diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 74 | ||||
| -rw-r--r-- | wqflask/runserver.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 58 | ||||
| -rw-r--r-- | wqflask/wqflask/parser.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 21 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 88 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 6 |
7 files changed, 138 insertions, 124 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4953e728..f75447f6 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -51,6 +51,9 @@ from maintenance import get_group_samplelists from MySQLdb import escape_string as escape from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + # Used by create_database to instantiate objects # Each subclass will add to this DS_NAME_MAP = {} @@ -59,7 +62,7 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) - print("dataset_type is:", dataset_type) + logger.debug("dataset_type is:", dataset_type) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] @@ -73,7 +76,7 @@ class Dataset_Types(object): with open(file_name, 'r') as fh: data = json.load(fh) - print("*" * 70) + logger.debug("*" * 70) for species in data['datasets']: for group in data['datasets'][species]: for dataset_type in data['datasets'][species][group]: @@ -98,7 +101,7 @@ def create_datasets_list(): result = Redis.get(key) if result: - print("Cache hit!!!") + logger.debug("Cache hit!!!") datasets = pickle.loads(result) else: @@ -113,7 +116,7 @@ def create_datasets_list(): for result in g.db.execute(query).fetchall(): #The query at the beginning of this function isn't necessary here, but still would #rather just reuse it - #print("type: {}\tname: {}".format(dataset_type, result.Name)) + #logger.debug("type: {}\tname: {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) @@ -133,7 +136,7 @@ def create_in_clause(items): def mescape(*items): """Multiple escape""" escaped = [escape(str(item)) for item in items] - #print("escaped is:", escaped) + #logger.debug("escaped is:", escaped) return escaped @@ -152,12 +155,12 @@ class Markers(object): marker['Mb'] = float(marker['Mb']) self.markers = markers - #print("self.markers:", self.markers) + #logger.debug("self.markers:", self.markers) def add_pvalues(self, p_values): - print("length of self.markers:", len(self.markers)) - print("length of p_values:", len(p_values)) + logger.debug("length of self.markers:", len(self.markers)) + logger.debug("length of p_values:", len(p_values)) if type(p_values) is list: # THIS IS only needed for the case when we are limiting the number of p-values calculated @@ -178,10 +181,10 @@ class Markers(object): elif type(p_values) is dict: filtered_markers = [] for marker in self.markers: - #print("marker[name]", marker['name']) - #print("p_values:", p_values) + #logger.debug("marker[name]", marker['name']) + #logger.debug("p_values:", p_values) if marker['name'] in p_values: - #print("marker {} IS in p_values".format(i)) + #logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -192,7 +195,7 @@ class Markers(object): marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 filtered_markers.append(marker) #else: - #print("marker {} NOT in p_values".format(i)) + #logger.debug("marker {} NOT in p_values".format(i)) #self.markers.remove(marker) #del self.markers[i] self.markers = filtered_markers @@ -204,7 +207,7 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - #print("splat:", splat) + #logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -220,7 +223,7 @@ class HumanMarkers(Markers): marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - #print("markers is: ", pf(self.markers)) + #logger.debug("markers is: ", pf(self.markers)) def add_pvalues(self, p_values): @@ -237,7 +240,7 @@ class DatasetGroup(object): """ def __init__(self, dataset): """This sets self.group and self.group_id""" - #print("DATASET NAME2:", dataset.name) + #logger.debug("DATASET NAME2:", dataset.name) self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() if self.name == 'BXD300': self.name = "BXD" @@ -245,7 +248,7 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.get_f1_parent_strains() - #print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list)) self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -257,7 +260,7 @@ class DatasetGroup(object): self.markers = HumanMarkers(self.name, markers) def get_markers(self): - #print("self.species is:", self.species) + #logger.debug("self.species is:", self.species) if self.species == "human": marker_class = HumanMarkers else: @@ -267,10 +270,10 @@ class DatasetGroup(object): def datasets(self): key = "group_dataset_menu:v2:" + self.name - print("key is2:", key) + logger.debug("key is2:", key) dataset_menu = [] - print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) - print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) + logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) + logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) results = g.db.execute(''' (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet @@ -317,7 +320,7 @@ class DatasetGroup(object): break if tissue_already_exists: - #print("dataset_menu:", dataset_menu[i]['datasets']) + #logger.debug("dataset_menu:", dataset_menu[i]['datasets']) dataset_menu[i]['datasets'].append((dataset, dataset_short)) else: dataset_menu.append(dict(tissue=tissue_name, @@ -343,18 +346,18 @@ class DatasetGroup(object): def get_samplelist(self): key = "samplelist:v2:" + self.name - #print("key is:", key) + #logger.debug("key is:", key) #with Bench("Loading cache"): result = Redis.get(key) if result: - #print("Sample List Cache hit!!!") - #print("Before unjsonifying {}: {}".format(type(result), result)) + #logger.debug("Sample List Cache hit!!!") + #logger.debug("Before unjsonifying {}: {}".format(type(result), result)) self.samplelist = json.loads(result) - #print(" type: ", type(self.samplelist)) - #print(" self.samplelist: ", self.samplelist) + #logger.debug(" type: ", type(self.samplelist)) + #logger.debug(" self.samplelist: ", self.samplelist) else: - print("Cache not hit") + logger.debug("Cache not hit") genotype_fn = locate_ignore_error(self.name+".geno",'genotype') mapping_fn = locate_ignore_error(self.name+".fam",'mapping') @@ -364,7 +367,7 @@ class DatasetGroup(object): self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - print("Sample list: ",self.samplelist) + logger.debug("Sample list: ",self.samplelist) Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) @@ -482,7 +485,7 @@ class DataSet(object): """ % (query_args)).fetchone() except TypeError: - print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) + logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass def get_trait_data(self, sample_list=None): @@ -549,10 +552,10 @@ class DataSet(object): """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) - #print("trait data query: ", query) + #logger.debug("trait data query: ", query) results = g.db.execute(query).fetchall() - #print("query results:", results) + #logger.debug("query results:", results) trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) @@ -571,7 +574,7 @@ class PhenotypeDataSet(DataSet): def setup(self): - #print("IS A PHENOTYPEDATASET") + #logger.debug("IS A PHENOTYPEDATASET") # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', @@ -967,7 +970,7 @@ class MrnaAssayDataSet(DataSet): """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - #print("query is:", pf(query)) + #logger.debug("query is:", pf(query)) result = g.db.execute(query).fetchone() @@ -1046,7 +1049,7 @@ class MrnaAssayDataSet(DataSet): Strain.Name """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() - #print("RETRIEVED RESULTS HERE:", results) + #logger.debug("RETRIEVED RESULTS HERE:", results) return results @@ -1130,7 +1133,7 @@ class TempDataSet(DataSet): def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" - #print("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) + #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table) @@ -1145,4 +1148,3 @@ def geno_mrna_confidentiality(ob): if confidential: return True - diff --git a/wqflask/runserver.py b/wqflask/runserver.py index bfc27827..4556056d 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -20,6 +20,7 @@ from wqflask import app #_ch = logging.StreamHandler() #_log.addHandler(_ch) +import logging import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -27,6 +28,8 @@ logger.info(app.config) from utility.tools import WEBSERVER_MODE +werkzeug_logger = logging.getLogger('werkzeug') + if WEBSERVER_MODE == 'DEBUG': app.run(host='0.0.0.0', port=app.config['SERVER_PORT'], @@ -35,6 +38,7 @@ if WEBSERVER_MODE == 'DEBUG': threaded=False, use_reloader=True) elif WEBSERVER_MODE == 'DEV': + werkzeug_logger.setLevel(logging.WARNING) app.run(host='0.0.0.0', port=app.config['SERVER_PORT'], debug=False, diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 04fd0688..48212877 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,6 +1,3 @@ -#!