name) + result = g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name) if this_trait: addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (self.dataset.group.name, 'dataInput')) addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") #addSelectionButton.append(addSelectionButton_img) addSelectionText = "Add" - elif self.cursor.fetchall(): + elif result.fetchall(): addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") #addSelectionButton.append(addSelectionButton_img) @@ -368,7 +368,7 @@ class ShowTrait(object): blatsequence = '' for seqt in seqs: if int(seqt[1][-1]) % 2 == 1: - blatsequence += string.strip(seqt[0]) + blatsequence += string.strip(seqt[0])## NEEDED FOR UCSC GENOME BROWSER LINK #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A' @@ -469,52 +469,25 @@ class ShowTrait(object): #XZ: Resource Links: if this_trait.symbol: - linkStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px") - #XZ,12/26/2008: Gene symbol may contain single quotation mark. #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) #I debug this by using double quotation marks. if _Species == "rat": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Rattus norvegicus" - - #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % this_trait.symbol) - self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % this_trait.symbol) - try: - kgId, chr, txst, txen = self.cursor.fetchall()[0] + result = g.db.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() + if result != None: + kgId, chr, txst, txen = result[0], result[1], result[2], result[3] if chr and txst and txen and kgId: txst = int(txst*1000000) txen = int(txen*1000000) - #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - # title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle) - # , " "*2) - except: - pass if _Species == "mouse": - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #symatlas_species = "Mus musculus" - - #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol) - #try: print("this_trait.symbol:", this_trait.symbol) result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() if result != None: this_chr, txst, txen = result[0], result[1], result[2] - #this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() if this_chr and txst and txen and this_trait.refseq_transcriptid : txst = int(txst*1000000) txen = int(txen*1000000) - #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\ - # title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9', - # this_trait.refseq_transcriptid, - # this_chr, - # txst, - # txen), - # Class="fs14 fwn"), style=linkStyle) - # , " "*2) + ## NEEDED FOR UCSC GENOME BROWSER LINK #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ -- cgit v1.2.3 From eef63adae30c1547f4c4189eb59a18d190c3aa08 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 11 May 2015 17:03:42 -0500 Subject: Moving pylmm out of the tree --- wqflask/base/data_set.py | 2 +- wqflask/utility/chunks.py | 96 ++++ wqflask/wqflask/heatmap/heatmap.py | 635 +++++++++++---------- .../wqflask/marker_regression/marker_regression.py | 4 +- 4 files changed, 417 insertions(+), 320 deletions(-) create mode 100644 wqflask/utility/chunks.py (limited to 'wqflask/base') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 489bd374..9f805fc3 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -42,7 +42,7 @@ from base import species from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench -from wqflask.my_pylmm.pyLMM import chunks +from wqflask.utility import chunks from maintenance import get_group_samplelists diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py new file mode 100644 index 00000000..9565fb96 --- /dev/null +++ b/wqflask/utility/chunks.py @@ -0,0 +1,96 @@ +from __future__ import absolute_import, print_function, division + +import math +import time + + +def divide_into_chunks(the_list, number_chunks): + """Divides a list into approximately number_chunks smaller lists + + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3) + [[1, 2, 7], [3, 22, 8], [5, 22, 333]] + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4) + [[1, 2, 7], [3, 22, 8], [5, 22, 333]] + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5) + [[1, 2], [7, 3], [22, 8], [5, 22], [333]] + >>> + + """ + length = len(the_list) + + if length == 0: + return [[]] + + if length <= number_chunks: + number_chunks = length + + chunksize = int(math.ceil(length / number_chunks)) + + chunks = [] + for counter in range(0, length, chunksize): + chunks.append(the_list[counter:counter+chunksize]) + + return chunks + +def _confirm_chunk(original, result): + all_chunked = [] + for chunk in result: + all_chunked.extend(chunk) + print("length of all chunked:", len(all_chunked)) + assert