diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 12 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py | 26 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py | 64 | ||||
| -rw-r--r-- | wqflask/utility/Plot.py | 98 | ||||
| -rw-r--r-- | wqflask/utility/__init__.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 150 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/collect.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 88 | ||||
| -rw-r--r-- | wqflask/wqflask/group_manager.py | 238 | ||||
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/interval_analyst/GeneUtil.py | 130 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 44 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 352 | ||||
| -rw-r--r-- | wqflask/wqflask/model.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/user_login.py | 70 |
19 files changed, 662 insertions, 662 deletions
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 27eb6553..c74489a8 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -113,13 +113,13 @@ class ConvertGenoFile: with open(self.output_file, 'w') as fh: json.dump(self.markers, fh, indent=" ", sort_keys=True) - # print('configurations:', str(configurations)) - #self.latest_col_pos = item_count + self.skipped_cols - #self.latest_col_value = item + # print('configurations:', str(configurations)) + #self.latest_col_pos = item_count + self.skipped_cols + #self.latest_col_value = item - # if item_count != 0: - # self.output_fh.write(" ") - # self.output_fh.write(self.configurations[item.upper()]) + # if item_count != 0: + # self.output_fh.write(" ") + # self.output_fh.write(self.configurations[item.upper()]) # self.output_fh.write("\n") diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index 1198740d..47377873 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -7,17 +7,17 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file class TestQtlReaperMapping(unittest.TestCase): - @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals = ["V1", "x", "V4", "V3","x"] - samples = ["S1", "S2", "S3", "S4","S5"] - trait_filename = "trait_file" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples, vals=vals, - trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") - filehandler = mock_open() - write_calls = [mock.call('Trait\t'), mock.call( - 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals = ["V1", "x", "V4", "V3","x"] + samples = ["S1", "S2", "S3", "S4","S5"] + trait_filename = "trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples, vals=vals, + trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") + filehandler = mock_open() + write_calls = [mock.call('Trait\t'), mock.call( + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] - filehandler.write.assert_has_calls(write_calls) + filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index d69a20d3..e518ec22 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -8,35 +8,35 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names class TestRqtlMapping(unittest.TestCase): - def setUp(self): - self.app_context = app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self, mock_logger, mock_db): - """test for getting trait data_type return True""" - query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value = [ - """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results = get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(query_value) - self.assertEqual(results, "fer434f") - - def test_sanitize_rqtl_phenotype(self): - """test for sanitizing rqtl phenotype""" - vals = ['f', "x", "r", "x","x"] - results = sanitize_rqtl_phenotype(vals) - expected_phenotype_string = 'c(f,NA,r,NA,NA)' - - self.assertEqual(results, expected_phenotype_string) - - def test_sanitize_rqtl_names(self): - """test for sanitzing rqtl names""" - vals = ['f', "x", "r", "x","x"] - expected_sanitized_name = "c('f',NA,'r',NA,NA)" - results = sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name, results) + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data(self, mock_logger, mock_db): + """test for getting trait data_type return True""" + query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value = [ + """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results = get_trait_data_type("traid_id") + mock_db.db.execute.assert_called_with(query_value) + self.assertEqual(results, "fer434f") + + def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" + vals = ['f', "x", "r", "x","x"] + results = sanitize_rqtl_phenotype(vals) + expected_phenotype_string = 'c(f,NA,r,NA,NA)' + + self.assertEqual(results, expected_phenotype_string) + + def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" + vals = ['f', "x", "r", "x","x"] + expected_sanitized_name = "c('f',NA,'r',NA,NA)" + results = sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name, results) diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 00658d10..f61e3b88 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -79,7 +79,7 @@ def frange(start, end=None, inc=1.0): start += 0.0 # force it to be a float count = int((end - start) / inc) if start + count * inc != end: - # Need to adjust the count. AFAICT, it always comes up one short. + # Need to adjust the count. AFAICT, it always comes up one short. count += 1 L = [start] * count for i in range(1, count): @@ -131,16 +131,16 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset if plotHeight <= 0 or plotWidth <= 0: - return + return if len(data) < 2: - return + return max_D = max(data) min_D = min(data) # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong if max_D == float('inf') or max_D > webqtlConfig.MAXLRS: - max_D = webqtlConfig.MAXLRS # maximum LRS value + max_D = webqtlConfig.MAXLRS # maximum LRS value xLow, xTop, stepX = detScale(min_D, max_D) @@ -151,15 +151,15 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab dataXY = [] Count = [] while j <= xTop: - dataXY.append(j) - Count.append(0) - j += step + dataXY.append(j) + Count.append(0) + j += step for i, item in enumerate(data): - if item == float('inf') or item > webqtlConfig.MAXLRS: - item = webqtlConfig.MAXLRS # maximum LRS value - j = int((item - xLow) / step) - Count[j] += 1 + if item == float('inf') or item > webqtlConfig.MAXLRS: + item = webqtlConfig.MAXLRS # maximum LRS value + j = int((item - xLow) / step) + Count[j] += 1 yLow, yTop, stepY = detScale(0, max(Count)) @@ -169,12 +169,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab barWidth = xScale * step for i, count in enumerate(Count): - if count: - xc = (dataXY[i] - xLow) * xScale + xLeftOffset - yc = -(count - yLow) * yScale + yTopOffset + plotHeight - im_drawer.rectangle( - xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)), - outline=barColor, fill=barColor) + if count: + xc = (dataXY[i] - xLow) * xScale + xLeftOffset + yc = -(count - yLow) * yScale + yTopOffset + plotHeight + im_drawer.rectangle( + xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)), + outline=barColor, fill=barColor) # draw drawing region im_drawer.rectangle( @@ -186,39 +186,39 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab scaleFont = ImageFont.truetype(font=COUR_FILE, size=11) x = xLow for i in range(int(stepX) + 1): - xc = xLeftOffset + (x - xLow) * xScale - im_drawer.line( - xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)), - fill=axesColor) - strX = cformat(d=x, rank=0) - im_drawer.text( - text=strX, - xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2, - yTopOffset + plotHeight + 14), font=scaleFont) - x += (xTop - xLow) / stepX + xc = xLeftOffset + (x - xLow) * xScale + im_drawer.line( + xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)), + fill=axesColor) + strX = cformat(d=x, rank=0) + im_drawer.text( + text=strX, + xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2, + yTopOffset + plotHeight + 14), font=scaleFont) + x += (xTop - xLow) / stepX y = yLow for i in range(int(stepY) + 1): - yc = yTopOffset + plotHeight - (y - yLow) * yScale - im_drawer.line( - xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) - strY = "%d" % y - im_drawer.text( - text=strY, - xy=(xLeftOffset - im_drawer.textsize(strY, - font=scaleFont)[0] - 6, yc + 5), - font=scaleFont) - y += (yTop - yLow) / stepY + yc = yTopOffset + plotHeight - (y - yLow) * yScale + im_drawer.line( + xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) + strY = "%d" % y + im_drawer.text( + text=strY, + xy=(xLeftOffset - im_drawer.textsize(strY, + font=scaleFont)[0] - 6, yc + 5), + font=scaleFont) + y += (yTop - yLow) / stepY # draw label labelFont = ImageFont.truetype(font=TAHOMA_FILE, size=17) if XLabel: - im_drawer.text( - text=XLabel, - xy=(xLeftOffset + ( - plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0, - yTopOffset + plotHeight + yBottomOffset-10), - font=labelFont, fill=labelColor) + im_drawer.text( + text=XLabel, + xy=(xLeftOffset + ( + plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0, + yTopOffset + plotHeight + yBottomOffset-10), + font=labelFont, fill=labelColor) if YLabel: draw_rotated_text(canvas, text=YLabel, @@ -230,12 +230,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab labelFont = ImageFont.truetype(font=VERDANA_FILE, size=16) if title: - im_drawer.text( - text=title, - xy=(xLeftOffset + (plotWidth - im_drawer.textsize( - title, font=labelFont)[0]) / 2.0, - 20), - font=labelFont, fill=labelColor) + im_drawer.text( + text=title, + xy=(xLeftOffset + (plotWidth - im_drawer.textsize( + title, font=labelFont)[0]) / 2.0, + 20), + font=labelFont, fill=labelColor) # This function determines the scale of the plot diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 816bc4df..6c8cd546 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -7,7 +7,7 @@ class Bunch: """Like a dictionary but using object notation""" def __init__(self, **kw): - self.__dict__ = kw + self.__dict__ = kw def __repr__(self): return pf(self.__dict__) diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index c0629b5d..eb545478 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -14,87 +14,87 @@ from pprint import pformat as pf class Marker: - def __init__(self): - self.name = None - self.chr = None - self.cM = None - self.Mb = None - self.genotypes = [] + def __init__(self): + self.name = None + self.chr = None + self.cM = None + self.Mb = None + self.genotypes = [] class ConvertGenoFile: - def __init__(self, input_file): - self.mb_exists = False - self.cm_exists = False - self.markers = [] + def __init__(self, input_file): + self.mb_exists = False + self.cm_exists = False + self.markers = [] - self.latest_row_pos = None - self.latest_col_pos = None + self.latest_row_pos = None + self.latest_col_pos = None - self.latest_row_value = None - self.latest_col_value = None - self.input_fh = open(input_file) - print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") - self.haplotype_notation = { - '@mat': "1", - '@pat': "2", - '@het': "-999", - '@unk': "-999" - } - self.configurations = {} + self.latest_row_value = None + self.latest_col_value = None + self.input_fh = open(input_file) + print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") + self.haplotype_notation = { + '@mat': "1", + '@pat': "2", + '@het': "-999", + '@unk': "-999" + } + self.configurations = {} - def process_rows(self): - for self.latest_row_pos, row in enumerate(self.input_fh): - self.latest_row_value = row - # Take care of headers - if not row.strip(): - continue - if row.startswith('#'): - continue - if row.startswith('Chr'): - if 'Mb' in row.split(): - self.mb_exists = True - if 'cM' in row.split(): - self.cm_exists = True - skip = 2 + self.cm_exists + self.mb_exists - self.individuals = row.split()[skip:] - continue - if row.startswith('@'): - key, _separater, value = row.partition(':') - key = key.strip() - value = value.strip() - if key in self.haplotype_notation: - self.configurations[value] = self.haplotype_notation[key] - continue - if not len(self.configurations): - raise EmptyConfigurations - yield row + def process_rows(self): + for self.latest_row_pos, row in enumerate(self.input_fh): + self.latest_row_value = row + # Take care of headers + if not row.strip(): + continue + if row.startswith('#'): + continue + if row.startswith('Chr'): + if 'Mb' in row.split(): + self.mb_exists = True + if 'cM' in row.split(): + self.cm_exists = True + skip = 2 + self.cm_exists + self.mb_exists + self.individuals = row.split()[skip:] + continue + if row.startswith('@'): + key, _separater, value = row.partition(':') + key = key.strip() + value = value.strip() + if key in self.haplotype_notation: + self.configurations[value] = self.haplotype_notation[key] + continue + if not len(self.configurations): + raise EmptyConfigurations + yield row - def process_csv(self): - for row in self.process_rows(): - row_items = row.split("\t") + def process_csv(self): + for row in self.process_rows(): + row_items = row.split("\t") - this_marker = Marker() - this_marker.name = row_items[1] - this_marker.chr = row_items[0] - if self.cm_exists and self.mb_exists: - this_marker.cM = row_items[2] - this_marker.Mb = row_items[3] - genotypes = row_items[4:] - elif self.cm_exists: - this_marker.cM = row_items[2] - genotypes = row_items[3:] - elif self.mb_exists: - this_marker.Mb = row_items[2] - genotypes = row_items[3:] - else: - genotypes = row_items[2:] - for item_count, genotype in enumerate(genotypes): - if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append( - self.configurations[genotype.upper().strip()]) - else: - print("WARNING:", genotype.upper()) - this_marker.genotypes.append("NA") - self.markers.append(this_marker.