/usr/bin/python - - from __future__ import print_function, division import string @@ -15,6 +12,9 @@ import sys from dbFunction import webqtlDatabaseFunction +import logging +from utility.logger import getLogger +logger = getLogger(__name__ , level = logging.INFO) class DoSearch(object): """Parent class containing parameters/functions used for all searches""" @@ -30,15 +30,15 @@ class DoSearch(object): self.dataset = dataset if self.dataset: - print("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) - print("self.dataset.group is: ", pf(self.dataset.group)) + logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) + logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): """Executes query and returns results""" query = self.normalize_spaces(query) - print("in do_search query is:", pf(query)) + logger.debug("in do_search query is:", pf(query)) results = g.db.execute(query, no_parameters=True).fetchall() return results @@ -56,7 +56,7 @@ class DoSearch(object): def mescape(self, *items): """Multiple escape""" escaped = [escape(str(item)) for item in items] - print("escaped is:", escaped) + logger.debug("escaped is:", escaped) return tuple(escaped) def normalize_spaces(self, stringy): @@ -66,13 +66,13 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): - print("search_types are:", pf(cls.search_types)) + logger.debug("search_types are:", pf(cls.search_types)) search_type_string = search_type['dataset_type'] if 'key' in search_type: search_type_string += '_' + search_type['key'] - print("search_type_string is:", search_type_string) + logger.debug("search_type_string is:", search_type_string) if search_type_string in cls.search_types: return cls.search_types[search_type_string] @@ -100,7 +100,7 @@ class QuickMrnaAssaySearch(DoSearch): def run(self): """Generates and runs a search for assays across all mRNA expression datasets""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") query = self.base_query + """WHERE (MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, @@ -108,7 +108,7 @@ class QuickMrnaAssaySearch(DoSearch): AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) - print("final query is:", pf(query)) + logger.debug("final query is:", pf(query)) return self.execute(query) @@ -176,14 +176,14 @@ class MrnaAssaySearch(DoSearch): where_clause, escape(str(self.dataset.id)))) - #print("query is:", pf(query)) + #logger.debug("query is:", pf(query)) return query def run_combined(self, from_clause = '', where_clause = ''): """Generates and runs a combined search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") #query = self.base_query + from_clause + " WHERE " + where_clause from_clause = self.normalize_spaces(from_clause) @@ -198,18 +198,18 @@ class MrnaAssaySearch(DoSearch): where_clause, escape(str(self.dataset.id)))) - print("final query is:", pf(query)) + logger.debug("final query is:", pf(query)) return self.execute(query) def run(self): """Generates and runs a simple search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") where_clause = self.get_where_clause() query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC" - #print("final query is:", pf(query)) + #logger.debug("final query is:", pf(query)) return self.execute(query) @@ -290,14 +290,14 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("query is:", pf(query)) + logger.debug("query is:", pf(query)) return query def run_combined(self, from_clause, where_clause): """Generates and runs a combined search of an phenotype dataset""" - print("Running PhenotypeSearch") + logger.debug("Running PhenotypeSearch") from_clause = self.normalize_spaces(from_clause) @@ -313,7 +313,7 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("final query is:", pf(query)) + logger.debug("final query is:", pf(query)) return self.execute(query) @@ -364,7 +364,7 @@ class QuickPhenotypeSearch(PhenotypeSearch): PublishXRef.InbredSetId = InbredSet.Id and InbredSet.SpeciesId = Species.Id""" % where_clause) - print("query