original == all_chunked, "You didn't chunk right" + + +def _chunk_test(divide_func): + import random + random.seed(7) + + number_exact = 0 + total_amount_off = 0 + + for test in range(1, 1001): + print("\n\ntest:", test) + number_chunks = random.randint(1, 20) + number_elements = random.randint(0, 100) + the_list = list(range(1, number_elements)) + result = divide_func(the_list, number_chunks) + + print("Dividing list of length {} into approximately {} chunks - got {} chunks".format( + len(the_list), number_chunks, len(result))) + print("result:", result) + + _confirm_chunk(the_list, result) + + amount_off = abs(number_chunks - len(result)) + if amount_off == 0: + number_exact += 1 + else: + total_amount_off += amount_off + + + print("\n{} exact out of {} [Total amount off: {}]".format(number_exact, + test, + total_amount_off)) + assert number_exact == 558 + assert total_amount_off == 1580 + return number_exact, total_amount_off + + +def _main(): + info = dict() + #funcs = (("sam", sam_divide_into_chunks), ("zach", zach_divide_into_chunks)) + funcs = (("only one", divide_into_chunks),) + for name, func in funcs: + start = time.time() + number_exact, total_amount_off = _chunk_test(func) + took = time.time() - start + info[name] = dict(number_exact=number_exact, + total_amount_off=total_amount_off, + took=took) + + print("info is:", info) + +if __name__ == '__main__': + _main() + print("\nConfirming doctests...") + import doctest + doctest.testmod() diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 9b6b1b69..035736fd 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,317 +1,318 @@ -from __future__ import absolute_import, print_function, division - -import sys -sys.path.append(".") - -import gc -import string -import cPickle -import os -import datetime -import time -import pp -import math -import collections -import resource - -import scipy -import numpy as np -from scipy import linalg - -from pprint import pformat as pf - -from htmlgen import HTMLgen2 as HT -import reaper - -from base.trait import GeneralTrait -from base import data_set -from base import species -from base import webqtlConfig -from utility import webqtlUtil -from wqflask.my_pylmm.data import prep_data -from wqflask.my_pylmm.pyLMM import lmm -from wqflask.my_pylmm.pyLMM import input -from utility import helper_functions -from utility import Plot, Bunch -from utility import temp_data - -from MySQLdb import escape_string as escape - -import cPickle as pickle -import simplejson as json - -from pprint import pformat as pf - -from redis import Redis -Redis = Redis() - -from flask import Flask, g - -class Heatmap(object): - - def __init__(self, start_vars, temp_uuid): - - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] - - helper_functions.get_trait_db_obs(self, trait_db_list) - - self.temp_uuid = temp_uuid - self.num_permutations = 5000 - self.dataset = self.trait_list[0][1] - - self.json_data = {} #The dictionary that will be used to create the json object that contains all the data needed to create the figure - - self.all_sample_list = [] - self.traits = [] - - chrnames = [] - self.species = species.TheSpecies(dataset=self.trait_list[0][1]) - for key in self.species.chromosomes.chromosomes.keys(): - chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) - - for trait_db in self.trait_list: - - this_trait = trait_db[0] - self.traits.append(this_trait.name) - this_sample_data = this_trait.data - - for sample in this_sample_data: - if sample not in self.all_sample_list: - self.all_sample_list.append(sample) - - self.sample_data = [] - for trait_db in self.trait_list: - this_trait = trait_db[0] - this_sample_data = this_trait.data - - #self.sample_data[this_trait.name] = [] - this_trait_vals = [] - for sample in self.all_sample_list: - if sample in this_sample_data: - this_trait_vals.append(this_sample_data[sample].value) - #self.sample_data[this_trait.name].append(this_sample_data[sample].value) - else: - this_trait_vals.append('') - #self.sample_data[this_trait.name].append('') - self.sample_data.append(this_trait_vals) - - self.gen_reaper_results() - #self.gen_pylmm_results() - - #chrnames = [] - lodnames = [] - chr_pos = [] - pos = [] - markernames = [] - - for trait in self.trait_results.keys(): - lodnames.append(trait) - - for marker in self.dataset.group.markers.markers: - #if marker['chr'] not in chrnames: - # chr_ob = [marker['chr'], "filler"] - # chrnames.append(chr_ob) - chr_pos.append(marker['chr']) - pos.append(marker['Mb']) - markernames.append(marker['name']) - - self.json_data['chrnames'] = chrnames - self.json_data['lodnames'] = lodnames - self.json_data['chr'] = chr_pos - self.json_data['pos'] = pos - self.json_data['markernames'] = markernames - - for trait in self.trait_results: - self.json_data[trait] = self.trait_results[trait] - - self.js_data = dict( - json_data = self.json_data - ) - - print("self.js_data:", self.js_data) - - - def gen_reaper_results(self): - self.trait_results = {} - for trait_db in self.trait_list: - self.dataset.group.get_markers() - this_trait = trait_db[0] - #this_db = trait_db[1] - genotype = self.dataset.group.read_genotype_file() - samples, values, variances = this_trait.export_informative() - - trimmed_samples = [] - trimmed_values = [] - for i in range(0, len(samples)): - if samples[i] in self.dataset.group.samplelist: - trimmed_samples.append(samples[i]) - trimmed_values.append(values[i]) - - self.lrs_array = genotype.permutation(strains = trimmed_samples, - trait = trimmed_values, - nperm= self.num_permutations) - - #self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)] - #self.significant = self.lrs_array[int(self.num_permutations*0.95-1)] - - reaper_results = genotype.regression(strains = trimmed_samples, - trait = trimmed_values) - - - lrs_values = [float(qtl.lrs) for qtl in reaper_results] - print("lrs_values:", lrs_values) - #self.dataset.group.markers.add_pvalues(p_values) - - self.trait_results[this_trait.name] = [] - for qtl in reaper_results: - if qtl.additive > 0: - self.trait_results[this_trait.name].append(-float(qtl.lrs)) - else: - self.trait_results[this_trait.name].append(float(qtl.lrs)) - #for lrs in lrs_values: - # if - # self.trait_results[this_trait.name].append(lrs) - - - #this_db_samples = self.dataset.group.samplelist - #this_sample_data = this_trait.data - ##print("this_sample_data", this_sample_data) - #this_trait_vals = [] - #for index, sample in enumerate(this_db_samples): - # if sample in this_sample_data: - # sample_value = this_sample_data[sample].value - # this_trait_vals.append(sample_value) - # else: - # this_trait_vals.append("x") - - #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) - - #key = "pylmm:input:" + str(self.temp_uuid) - #print("key is:", pf(key)) - - #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - - #no_val_samples = self.identify_empty_samples(this_trait_vals) - #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - - #genotype_matrix = np.array(trimmed_genotype_data).T - - #print("genotype_matrix:", str(genotype_matrix.tolist())) - #print("pheno_vector:", str(pheno_vector.tolist())) - - #params = dict(pheno_vector = pheno_vector.tolist(), - # genotype_matrix = genotype_matrix.tolist(), - # restricted_max_likelihood = True, - # refit = False, - # temp_uuid = str(self.temp_uuid), - # - # # meta data - # timestamp = datetime.datetime.now().isoformat(), - # ) - # - #json_params = json.dumps(params) - ##print("json_params:", json_params) - #Redis.set(key, json_params) - #Redis.expire(key, 60*60) - #print("before printing command") - # - #command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key, - # "other") - #print("command is:", command) - #print("after printing command") - # - #os.system(command) - # - #json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) - - def gen_pylmm_results(self): - self.trait_results = {} - for trait_db in self.trait_list: - this_trait = trait_db[0] - #this_db = trait_db[1] - self.dataset.group.get_markers() - - this_db_samples = self.dataset.group.samplelist - this_sample_data = this_trait.data - #print("this_sample_data", this_sample_data) - this_trait_vals = [] - for index, sample in enumerate(this_db_samples): - if sample in this_sample_data: - sample_value = this_sample_data[sample].value - this_trait_vals.append(sample_value) - else: - this_trait_vals.append("x") - - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) - - key = "pylmm:input:" + str(self.temp_uuid) - #print("key is:", pf(key)) - - genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - - no_val_samples = self.identify_empty_samples(this_trait_vals) - trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - - genotype_matrix = np.array(trimmed_genotype_data).T - - #print("genotype_matrix:", str(genotype_matrix.tolist())) - #print("pheno_vector:", str(pheno_vector.tolist())) - - params = dict(pheno_vector = pheno_vector.tolist(), - genotype_matrix = genotype_matrix.tolist(), - restricted_max_likelihood = True, - refit = False, - temp_uuid = str(self.temp_uuid), - - # meta data - timestamp = datetime.datetime.now().isoformat(), - ) - - json_params = json.dumps(params) - #print("json_params:", json_params) - Redis.set(key, json_params) - Redis.expire(key, 60*60) - print("before printing command") - - command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key, - "other") - print("command is:", command) - print("after printing