From 1cf4b598dd986760627eef4144c0445679c97866 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 9 Apr 2018 17:25:15 +0000 Subject: Removed unused code from get_select_dataset.py and get_group_samplelists.py scripts --- wqflask/maintenance/gen_select_dataset.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index f62d0cc1..16dcebc5 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -66,7 +66,7 @@ from pprint import pformat as pf print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') -def parse_db_uri(db_uri): +def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" parsed_uri = urlparse.urlparse(SQL_URI) @@ -81,7 +81,6 @@ def parse_db_uri(db_uri): return db_conn_info - def get_species(): """Build species list""" Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId") @@ -268,7 +267,7 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - parse_db_uri(SQL_URI) + parse_db_uri() species = get_species() groups = get_groups(species) @@ -307,6 +306,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI)) + Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() + main() \ No newline at end of file -- cgit v1.2.3 From 9bb60bb18ae5ac70fe480095554796b7c18f1b6c Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 25 May 2018 15:52:40 +0000 Subject: Fixed issue causing anonymous collections to not work on my branch and staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable --- wqflask/maintenance/convert_dryad_to_bimbam.py | 70 ++++++++++++++++++++++ wqflask/maintenance/gen_select_dataset.py | 2 +- wqflask/maintenance/quantile_normalize.py | 4 +- .../new/javascript/dataset_menu_structure.json | 34 +++++++++++ wqflask/wqflask/user_manager.py | 10 +++- 5 files changed, 116 insertions(+), 4 deletions(-) create mode 100644 wqflask/maintenance/convert_dryad_to_bimbam.py (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py new file mode 100644 index 00000000..e833b395 --- /dev/null +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -0,0 +1,70 @@ +#!/usr/bin/python + +""" +Convert data dryad files to a BIMBAM _geno and _snps file + + +""" + +from __future__ import print_function, division, absolute_import +import sys +sys.path.append("..") + + +def read_dryad_file(filename): + exclude_count = 0 + marker_list = [] + sample_dict = {} + sample_list = [] + geno_rows = [] + with open(filename, 'r') as the_file: + for i, line in enumerate(the_file): + if i > 0: + if line.split(" ")[1] == "no": + sample_name = line.split(" ")[0] + sample_list.append(sample_name) + sample_dict[sample_name] = line.split(" ")[2:] + else: + exclude_count += 1 + else: + marker_list = line.split(" ")[2:] + + for i, marker in enumerate(marker_list): + this_row = [] + this_row.append(marker) + this_row.append("X") + this_row.append("Y") + for sample in sample_list: + this_row.append(sample_dict[sample][i]) + geno_rows.append(this_row) + + print(exclude_count) + + return geno_rows + + #for i, marker in enumerate(marker_list): + # this_row = [] + # this_row.append(marker) + # this_row.append("X") + # this_row.append("Y") + # with open(filename, 'r') as the_file: + # for j, line in enumerate(the_file): + # if j > 0: + # this_row.append(line.split(" ")[i+2]) + # print("row: " + str(i)) + # geno_rows.append(this_row) + # + #return geno_rows + +def write_bimbam_files(geno_rows): + with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh: + for row in geno_rows: + geno_fh.write(", ".join(row) + "\n") + +def convert_dryad_to_bimbam(filename): + geno_file_rows = read_dryad_file(filename) + write_bimbam_files(geno_file_rows) + +if __name__=="__main__": + input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" + convert_dryad_to_bimbam(input_filename) \ No newline at end of file diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 2825c6ea..18b2dac9 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -63,7 +63,7 @@ from pprint import pformat as pf #conn = Engine.connect() -def parse_db_uri(db_uri): +def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" parsed_uri = urlparse.urlparse(SQL_URI) diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index c11073fb..41a3aad8 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -59,7 +59,7 @@ def set_data(dataset_name): orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt" sample_list = [] - with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh: + with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] @@ -118,7 +118,7 @@ if __name__ == '__main__': #out_filename = sys.argv[1][:-4] + '_quantnorm.txt' - #success, _ = bulk(es, set_data(sys.argv[1])) + success, _ = bulk(es, set_data(sys.argv[1])) response = es.search( index = "traits", doc_type = "trait", body = { diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index d00b52b8..c605329b 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1966,6 +1966,21 @@ "470", "EPFLADEL1013", "EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Exon Level (Oct13) RMA" + ], + [ + "777", + "EL_BXDCDHFDScWAT_0216", + "EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA" + ], + [ + "778", + "EL_BXDHFDScWAT_0216", + "EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA" + ], + [ + "779", + "EL_BXDCDScWAT_0216", + "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA **" ] ], "Adrenal Gland mRNA": [ @@ -3355,6 +3370,15 @@ ] ] }, + "D2GM": { + "Retina mRNA": [ + [ + "847", + "JAX_D2GM_RSeq_log2Z_0418", + "JAX Retina (Apr18) RNA-Seq log2-Z" + ] + ] + }, "EMSR": {}, "HS": { "Hippocampus mRNA": [ @@ -3954,6 +3978,10 @@ "CXB", "CXB" ], + [ + "D2GM", + "D2 Glaucoma Model" + ], [ "EMSR", "Ethanol-Medicated Stress Reduction" @@ -5236,6 +5264,12 @@ "Spleen mRNA" ] ], + "D2GM": [ + [ + "Retina mRNA", + "Retina mRNA" + ] + ], "EMSR": [], "HS": [ [ diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index d652f2e9..132bae90 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -62,9 +62,17 @@ class AnonUser(object): self.anon_id, self.cookie = create_signed_cookie() self.key = "anon_collection:v1:{}".format(self.anon_id) - @after.after_this_request + #ZS: This was originally the commented out function below + # For some reason I don't yet understand the commented out code works on production, + # but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work. + @app.after_request def set_cookie(response): response.set_cookie(self.cookie_name, self.cookie) + return response + + #@after.after_this_request + #def set_cookie(response): + # response.set_cookie(self.cookie_name, self.cookie) def add_collection(self, new_collection): collection_dict = dict(name = new_collection.name, -- cgit v1.2.3