is:", pf(query)) + logger.debug("query is:", pf(query)) return query @@ -408,7 +408,7 @@ class GenotypeSearch(DoSearch): where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, field), self.search_term)) - print("hello ;where_clause is:", pf(where_clause)) + logger.debug("hello ;where_clause is:", pf(where_clause)) where_clause = "(%s) " % ' OR '.join(where_clause) return where_clause @@ -432,7 +432,7 @@ class GenotypeSearch(DoSearch): and GenoFreeze.Id = %s"""% (where_clause, escape(str(self.dataset.id)))) - print("query is:", pf(query)) + logger.debug("query is:", pf(query)) return query @@ -586,7 +586,7 @@ class LrsSearch(DoSearch): self.species_id) else: # Deal with >, <, >=, and <= - print("self.search_term is:", self.search_term) + logger.debug("self.search_term is:", self.search_term) where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) @@ -787,7 +787,7 @@ class MeanSearch(MrnaAssaySearch): def get_final_query(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -795,7 +795,7 @@ class MeanSearch(MrnaAssaySearch): def run(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -825,7 +825,7 @@ class RangeSearch(MrnaAssaySearch): WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s """ % (escape(self.search_term[0])) - print("where_clause is:", pf(where_clause)) + logger.debug("where_clause is:", pf(where_clause)) return where_clause @@ -927,7 +927,7 @@ class PvalueSearch(MrnaAssaySearch): self.search_operator, self.search_term[0]) - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -992,7 +992,7 @@ if __name__ == "__main__": # ProbeSet.Id = ProbeSetXRef.ProbeSetId and # ProbeSetXRef.ProbeSetFreezeId = 112""") - #print(pf(cursor.fetchall())) + #logger.debug(pf(cursor.fetchall())) #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run() #results = RifSearch("diabetes", dataset, cursor, db_conn).run() @@ -1004,4 +1004,4 @@ if __name__ == "__main__": #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - print("results are:", pf(results)) + logger.debug("results are:", pf(results)) diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 35070b8c..ea7ab1b9 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -23,6 +23,9 @@ import re from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + def parse(pstring): """ @@ -40,13 +43,13 @@ def parse(pstring): separators = [re.escape(x) for x in ("<=", ">=", ":", "=", "<", ">")] separators = '(%s)' % ("|".join(separators)) - print("separators:", separators) + logger.debug("separators:", separators) for item in pstring: splat = re.split(separators, item) - print("splat is:", splat) + logger.debug("splat is:", splat) # splat is an array of 1 if no match, otherwise more than 1 if len(splat) > 1: @@ -72,7 +75,7 @@ def parse(pstring): search_term=[item]) items.append(term) - print("* items are:", pf(items) + "\n") + logger.debug("* items are:", pf(items) + "\n") return(items) #def encregexp(self,str): @@ -108,4 +111,4 @@ if __name__ == '__main__': parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)") parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)") parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)") - parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)")
\ No newline at end of file + parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)") diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index f04881a6..30b65e80 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -36,6 +36,9 @@ from dbFunction import webqtlDatabaseFunction from utility import formatting +from utility.logger import getLogger +logger = getLogger(__name__ ) + #class QuickSearchResult(object): #def __init__(self, key, result_fields): # self.key = key @@ -64,9 +67,9 @@ class SearchResultPage(object): #else: self.uc_id = uuid.uuid4() - print("uc_id:", self.uc_id) + logger.debug("uc_id:", self.uc_id) - print("kw is:", kw) + logger.debug("kw is:", kw) if kw['search_terms_or']: self.and_or = "or" self.search_terms = kw['search_terms_or'] @@ -82,7 +85,7 @@ class SearchResultPage(object): else: dataset_type = "ProbeSet" self.dataset = create_dataset(kw['dataset'], dataset_type) - print("KEYWORD:", self.search_terms) + logger.debug("KEYWORD:", self.search_terms) self.search() if self.search_term_exists: self.gen_search_result() @@ -100,14 +103,14 @@ class