command") - - os.system(command) - - json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) - results = json.loads(json_results[1]) - p_values = [float(result) for result in results['p_values']] - #print("p_values:", p_values) - self.dataset.group.markers.add_pvalues(p_values) - - self.trait_results[this_trait.name] = [] - for marker in self.dataset.group.markers.markers: - self.trait_results[this_trait.name].append(marker['lod_score']) - - - def identify_empty_samples(self, values): - no_val_samples = [] - for sample_count, val in enumerate(values): - if val == "x": - no_val_samples.append(sample_count) - return no_val_samples - - def trim_genotypes(self, genotype_data, no_value_samples): - trimmed_genotype_data = [] - for marker in genotype_data: - new_genotypes = [] - for item_count, genotype in enumerate(marker): - if item_count in no_value_samples: - continue - try: - genotype = float(genotype) - except ValueError: - genotype = np.nan - pass - new_genotypes.append(genotype) - trimmed_genotype_data.append(new_genotypes) - return trimmed_genotype_data - - \ No newline at end of file +from __future__ import absolute_import, print_function, division + +import sys +sys.path.append(".") + +import gc +import string +import cPickle +import os +import datetime +import time +import pp +import math +import collections +import resource + +import scipy +import numpy as np +from scipy import linalg + +from pprint import pformat as pf + +from htmlgen import HTMLgen2 as HT +import reaper + +from base.trait import GeneralTrait +from base import data_set +from base import species +from base import webqtlConfig +from utility import webqtlUtil +from wqflask.my_pylmm.data import prep_data +# from wqflask.my_pylmm.pyLMM import lmm +# from wqflask.my_pylmm.pyLMM import input +from utility import helper_functions +from utility import Plot, Bunch +from utility import temp_data + +from MySQLdb import escape_string as escape + +import cPickle as pickle +import simplejson as json + +from pprint import pformat as pf + +from redis import Redis +Redis = Redis() + +from flask import Flask, g + +class Heatmap(object): + + def __init__(self, start_vars, temp_uuid): + + trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + + helper_functions.get_trait_db_obs(self, trait_db_list) + + self.temp_uuid = temp_uuid + self.num_permutations = 5000 + self.dataset = self.trait_list[0][1] + + self.json_data = {} #The dictionary that will be used to create the json object that contains all the data needed to create the figure + + self.all_sample_list = [] + self.traits = [] + + chrnames = [] + self.species = species.TheSpecies(dataset=self.trait_list[0][1]) + for key in self.species.chromosomes.chromosomes.keys(): + chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) + + for trait_db in self.trait_list: + + this_trait = trait_db[0] + self.traits.append(this_trait.name) + this_sample_data = this_trait.data + + for sample in this_sample_data: + if sample not in self.all_sample_list: + self.all_sample_list.append(sample) + + self.sample_data = [] + for trait_db in self.trait_list: + this_trait = trait_db[0] + this_sample_data = this_trait.data + + #self.sample_data[this_trait.name] = [] + this_trait_vals = [] + for sample in self.all_sample_list: + if sample in this_sample_data: + this_trait_vals.append(this_sample_data[sample].value) + #self.sample_data[this_trait.name].append(this_sample_data[sample].value) + else: + this_trait_vals.append('') + #self.sample_data[this_trait.name].append('') + self.sample_data.append(this_trait_vals) + + self.gen_reaper_results() + #self.gen_pylmm_results() + + #chrnames = [] + lodnames = [] + chr_pos = [] + pos = [] + markernames = [] + + for trait in self.trait_results.keys(): + lodnames.append(trait) + + for marker in self.dataset.group.markers.markers: + #if marker['chr'] not in chrnames: + # chr_ob = [marker['chr'], "filler"] + # chrnames.append(chr_ob) + chr_pos.append(marker['chr']) + pos.append(marker['Mb']) + markernames.append(marker['name']) + + self.json_data['chrnames'] = chrnames + self.json_data['lodnames'] = lodnames + self.json_data['chr'] = chr_pos + self.json_data['pos'] = pos + self.json_data['markernames'] = markernames + + for trait in self.trait_results: + self.json_data[trait] = self.trait_results[trait] + + self.js_data = dict( + json_data = self.json_data + ) + + print("self.js_data:", self.js_data) + + + def gen_reaper_results(self): + self.trait_results = {} + for trait_db in self.trait_list: + self.dataset.group.get_markers() + this_trait = trait_db[0] + #this_db = trait_db[1] + genotype = self.dataset.group.read_genotype_file() + samples, values, variances = this_trait.export_informative() + + trimmed_samples = [] + trimmed_values = [] + for i in range(0, len(samples)): + if samples[i] in self.dataset.group.samplelist: + trimmed_samples.append(samples[i]) + trimmed_values.append(values[i]) + + self.lrs_array = genotype.permutation(strains = trimmed_samples, + trait = trimmed_values, + nperm= self.num_permutations) + + #self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)] + #self.significant = self.lrs_array[int(self.num_permutations*0.95-1)] + + reaper_results = genotype.regression(strains = trimmed_samples, + trait = trimmed_values) + + + lrs_values = [float(qtl.lrs) for qtl in reaper_results] + print("lrs_values:", lrs_values) + #self.dataset.group.markers.add_pvalues(p_values) + + self.trait_results[this_trait.name] = [] + for qtl in reaper_results: + if qtl.additive > 0: + self.trait_results[this_trait.name].append(-float(qtl.lrs)) + else: + self.trait_results[this_trait.name].append(float(qtl.lrs)) + #for lrs in lrs_values: + # if + # self.trait_results[this_trait.name].append(lrs) + + + #this_db_samples = self.dataset.group.samplelist + #this_sample_data = this_trait.data + ##print("this_sample_data", this_sample_data) + #this_trait_vals = [] + #for index, sample in enumerate(this_db_samples): + # if sample in this_sample_data: + # sample_value = this_sample_data[sample].value + # this_trait_vals.append(sample_value) + # else: + # this_trait_vals.append("x") + + #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) + + #key = "pylmm:input:" + str(self.temp_uuid) + #print("key is:", pf(key)) + + #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + #no_val_samples = self.identify_empty_samples(this_trait_vals) + #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + #genotype_matrix = np.array(trimmed_genotype_data).T + + #print("genotype_matrix:", str(genotype_matrix.tolist())) + #print("pheno_vector:", str(pheno_vector.tolist())) + + #params = dict(pheno_vector = pheno_vector.tolist(), + # genotype_matrix = genotype_matrix.tolist(), + # restricted_max_likelihood = True, + # refit = False, + # temp_uuid = str(self.temp_uuid), + # + # # meta data + # timestamp = datetime.datetime.now().isoformat(), + # ) + # + #json_params = json.dumps(params) + ##print("json_params:", json_params) + #Redis.set(key, json_params) + #Redis.expire(key, 60*60) + #print("before printing command") + # + #command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key, + # "other") + #print("command is:", command) + #print("after printing command") + # + #os.system(command) + # + #json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) + + def gen_pylmm_results(self): + # This function is NOT used. If it is, we should use a shared function with marker_regression.py + self.trait_results = {} + for trait_db in self.trait_list: + this_trait = trait_db[0] + #this_db = trait_db[1] + self.dataset.group.get_markers() + + this_db_samples = self.dataset.group.samplelist + this_sample_data = this_trait.data + #print("this_sample_data", this_sample_data) + this_trait_vals = [] + for index, sample in enumerate(this_db_samples): + if sample in this_sample_data: + sample_value = this_sample_data[sample].value + this_trait_vals.append(sample_value) + else: + this_trait_vals.append("x") + + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) + + key = "pylmm:input:" + str(self.temp_uuid) + #print("key is:", pf(key)) + + genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + no_val_samples = self.identify_empty_samples(this_trait_vals) + trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + genotype_matrix = np.array(trimmed_genotype_data).T + + #print("genotype_matrix:", str(genotype_matrix.tolist())) + #print("pheno_vector:", str(pheno_vector.tolist())) + + params = dict(pheno_vector = pheno_vector.tolist(), + genotype_matrix = genotype_matrix.tolist(), + restricted_max_likelihood = True, + refit = False, + temp_uuid = str(self.temp_uuid), + + # meta data + timestamp = datetime.datetime.now().isoformat(), + ) + + json_params = json.dumps(params) + #print("json_params:", json_params) + Redis.set(key, json_params) + Redis.expire(key, 60*60) + print("before printing command") + + command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key, + "other") + print("command is:", command) + print("after printing command") + + os.system(command) + + json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) + results = json.loads(json_results[1]) + p_values = [float(result) for result in results['p_values']] + #print("p_values:", p_values) + self.dataset.group.markers.add_pvalues(p_values) + + self.trait_results[this_trait.name] = [] + for marker in self.dataset.group.markers.markers: + self.trait_results[this_trait.name].append(marker['lod_score']) + + + def