__dict__) + this_marker = Marker() + this_marker.name = row_items[1] + this_marker.chr = row_items[0] + if self.cm_exists and self.mb_exists: + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] + genotypes = row_items[3:] + elif self.mb_exists: + this_marker.Mb = row_items[2] + genotypes = row_items[3:] + else: + genotypes = row_items[2:] + for item_count, genotype in enumerate(genotypes): + if genotype.upper().strip() in self.configurations: + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) + else: + print("WARNING:", genotype.upper()) + this_marker.genotypes.append("NA") + self.markers.append(this_marker.__dict__) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index d82e478d..4f09176a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -73,7 +73,7 @@ def get_setting(command_id, guess=None): def get_setting_bool(id): v = get_setting(id) if v not in [0, False, 'False', 'FALSE', None]: - return True + return True return False diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 9fd89524..b06d84ff 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -35,7 +35,7 @@ def process_traits(unprocessed_traits): data, _separator, the_hmac = trait.rpartition(':') data = data.strip() if g.user_session.logged_in: - assert the_hmac == hmac.hmac_creation(data), "Data tampering?" + assert the_hmac == hmac.hmac_creation(data), "Data tampering?" traits.add(str(data)) return traits @@ -52,14 +52,14 @@ def report_change(len_before, len_now): @app.route("/collections/store_trait_list", methods=('POST',)) def store_traits_list(): - params = request.form + params = request.form - traits = params['traits'] - hash = params['hash'] + traits = params['traits'] + hash = params['hash'] - Redis.set(hash, traits) + Redis.set(hash, traits) - return hash + return hash @app.route("/collections/add") diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 59469428..c04b17be 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -238,9 +238,9 @@ class CorrelationMatrix: for i in range(len(self.trait_list)): loadings_row = [] if len(self.trait_list) > 2: - the_range = 3 + the_range = 3 else: - the_range = 2 + the_range = 2 for j in range(the_range): position = i + len(self.trait_list) * j loadings_row.append(self.loadings[0][position]) diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index f4eafbe7..820e81bc 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -115,8 +115,8 @@ class CTL: markers = [] markernames = [] for marker in parser.markers: - markernames.append(marker["name"]) - markers.append(marker["genotypes"]) + markernames.append(marker["name"]) + markers.append(marker["genotypes"]) genotypes = list(itertools.chain(*markers)) logger.debug(len(genotypes) / len(individuals), @@ -128,16 +128,16 @@ class CTL: # Create a phenotype matrix traits = [] for trait in self.trait_db_list: - logger.debug("retrieving data for", trait) - if trait != "": - ts = trait.split(':') - gt = create_trait(name=ts[0], dataset_name=ts[1]) - gt = retrieve_sample_data(gt, dataset, individuals) - for ind in individuals: - if ind in list(gt.data.keys()): - traits.append(gt.data[ind].value) - else: - traits.append("-999") + logger.debug("retrieving data for", trait) + if trait != "": + ts = trait.split(':') + gt = create_trait(name=ts[0], dataset_name=ts[1]) + gt = retrieve_sample_data(gt, dataset, individuals) + for ind in individuals: + if ind in list(gt.data.keys()): + traits.append(gt.data[ind].value) + else: + traits.append("-999") rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len( individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) @@ -177,42 +177,42 @@ class CTL: # We start from 2, since R starts from 1 :) n = 2 for trait in self.trait_db_list: - # Create the QTL like CTL plots - self.results['imgurl' + \ - str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" - self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \ - self.results['imgurl' + str(n)] - r_png(self.results['imgloc' + str(n)], - width=1000, height=600, type='cairo-png') - self.r_plotCTLobject( - res, (n - 1), significance=significance, main='Phenotype ' + trait) - r_dev_off() - n = n + 1 + # Create the QTL like CTL plots + self.results['imgurl' + \ + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" + self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \ + self.results['imgurl' + str(n)] + r_png(self.results['imgloc' + str(n)], + width=1000, height=600, type='cairo-png') + self.r_plotCTLobject( + res, (n - 1), significance=significance, main='Phenotype ' + trait) + r_dev_off() + n = n + 1 # Flush any output from R sys.stdout.flush() # Create the interactive graph for cytoscape visualization (Nodes and Edges) if not isinstance(significant, ri.RNULLType): - for x in range(len(significant[0])): - logger.debug(significant[0][x], significant[1] - [x], significant[2][x]) # Debug to console - # Source - tsS = significant[0][x].split(':') - # Target - tsT = significant[2][x].split(':') - # Retrieve Source info from the DB - gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) - # Retrieve Target info from the DB - gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) - self.addNode(gtS) - self.addNode(gtT) - self.addEdge(gtS, gtT, significant, x) - - # Update the trait name for the displayed table - significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) - # Update the trait name for the displayed table - significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) + for x in range(len(significant[0])): + logger.debug(significant[0][x], significant[1] + [x], significant[2][x]) # Debug to console + # Source + tsS = significant[0][x].split(':') + # Target + tsT = significant[2][x].split(':') + # Retrieve Source info from the DB + gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) + # Retrieve Target info from the DB + gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) + self.addNode(gtS) + self.addNode(gtT) + self.addEdge(gtS, gtT, significant, x) + + # Update the trait name for the displayed table + significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) + # Update the trait name for the displayed table + significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) self.elements = json.dumps(self.nodes_list + self.edges_list) @@ -227,8 +227,8 @@ class CTL: self.loadImage("imgloc1", "imgdata1") n = 2 for trait in self.trait_db_list: - self.loadImage("imgloc" + str(n), "imgdata" + str(n)) - n = n + 1 + self.loadImage("imgloc" + str(n), "imgdata" + str(n)) + n = n + 1 def process_results(self, results): logger.info("Processing CTL output") diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 55a7da0e..995915a9 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -16,158 +16,158 @@ logger = getLogger(__name__) @app.route("/groups/manage", methods=('GET', 