From e695e8d162ca04f41694a525e93ced1b9d23a85b Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 16 Aug 2016 20:30:38 +0000 Subject: Users can now select specific traits from collection when using collection tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc). --- wqflask/utility/helper_functions.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 15f60765..149ee553 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -4,6 +4,8 @@ from base.trait import GeneralTrait from base import data_set from base.species import TheSpecies +from wqflask import user_manager + def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" @@ -23,13 +25,15 @@ def get_species_dataset_trait(self, start_vars): def get_trait_db_obs(self, trait_db_list): - + if isinstance(trait_db_list, basestring): + trait_db_list = trait_db_list.split(",") + self.trait_list = [] - for i, trait_db in enumerate(trait_db_list): - if i == (len(trait_db_list) - 1): - break - trait_name, dataset_name = trait_db.split(":") - #print("dataset_name:", dataset_name) + for trait in trait_db_list: + data, _separator, hmac = trait.rpartition(':') + data = data.strip() + assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" + trait_name, dataset_name = data.split(":") dataset_ob = data_set.create_dataset(dataset_name) trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, -- cgit 1.4.1 From ec7d4e1198bc8d2f83ce99b41e2084fbce6a0be7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 10 Sep 2016 11:43:21 +0200 Subject: Support for running maintenance scripts so they can pick up all webserver settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py --- bin/genenetwork2 | 27 ++++++++++++++++++++++++--- wqflask/base/data_set.py | 2 +- wqflask/base/webqtlConfig.py | 1 - wqflask/maintenance/gen_select_dataset.py | 26 +++++++++++++++++--------- wqflask/utility/tools.py | 1 + 5 files changed, 43 insertions(+), 14 deletions(-) (limited to 'wqflask/utility') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index d3bf3299..3a8c3ff4 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,6 +1,14 @@ #! /bin/bash # -# This will run the GN2 server (with default settings if none supplied). +# This will run the GN2 server (with default settings if none supplied). Pass in +# your own settings file, e.g. +# +# ./bin/genenetwork2 ~/my_settings.py +# +# To run a maintenance script with settings (instead of the webserver) add that with +# a -c switch, e.g. +# +# ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py # # Environment settings can be used to preconfigure as well as a # settings.py file. @@ -18,7 +26,12 @@ echo $GN2_BASE_PATH # Handle settings parameter settings=$1 -if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi +if [ -z $settings ]; then + # get default + settings=$GN2_BASE_PATH/etc/default_settings.py +else + shift +fi if [ ! -e $settings ]; then echo "ERROR: can not locate settings file - pass it in the command line" exit 1 @@ -32,7 +45,15 @@ export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH if [ -z $TEMPDIR ]; then TEMPDIR="/tmp" fi - + +# Now handle command parameter -c +if [ $1 = '-c' ] ; then + echo PYTHONPATH=$PYTHONPATH + echo RUNNING COMMAND $2 + /usr/bin/env python $2 + exit 0 +fi + echo "Starting the redis server:" echo -n "dir $TEMPDIR dbfilename gn2.rdb diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1b4e1195..6cd3c8e6 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -91,7 +91,7 @@ Publish or ProbeSet. E.g. if USE_GN_SERVER: data = menu_main() else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index f76d8140..8c67a6fd 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -80,4 +80,3 @@ PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' SCRIPTFILE = 'main.py' - diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index d39bf4a5..5c25c15b 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -1,7 +1,9 @@ """Script that generates the data for the main dropdown menus on the home page Writes out data as /static/new/javascript/dataset_menu_structure.json -It needs to be run manually when database has been changed. +It needs to be run manually when database has been changed. Run it as + + python gen_select_dataset.py """ @@ -37,9 +39,15 @@ from __future__ import print_function, division #print("cdict is:", cdict) import sys -# import zach_settings # no hard code paths! -# import MySQLdb +# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead +sys.path.insert(0,'./wqflask') +# NEW: import app to avoid a circular dependency on utility.tools +from wqflask import app + +from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI + +import MySQLdb # import simplejson as json import urlparse @@ -55,14 +63,13 @@ from pprint import pformat as pf #conn = Engine.connect() -print('ERROR: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') -sys.exit() +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): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(zach_settings.DB_URI) + parsed_uri = urlparse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -70,6 +77,7 @@ def parse_db_uri(db_uri): user = parsed_uri.username, passwd = parsed_uri.password) + print(db_conn_info) return db_conn_info @@ -258,7 +266,7 @@ 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(zach_settings.SQL_URI) + parse_db_uri(SQL_URI) species = get_species() groups = get_groups(species) @@ -281,7 +289,7 @@ def main(): #print("data:", data) - output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" + output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) @@ -297,6 +305,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.SQL_URI)) + Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI)) Cursor = Conn.cursor() main() diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index bb8241f5..2c8cc5c5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,6 +3,7 @@ import os import sys + from wqflask import app # Use the standard logger here to avoid a circular dependency -- cgit 1.4.1 From e7693e53821747d294452c9bff7e8b0f38a0eb8e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 24 Sep 2016 07:41:39 +0000 Subject: tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2 --- etc/default_settings.py | 13 ++++++++----- wqflask/base/webqtlConfig.py | 5 +++-- wqflask/utility/tools.py | 7 +++++-- 3 files changed, 16 insertions(+), 9 deletions(-) (limited to 'wqflask/utility') diff --git a/etc/default_settings.py b/etc/default_settings.py index df734f7c..9dddd0ad 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -22,7 +22,7 @@ SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' SQLALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" -# Flask configuration (see website) +# ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True SECURITY_CONFIRMABLE = True SECURITY_TRACKABLE = True @@ -34,8 +34,8 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you" SERVER_PORT = 5003 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' -# Behavioural settings (defaults) note that logger and log levels can -# be overridden at the module level and with enviroment settings +# ---- Behavioural settings (defaults) note that logger and log levels can +# be overridden at the module level and with enviroment settings WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) WEBSERVER_BRANDING = None # Set the branding (nyi) WEBSERVER_DEPLOY = None # Deployment specifics (nyi) @@ -49,10 +49,13 @@ LOG_BENCH = True # Log bench marks USE_REDIS = True # REDIS caching (note that redis will be phased out) USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls -# Path overrides for Genenetwork +# ---- Path overrides for Genenetwork +# TMPDIR is normally picked up from the environment HOME=os.environ['HOME'] LOGFILE = HOME+"/genenetwork2.log" -GENENETWORK_FILES = HOME+"/gn2_data" +GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files + +# ---- GN2 Executables PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 8c67a6fd..6bbabdec 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -60,9 +60,10 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp # HTMLPATH is replaced by GENODIR # IMGDIR is replaced by GENERATED_IMAGE_DIR -# Temporary storage: +# Temporary storage (note that this TMPDIR is not the same directory +# as the UNIX TMPDIR) TMPDIR = mk_dir(TEMPDIR+'/gn2/') -CACHEDIR = mk_dir(TEMPDIR+'/cache/') +CACHEDIR = mk_dir(TMPDIR+'/cache/') # We can no longer write into the git tree: GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/') GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 2c8cc5c5..907b0d6a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -147,7 +147,10 @@ def locate_ignore_error(name, subdir=None): return None def tempdir(): - return valid_path(get_setting("TEMPDIR","/tmp")) + """ + Get UNIX TMPDIR by default + """ + return valid_path(get_setting("TMPDIR","/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' @@ -184,9 +187,9 @@ LOG_BENCH = get_setting_bool('LOG_BENCH') LOG_FORMAT = "%(message)s" # not yet in use USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') +GENENETWORK_FILES = get_setting_bool('GENENETWORK_FILES') PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() -FLAT_FILES = flat_files() TEMPDIR = tempdir() -- cgit 1.4.1