identify_empty_samples(self, values): + no_val_samples = [] + for sample_count, val in enumerate(values): + if val == "x": + no_val_samples.append(sample_count) + return no_val_samples + + def trim_genotypes(self, genotype_data, no_value_samples): + trimmed_genotype_data = [] + for marker in genotype_data: + new_genotypes = [] + for item_count, genotype in enumerate(marker): + if item_count in no_value_samples: + continue + try: + genotype = float(genotype) + except ValueError: + genotype = np.nan + pass + new_genotypes.append(genotype) + trimmed_genotype_data.append(new_genotypes) + return trimmed_genotype_data + + diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 49521bd6..c5fab4ee 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -37,8 +37,8 @@ from utility import webqtlUtil from wqflask.marker_regression import gemma_mapping #from wqflask.marker_regression import rqtl_mapping from wqflask.my_pylmm.data import prep_data -from wqflask.my_pylmm.pyLMM import lmm -from wqflask.my_pylmm.pyLMM import input +# from wqflask.my_pylmm.pyLMM import lmm +# from wqflask.my_pylmm.pyLMM import input from utility import helper_functions from utility import Plot, Bunch from utility import temp_data -- cgit v1.2.3 From bc98e46fc910357ea3aeca5950e94e38d9584f9e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 11 May 2015 22:44:18 +0000 Subject: Moved chunks --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9f805fc3..1cd57b4b 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -42,7 +42,7 @@ from base import species from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench -from wqflask.utility import chunks +from utility import chunks from maintenance import get_group_samplelists -- cgit v1.2.3 From 2eeaf2f6df9deb3f89db0b5821d784b93eb4bc36 Mon Sep 17 00:00:00 2001 From: Artem Tarasov Date: Tue, 12 May 2015 14:10:04 +0300 Subject: Fix #35 * 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top --- wqflask/base/trait.py | 28 ++++++++++++++++++----- wqflask/wqflask/templates/show_trait.html | 10 +++++--- wqflask/wqflask/templates/show_trait_details.html | 6 ++++- 3 files changed, 34 insertions(+), 10 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index f3648b80..8930c917 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -53,7 +53,8 @@ class GeneralTrait(object): self.pvalue = None self.mean = None self.num_overlap = None - + self.strand_probe = None + self.symbol = None if kw.get('fullname'): name2 = value.split("::") @@ -532,13 +533,28 @@ class GeneralTrait(object): setDescription.append(self.dataset.genHTML(Class='cori')) return setDescription + @property + def name_header_fmt(self): + '''Return a human-readable name for use in page header''' + if self.dataset.type == 'ProbeSet': + return self.symbol + elif self.dataset.type == 'Geno': + return self.name + elif self.dataset.type == 'Publish': + return self.post_publication_abbreviation + else: + return "unnamed" + @property def description_fmt(self): '''Return a text formated description''' - if self.description: - formatted = self.description - if self.probe_target_description: - formatted += "; " + self.probe_target_description + if self.dataset.type == 'ProbeSet': + if self.description: + formatted = self.description + if self.probe_target_description: + formatted += "; " + self.probe_target_description + elif self.dataset.type == 'Publish': + formatted = self.post_publication_description else: formatted = "Not available" return formatted.capitalize() @@ -652,4 +668,4 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data - \ No newline at end of file + diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index a1723ef8..d6f22f41 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -13,8 +13,12 @@ {% endblock %} {% block content %} - {{ header("{}".format(this_trait.symbol), - '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} + {% if this_trait.dataset.type != 'Geno' %} + {{ header("{}".format(this_trait.name_header_fmt), + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} + {% else %} + {{ header("{}".format(this_trait.name_header_fmt)) }} + {% endif %}

{{ dataset.group.species.capitalize() }} - {{ dataset.group.name }} - - {{ this_trait.symbol }} + {{ this_trait.name_header_fmt }}

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 0afac1f7..e1780e42 100755 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,9 +1,13 @@
+ {% if this_trait.dataset.type == 'ProbeSet' %}
Aliases
{{ this_trait.alias_fmt }}
+ {% endif %} + {% if this_trait.dataset.type != 'Publish' %}
Location
{{ this_trait.location_fmt }}
+ {% endif %}
Database
@@ -16,7 +20,7 @@
- BLAT Specifity + BLAT Specificity
{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}
-- cgit v1.2.3