'POST')) def manage_groups(): - params = request.form if request.form else request.args - if "add_new_group" in params: - return redirect(url_for('add_group')) - else: - admin_groups, member_groups = get_user_groups(g.user_session.user_id) - return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups) + params = request.form if request.form else request.args + if "add_new_group" in params: + return redirect(url_for('add_group')) + else: + admin_groups, member_groups = get_user_groups(g.user_session.user_id) + return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups) @app.route("/groups/view", methods=('GET', 'POST')) def view_group(): - params = request.form if request.form else request.args - group_id = params['id'] - group_info = get_group_info(group_id) - admins_info = [] - user_is_admin = False - if g.user_session.user_id in group_info['admins']: - user_is_admin = True - for user_id in group_info['admins']: - if user_id: - user_info = get_user_by_unique_column("user_id", user_id) - admins_info.append(user_info) - members_info = [] - for user_id in group_info['members']: - if user_id: - user_info = get_user_by_unique_column("user_id", user_id) - members_info.append(user_info) - - # ZS: This whole part might not scale well with many resources - resources_info = [] - all_resources = get_resources() - for resource_id in all_resources: - resource_info = get_resource_info(resource_id) - group_masks = resource_info['group_masks'] - if group_id in group_masks: - this_resource = {} - privileges = group_masks[group_id] - this_resource['id'] = resource_id - this_resource['name'] = resource_info['name'] - this_resource['data'] = privileges['data'] - this_resource['metadata'] = privileges['metadata'] - this_resource['admin'] = privileges['admin'] - resources_info.append(this_resource) - - return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info) + params = request.form if request.form else request.args + group_id = params['id'] + group_info = get_group_info(group_id) + admins_info = [] + user_is_admin = False + if g.user_session.user_id in group_info['admins']: + user_is_admin = True + for user_id in group_info['admins']: + if user_id: + user_info = get_user_by_unique_column("user_id", user_id) + admins_info.append(user_info) + members_info = [] + for user_id in group_info['members']: + if user_id: + user_info = get_user_by_unique_column("user_id", user_id) + members_info.append(user_info) + + # ZS: This whole part might not scale well with many resources + resources_info = [] + all_resources = get_resources() + for resource_id in all_resources: + resource_info = get_resource_info(resource_id) + group_masks = resource_info['group_masks'] + if group_id in group_masks: + this_resource = {} + privileges = group_masks[group_id] + this_resource['id'] = resource_id + this_resource['name'] = resource_info['name'] + this_resource['data'] = privileges['data'] + this_resource['metadata'] = privileges['metadata'] + this_resource['admin'] = privileges['admin'] + resources_info.append(this_resource) + + return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info) @app.route("/groups/remove", methods=('POST',)) def remove_groups(): - group_ids_to_remove = request.form['selected_group_ids'] - for group_id in group_ids_to_remove.split(":"): - delete_group(g.user_session.user_id, group_id) + group_ids_to_remove = request.form['selected_group_ids'] + for group_id in group_ids_to_remove.split(":"): + delete_group(g.user_session.user_id, group_id) - return redirect(url_for('manage_groups')) + return redirect(url_for('manage_groups')) @app.route("/groups/remove_users", methods=('POST',)) def remove_users(): - group_id = request.form['group_id'] - admin_ids_to_remove = request.form['selected_admin_ids'] - member_ids_to_remove = request.form['selected_member_ids'] + group_id = request.form['group_id'] + admin_ids_to_remove = request.form['selected_admin_ids'] + member_ids_to_remove = request.form['selected_member_ids'] - remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( - ":"), group_id, user_type="admins") - remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( - ":"), group_id, user_type="members") + remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( + ":"), group_id, user_type="admins") + remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( + ":"), group_id, user_type="members") - return redirect(url_for('view_group', id=group_id)) + return redirect(url_for('view_group', id=group_id)) @app.route("/groups/add_<path:user_type>", methods=('POST',)) def add_users(user_type='members'): - group_id = request.form['group_id'] - if user_type == "admins": - user_emails = request.form['admin_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, - user_emails, admins=True) - elif user_type == "members": - user_emails = request.form['member_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, - user_emails, admins=False) + group_id = request.form['group_id'] + if user_type == "admins": + user_emails = request.form['admin_emails_to_add'].split(",") + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=True) + elif user_type == "members": + user_emails = request.form['member_emails_to_add'].split(",") + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=False) - return redirect(url_for('view_group', id=group_id)) + return redirect(url_for('view_group', id=group_id)) @app.route("/groups/change_name", methods=('POST',)) def change_name(): - group_id = request.form['group_id'] - new_name = request.form['new_name'] - group_info = change_group_name(g.user_session.user_id, group_id, new_name) + group_id = request.form['group_id'] + new_name = request.form['new_name'] + group_info = change_group_name(g.user_session.user_id, group_id, new_name) - return new_name + return new_name @app.route("/groups/create", methods=('GET', 'POST')) def add_or_edit_group(): - params = request.form if request.form else request.args - if "group_name" in params: - member_user_ids = set() - admin_user_ids = set() - # ZS: Always add the user creating the group as an admin - admin_user_ids.add(g.user_session.user_id) - if "admin_emails_to_add" in params: - admin_emails = params['admin_emails_to_add'].split(",") - for email in admin_emails: - user_details = get_user_by_unique_column("email_address", email) - if user_details: - admin_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") - if "member_emails_to_add" in params: - member_emails = params['member_emails_to_add'].split(",") - for email in member_emails: - user_details = get_user_by_unique_column("email_address", email) - if user_details: - member_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") - - create_group(list(admin_user_ids), list( - member_user_ids), params['group_name']) - return redirect(url_for('manage_groups')) - else: - return render_template("admin/create_group.html") + params = request.form if request.form else request.args + if "group_name" in params: + member_user_ids = set() + admin_user_ids = set() + # ZS: Always add the user creating the group as an admin + admin_user_ids.add(g.user_session.user_id) + if "admin_emails_to_add" in params: + admin_emails = params['admin_emails_to_add'].split(",") + for email in admin_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + admin_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") + if "member_emails_to_add" in params: + member_emails = params['member_emails_to_add'].split(",") + for email in member_emails: + user_details = get_user_by_unique_column("email_address", email) + if user_details: + member_user_ids.add(user_details['user_id']) + #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") + + create_group(list(admin_user_ids), list( + member_user_ids), params['group_name']) + return redirect(url_for('manage_groups')) + else: + return render_template("admin/create_group.html") # ZS: Will integrate this later, for now just letting users be added directly def send_group_invites(group_id, user_email_list=[], user_type="members"): - for user_email in user_email_list: - user_details = get_user_by_unique_column("email_address", user_email) - if user_details: - group_info = get_group_info(group_id) - # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, - # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something - if group_info: - # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, - # but do add them if they're a regular user and are added as an admin - if (user_details['user_id'] in group_info['admins']) or \ - ((user_type == "members") and (user_details['user_id'] in group_info['members'])): - continue - else: - send_verification_email(user_details, template_name="email/group_verification.txt", - key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") - else: - temp_password = ''.join(random.choice( - string.ascii_uppercase + string.digits) for _ in range(6)) - user_details = { - 'user_id': str(uuid.uuid4()), - 'email_address': user_email, - 'registration_info': basic_info(), - 'password': set_password(temp_password), - 'confirmed': 0 - } - save_user(user_details, user_details['user_id']) - send_invitation_email(user_email, temp_password) + for user_email in user_email_list: + user_details = get_user_by_unique_column("email_address", user_email) + if user_details: + group_info = get_group_info(group_id) + # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, + # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something + if group_info: + # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, + # but do add them if they're a regular user and are added as an admin + if (user_details['user_id'] in group_info['admins']) or \ + ((user_type == "members") and (user_details['user_id'] in group_info['members'])): + continue + else: + send_verification_email(user_details, template_name="email/group_verification.txt", + key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") + else: + temp_password = ''.join(random.choice( + string.ascii_uppercase + string.digits) for _ in range(6)) + user_details = { + 'user_id': str(uuid.uuid4()), + 'email_address': user_email, + 'registration_info': basic_info(), + 'password': set_password(temp_password), + 'confirmed': 0 + } + save_user(user_details, user_details['user_id']) + send_invitation_email(user_email, temp_password) # @app.route() diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 9548d130..f02da27c 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -247,13 +247,13 @@ class GSearch: if not trait_ob: continue if this_trait['dataset'] == this_trait['group'] + "Publish": - try: - if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + \ - str(trait_ob.locus_chr) + \ - ": " + str(trait_ob.locus_mb) - except: - this_trait['max_lrs_text'] = "N/A" + try: + if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": + this_trait['max_lrs_text'] = "Chr" + \ + str(trait_ob.locus_chr) + \ + ": " + str(trait_ob.locus_mb) + except: + this_trait['max_lrs_text'] = "N/A" trait_list.append(this_trait) diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index e624a146..2f1c142c 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -7,79 +7,79 @@ from flask import Flask, g def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): - fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', - 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', - 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] + fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', + 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', + 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] - # List All Species in the Gene Table - speciesDict = {} - results = g.db.execute(""" + # List All Species in the Gene Table + speciesDict = {} + results = g.db.execute(""" SELECT Species.Name, GeneList.SpeciesId FROM Species, GeneList WHERE GeneList.SpeciesId = Species.Id GROUP BY GeneList.SpeciesId""").fetchall() - for item in results: - speciesDict[item[0]] = item[1] + for item in results: + speciesDict[item[0]] = item[1] - # List current Species and other Species - speciesId = speciesDict[species] - otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] - otherSpecies.remove([species, speciesId]) + # List current Species and other Species + speciesId = speciesDict[species] + otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] + otherSpecies.remove([species, speciesId]) - results = g.db.execute(""" + results = g.db.execute(""" SELECT %s FROM GeneList WHERE SpeciesId = %d AND Chromosome = '%s' AND ((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f)) ORDER BY txStart """ % (", ".join(fetchFields), - speciesId, chrName, - startMb, endMb, - startMb, endMb)).fetchall() - - GeneList = [] - - if results: - for result in results: - newdict = {} - for j, item in enumerate(fetchFields): - newdict[item] = result[j] - # count SNPs if possible - if diffCol and species == 'mouse': - newdict["snpCount"] = g.db.execute(""" + speciesId, chrName, + startMb, endMb, + startMb, endMb)).fetchall() + + GeneList = [] + + if results: + for result in results: + newdict = {} + for j, item in enumerate(fetchFields): + newdict[item] = result[j] + # count SNPs if possible + if diffCol and species == 'mouse': + newdict["snpCount"] = g.db.execute(""" SELECT count(*) FROM BXDSnpPosition WHERE Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict["snpDensity"] = newdict["snpCount"] / \ - (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 - else: - newdict["snpDensity"] = newdict["snpCount"] = 0 - - try: - newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart']) - except: - pass - - # load gene from other Species by the same name - for item in otherSpecies: - othSpec, othSpecId = item - newdict2 = {} - - resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields), - othSpecId, - newdict["GeneSymbol"])).fetchone() - - if resultsOther: - for j, item in enumerate(fetchFields): - newdict2[item] = resultsOther[j] - - # count SNPs if possible, could be a separate function - if diffCol and othSpec == 'mouse': - newdict2["snpCount"] = g.db.execute(""" + newdict["snpDensity"] = newdict["snpCount"] / \ + (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 + else: + newdict["snpDensity"] = newdict["snpCount"] = 0 + + try: + newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart']) + except: + pass + + # load gene from other Species by the same name + for item in otherSpecies: + othSpec, othSpecId = item + newdict2 = {} + + resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields), + othSpecId, + newdict["GeneSymbol"])).fetchone() + + if resultsOther: + for j, item in enumerate(fetchFields): + newdict2[item] = resultsOther[j] + + # count SNPs if possible, could be a separate function + if diffCol and othSpec == 'mouse': + newdict2["snpCount"] = g.db.execute(""" SELECT count(*) FROM BXDSnpPosition WHERE Chr = '%s' AND @@ -87,19 +87,19 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict2["snpDensity"] = newdict2["snpCount"] / \ - (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 - else: - newdict2["snpDensity"] = newdict2["snpCount"] = 0 + newdict2["snpDensity"] = newdict2["snpCount"] / \ + (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 + else: + newdict2["snpDensity"] = newdict2["snpCount"] = 0 - try: - newdict2['GeneLength'] = 1000.0 * \ - (newdict2['TxEnd'] - newdict2['TxStart']) - except: - pass + try: + newdict2['GeneLength'] = 1000.0 * \ + (newdict2['TxEnd'] - newdict2['TxStart']) + except: + pass - newdict['%sGene' % othSpec] = newdict2 + newdict['%sGene' % othSpec] = newdict2 - GeneList.append(newdict) + GeneList.append(newdict) - return GeneList + return GeneList diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 8d0134d8..c68e0fde 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -395,17 +395,17 @@ class DisplayMappingResults: # Darwing Options try: - if self.selectedChr > -1: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( - self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) - else: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( - self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + if self.selectedChr > -1: + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + else: + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) except: - if self.selectedChr > -1: - self.graphWidth = self.GRAPH_DEFAULT_WIDTH - else: - self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH + if self.selectedChr > -1: + self.graphWidth = self.GRAPH_DEFAULT_WIDTH + else: + self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH # BEGIN HaplotypeAnalyst if 'haplotypeAnalystCheck' in list(start_vars.keys()): @@ -574,15 +574,15 @@ class DisplayMappingResults: chrName, self.diffCol, self.startMb, self.endMb, "rat") if self.geneCol and self.intervalAnalystChecked: - ####################################################################### - #Nick use GENEID as RefGene to get Literature Correlation Informations# - #For Interval Mapping, Literature Correlation isn't useful, so skip it# - #through set GENEID is None # - ####################################################################### + ####################################################################### + #Nick use GENEID as RefGene to get Literature Correlation Informations# + #For Interval Mapping, Literature Correlation isn't useful, so skip it# + #through set GENEID is None # + ####################################################################### - GENEID = None + GENEID = None - self.geneTable(self.geneCol, GENEID) + self.geneTable(self.geneCol, GENEID) ################################################################ # Plots goes here @@ -2636,11 +2636,11 @@ class DisplayMappingResults: LRSCoordXY.append((Xc, Yc)) if not self.multipleInterval and self.additiveChecked: - if additiveMax == 0.0: - additiveMax = 0.000001 - Yc = yZero - qtlresult['additive'] * \ - AdditiveHeightThresh / additiveMax - AdditiveCoordXY.append((Xc, Yc)) + if additiveMax == 0.0: + additiveMax = 0.000001 + Yc = yZero - qtlresult['additive'] * \ + AdditiveHeightThresh / additiveMax + AdditiveCoordXY.append((Xc, Yc)) m += 1 diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index b3c9fddf..32dbad1f 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -294,13 +294,13 @@ def add_categorical_covar(cross, covar_as_string, i): col_names = [] # logger.info("loop") for x in range(1, (nCol + 1)): - #logger.info("loop" + str(x)); - col_name = "covar_" + str(i) + "_" + str(x) - #logger.info("col_name" + col_name); - ro.r('the_cross$pheno <- cbind(pheno, ' + \ - col_name + ' = newcovar[,' + str(x) + '])') - col_names.append(col_name) - #logger.info("loop" + str(x) + "done"); + #logger.info("loop" + str(x)); + col_name = "covar_" + str(i) + "_" + str(x) + #logger.info("col_name" + col_name); + ro.r('the_cross$pheno <- cbind(pheno, ' + \ + col_name + ' = newcovar[,' + str(x) + '])') + col_names.append(col_name) + #logger.info("loop" + str(x) + "done"); logger.info("returning from add_categorical_covar") return ro.r["the_cross"], col_names diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index d9b28fba..041f4348 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -65,10 +65,10 @@ class RunMapping: # ZS: Sometimes a group may have a genofile that only includes a subset of samples genofile_samplelist = [] if 'genofile' in start_vars: - if start_vars['genofile'] != "": - self.genofile_string = start_vars['genofile'] - self.dataset.group.genofile = self.genofile_string.split(":")[0] - genofile_samplelist = get_genofile_samplelist(self.dataset) + if start_vars['genofile'] != "": + self.genofile_string = start_vars['genofile'] + self.dataset.group.genofile = self.genofile_string.split(":")[0] + genofile_samplelist = get_genofile_samplelist(self.dataset) all_samples_ordered = self.dataset.group.all_samples_ordered() @@ -324,182 +324,182 @@ class RunMapping: self.no_results = False if len(results) == 0: - self.no_results = True + self.no_results = True else: - if self.pair_scan == True: - self.qtl_results = [] - highest_chr = 1 # This is needed in order to convert the highest chr to X/Y - for marker in results: - if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": - if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": - highest_chr = marker['chr1'] - if 'lod_score' in list(marker.keys()): - self.qtl_results.append(marker) - - self.trimmed_markers = results - - for qtl in enumerate(self.qtl_results): - self.json_data['chr1'].append(str(qtl['chr1'])) - self.json_data['chr2'].append(str(qtl['chr2'])) - self.json_data['Mb'].append(qtl['Mb']) - self.json_data['markernames'].append(qtl['name']) - - self.js_data = dict( - json_data=self.json_data, - this_trait=self.this_trait.name, - data_set=self.dataset.name, - maf=self.maf, - manhattan_plot=self.manhattan_plot, - mapping_scale=self.mapping_scale, - qtl_results=self.qtl_results - ) - - else: - self.qtl_results = [] - self.results_for_browser = [] - self.annotations_for_browser = [] - highest_chr = 1 # This is needed in order to convert the highest chr to X/Y - for marker in results: - if 'Mb' in marker: - this_ps = marker['Mb'] * 1000000 - else: - this_ps = marker['cM'] * 1000000 - - browser_marker = dict( - chr=str(marker['chr']), - rs=marker['name'], - ps=this_ps, - url="/show_trait?trait_id=" + \ - marker['name'] + "&dataset=" + \ - self.dataset.group.name + "Geno" - ) - - if self.geno_db_exists == "True": - annot_marker = dict( - name=str(marker['name']), - chr=str(marker['chr']), - rs=marker['name'], - pos=this_ps, - url="/show_trait?trait_id=" + \ - marker['name'] + "&dataset=" + \ - self.dataset.group.name + "Geno" - ) - else: - annot_marker = dict( - name=str(marker['name']), - chr=str(marker['chr']), - rs=marker['name'], - pos=this_ps - ) - - if 'lrs_value' in marker and marker['lrs_value'] > 0: - browser_marker['p_wald'] = 10**- \ - (marker['lrs_value'] / 4.61) - elif 'lod_score' in marker and marker['lod_score'] > 0: - browser_marker['p_wald'] = 10**-(marker['lod_score']) - else: - browser_marker['p_wald'] = 0 - - self.results_for_browser.append(browser_marker) - self.annotations_for_browser.append(annot_marker) - if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": - if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": - highest_chr = marker['chr'] - if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): - if 'Mb' in marker.keys(): - marker['display_pos'] = "Chr" + \ - str(marker['chr']) + ": " + \ - "{:.6f}".format(marker['Mb']) - elif 'cM' in marker.keys(): - marker['display_pos'] = "Chr" + \ - str(marker['chr']) + ": " + \ - "{:.3f}".format(marker['cM']) - else: - marker['display_pos'] = "N/A" - self.qtl_results.append(marker) - - total_markers = len(self.qtl_results) - - with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, - self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) - - with Bench("Trimming Markers for Figure"): - if len(self.qtl_results) > 30000: - self.qtl_results = trim_markers_for_figure( - self.qtl_results) - self.results_for_browser = trim_markers_for_figure( - self.results_for_browser) - filtered_annotations = [] - for marker in self.results_for_browser: - for annot_marker in self.annotations_for_browser: - if annot_marker['rs'] == marker['rs']: - filtered_annotations.append(annot_marker) - break - self.annotations_for_browser = filtered_annotations - browser_files = write_input_for_browser( - self.dataset, self.results_for_browser, self.annotations_for_browser) - else: - browser_files = write_input_for_browser( - self.dataset, self.results_for_browser, self.annotations_for_browser) - - with Bench("Trimming Markers for Table"): - self.trimmed_markers = trim_markers_for_table(results) - - chr_lengths = get_chr_lengths( - self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) - - # ZS: For zooming into genome browser, need to pass chromosome name instead of number - if self.dataset.group.species == "mouse": - if self.selected_chr == 20: - this_chr = "X" - else: - this_chr = str(self.selected_chr) - elif self.dataset.group.species == "rat": - if self.selected_chr == 21: - this_chr = "X" - else: - this_chr = str(self.selected_chr) - else: - if self.selected_chr == 22: - this_chr = "X" - elif self.selected_chr == 23: - this_chr = "Y" - else: - this_chr = str(self.selected_chr) - - if self.mapping_method != "gemma": - if self.score_type == "LRS": - significant_for_browser = self.significant / 4.61 - else: - significant_for_browser = self.significant - - self.js_data = dict( - #result_score_type = self.score_type, - #this_trait = self.this_trait.name, - #data_set = self.dataset.name, - #maf = self.maf, - #manhattan_plot = self.manhattan_plot, - #mapping_scale = self.mapping_scale, - #chromosomes = chromosome_mb_lengths, - #qtl_results = self.qtl_results, - categorical_vars=self.categorical_vars, - chr_lengths=chr_lengths, - num_perm=self.num_perm, - perm_results=self.perm_output, - significant=significant_for_browser, - browser_files=browser_files, - selected_chr=this_chr, - total_markers=total_markers - ) - else: + if self.pair_scan == True: + self.qtl_results = [] + highest_chr = 1 # This is needed in order to convert the highest chr to X/Y + for marker in results: + if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": + if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": + highest_chr = marker['chr1'] + if 'lod_score' in list(marker.keys()): + self.qtl_results.append(marker) + + self.trimmed_markers = results + + for qtl in enumerate(self.qtl_results): + self.json_data['chr1'].append(str(qtl['chr1'])) + self.json_data['chr2'].append(str(qtl['chr2'])) + self.json_data['Mb'].append(qtl['Mb']) + self.json_data['markernames'].append(qtl['name']) + self.js_data = dict( - chr_lengths=chr_lengths, - browser_files=browser_files, - selected_chr=this_chr, - total_markers=total_markers + json_data=self.json_data, + this_trait=self.this_trait.name, + data_set=self.dataset.name, + maf=self.maf, + manhattan_plot=self.manhattan_plot, + mapping_scale=self.mapping_scale, + qtl_results=self.qtl_results ) + else: + self.qtl_results = [] + self.results_for_browser = [] + self.annotations_for_browser = [] + highest_chr = 1 # This is needed in order to convert the highest chr to X/Y + for marker in results: + if 'Mb' in marker: + this_ps = marker['Mb'] * 1000000 + else: + this_ps = marker['cM'] * 1000000 + + browser_marker = dict( + chr=str(marker['chr']), + rs=marker['name'], + ps=this_ps, + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" + ) + + if self.geno_db_exists == "True": + annot_marker = dict( + name=str(marker['name']), + chr=str(marker['chr']), + rs=marker['name'], + pos=this_ps, + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" + ) + else: + annot_marker = dict( + name=str(marker['name']), + chr=str(marker['chr']), + rs=marker['name'], + pos=this_ps + ) + + if 'lrs_value' in marker and marker['lrs_value'] > 0: + browser_marker['p_wald'] = 10**- \ + (marker['lrs_value'] / 4.61) + elif 'lod_score' in marker and marker['lod_score'] > 0: + browser_marker['p_wald'] = 10**-(marker['lod_score']) + else: + browser_marker['p_wald'] = 0 + + self.results_for_browser.append(browser_marker) + self.annotations_for_browser.append(annot_marker) + if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": + if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": + highest_chr = marker['chr'] + if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): + if 'Mb' in marker.keys(): + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.6f}".format(marker['Mb']) + elif 'cM' in marker.keys(): + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.3f}".format(marker['cM']) + else: + marker['display_pos'] = "N/A" + self.qtl_results.append(marker) + + total_markers = len(self.qtl_results) + + with Bench("Exporting Results"): + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, + self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + + with Bench("Trimming Markers for Figure"): + if len(self.qtl_results) > 30000: + self.qtl_results = trim_markers_for_figure( + self.qtl_results) + self.results_for_browser = trim_markers_for_figure( + self.results_for_browser) + filtered_annotations = [] + for marker in self.results_for_browser: + for annot_marker in self.annotations_for_browser: + if annot_marker['rs'] == marker['rs']: + filtered_annotations.append(annot_marker) + break + self.annotations_for_browser = filtered_annotations + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) + else: + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) + + with Bench("Trimming Markers for Table"): + self.trimmed_markers = trim_markers_for_table(results) + + chr_lengths = get_chr_lengths( + self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) + + # ZS: For zooming into genome browser, need to pass chromosome name instead of number + if self.dataset.group.species == "mouse": + if self.selected_chr == 20: + this_chr = "X" + else: + this_chr = str(self.selected_chr) + elif self.dataset.group.species == "rat": + if self.selected_chr == 21: + this_chr = "X" + else: + this_chr = str(self.selected_chr) + else: + if self.selected_chr == 22: + this_chr = "X" + elif self.selected_chr == 23: + this_chr = "Y" + else: + this_chr = str(self.selected_chr) + + if self.mapping_method != "gemma": + if self.score_type == "LRS": + significant_for_browser = self.significant / 4.61 + else: + significant_for_browser = self.significant + + self.js_data = dict( + #result_score_type = self.score_type, + #this_trait = self.this_trait.name, + #data_set = self.dataset.name, + #maf = self.maf, + #manhattan_plot = self.manhattan_plot, + #mapping_scale = self.mapping_scale, + #chromosomes = chromosome_mb_lengths, + #qtl_results = self.qtl_results, + categorical_vars=self.categorical_vars, + chr_lengths=chr_lengths, + num_perm=self.num_perm, + perm_results=self.perm_output, + significant=significant_for_browser, + browser_files=browser_files, + selected_chr=this_chr, + total_markers=total_markers + ) + else: + self.js_data = dict( + chr_lengths=chr_lengths, + browser_files=browser_files, + selected_chr=this_chr, + total_markers=total_markers + ) + def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 7b9ff8fe..55b0278a 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -36,7 +36,7 @@ class User(Base): # json detailing when they became a superuser, otherwise empty superuser = Column(Text) - # if not superuser + # if not superuser logins = relationship("Login", order_by="desc(Login.timestamp)", diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 0d2fb2f8..2e1cb992 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -78,7 +78,7 @@ class SearchResultPage: try: self.search() except: - self.search_term_exists = False + self.search_term_exists = False self.too_many_results = False if self.search_term_exists: diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index bfaed9c2..725e7c9e 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -464,49 +464,49 @@ def password_reset_step2(): def register_user(params): - thank_you_mode = False - errors = [] - user_details = {} - - user_details['email_address'] = params.get( - 'email_address', '').encode("utf-8").strip() - if not (5 <= len(user_details['email_address']) <= 50): - errors.append( - 'Email Address needs to be between 5 and 50 characters.') - else: - email_exists = get_user_by_unique_column( - "email_address", user_details['email_address']) - if email_exists: - errors.append('User already exists with that email') + thank_you_mode = False + errors = [] + user_details = {} - user_details['full_name'] = params.get( - 'full_name', '').encode("utf-8").strip() - if not (5 <= len(user_details['full_name']) <= 50): - errors.append('Full Name needs to be between 5 and 50 characters.') + user_details['email_address'] = params.get( + 'email_address', '').encode("utf-8").strip() + if not (5 <= len(user_details['email_address']) <= 50): + errors.append( + 'Email Address needs to be between 5 and 50 characters.') + else: + email_exists = get_user_by_unique_column( + "email_address", user_details['email_address']) + if email_exists: + errors.append('User already exists with that email') - user_details['organization'] = params.get( - 'organization', '').encode("utf-8").strip() - if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50): - errors.append( - 'Organization needs to be empty or between 5 and 50 characters.') + user_details['full_name'] = params.get( + 'full_name', '').encode("utf-8").strip() + if not (5 <= len(user_details['full_name']) <= 50): + errors.append('Full Name needs to be between 5 and 50 characters.') - password = str(params.get('password', '')) - if not (6 <= len(password)): - errors.append('Password needs to be at least 6 characters.') + user_details['organization'] = params.get( + 'organization', '').encode("utf-8").strip() + if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50): + errors.append( + 'Organization needs to be empty or between 5 and 50 characters.') - if params.get('password_confirm') != password: - errors.append("Passwords don't match.") + password = str(params.get('password', '')) + if not (6 <= len(password)): + errors.append('Password needs to be at least 6 characters.') - user_details['password'] = set_password(password) - user_details['user_id'] = str(uuid.uuid4()) - user_details['confirmed'] = 1 + if params.get('password_confirm') != password: + errors.append("Passwords don't match.") - user_details['registration_info'] = basic_info() + user_details['password'] = set_password(password) + user_details['user_id'] = str(uuid.uuid4()) + user_details['confirmed'] = 1 - if len(errors) == 0: - save_user(user_details, user_details['user_id']) + user_details['registration_info'] = basic_info() + + if len(errors) == 0: + save_user(user_details, user_details['user_id']) - return errors + return errors @app.route("/n/register", methods=('GET', 'POST')) |