SearchResultPage(object): # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term - print("self.results is:", pf(self.results)) + logger.debug("self.results is:", pf(self.results)) for result in self.results: if not result: continue #### Excel file needs to be generated #### - #print("foo locals are:", locals()) + #logger.debug("foo locals are:", locals()) trait_id = result[0] this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) @@ -124,7 +127,7 @@ class SearchResultPage(object): def search(self): self.search_terms = parser.parse(self.search_terms) - print("After parsing:", self.search_terms) + logger.debug("After parsing:", self.search_terms) if len(self.search_terms) > 1: combined_from_clause = "" @@ -171,19 +174,19 @@ class SearchResultPage(object): self.header_fields = the_search.header_fields def get_search_ob(self, a_search): - print("[kodak] item is:", pf(a_search)) + logger.debug("[kodak] item is:", pf(a_search)) search_term = a_search['search_term'] search_operator = a_search['separator'] search_type = {} search_type['dataset_type'] = self.dataset.type if a_search['key']: search_type['key'] = a_search['key'].upper() - print("search_type is:", pf(search_type)) + logger.debug("search_type is:", pf(search_type)) search_ob = do_search.DoSearch.get_search(search_type) if search_ob: search_class = getattr(do_search, search_ob) - print("search_class is: ", pf(search_class)) + logger.debug("search_class is: ", pf(search_class)) the_search = search_class(search_term, search_operator, self.dataset, diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 1e454292..557708e9 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -47,7 +47,9 @@ from wqflask import model from utility import Bunch, Struct, after - +import logging +from utility.logger import getLogger +logger = getLogger(__name__) from base.data_set import create_datasets_list @@ -64,10 +66,10 @@ class AnonUser(object): def __init__(self): self.cookie = request.cookies.get(self.cookie_name) if self.cookie: - print("already is cookie") + logger.debug("already is cookie") self.anon_id = verify_cookie(self.cookie) else: - print("creating new cookie") + logger.debug("creating new cookie") self.anon_id, self.cookie = create_signed_cookie() @after.after_this_request @@ -87,7 +89,7 @@ def create_signed_cookie(): the_uuid = str(uuid.uuid4()) signature = actual_hmac_creation(the_uuid) uuid_signed = the_uuid + ":" + signature - print("uuid_signed:", uuid_signed) + logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed class UserSession(object): @@ -102,7 +104,7 @@ class UserSession(object): session_id = verify_cookie(cookie) self.redis_key = self.cookie_name + ":" + session_id - print("self.redis_key is:", self.redis_key) + logger.debug("self.redis_key is:", self.redis_key) self.session_id = session_id self.record = Redis.hgetall(self.redis_key) @@ -123,10 +125,10 @@ class UserSession(object): if Redis.ttl(self.redis_key) < THREE_DAYS: # (Almost) everytime the user does something we extend the session_id in Redis... - print("Extending ttl...") + logger.debug("Extending ttl...") Redis.expire(self.redis_key, THREE_DAYS) - print("record is:", self.record) + logger.debug("record is:", self.record) self.logged_in = True @property @@ -156,7 +158,7 @@ class UserSession(object): def delete_session(self): # And more importantly delete the redis record Redis.delete(self.cookie_name) - print("At end of delete_session") + logger.debug("At end of delete_session") @app.before_request def before_request(): @@ -165,26 +167,26 @@ def before_request(): class UsersManager(object): def __init__(self): self.users = model.User.query.all() - print("Users are:", self.users) + logger.debug("Users are:", self.users) class UserManager(object): def __init__(self, kw): self.user_id = kw['user_id'] - print("In UserManager locals are:", pf(locals())) + logger.debug("In UserManager locals are:", pf(locals())) #self.user = model.User.get(user_id) - #print("user is:", user) + #logger.debug("user is:", user) self.user = model.User.query.get(self.user_id) - print("user is:", self.user) + logger.debug("user is:", self.user) datasets = create_datasets_list() for dataset in datasets: if not dataset.check_confidentiality(): continue - print("\n Name:", dataset.name) - print(" Type:", dataset.type) - print(" ID:", dataset.id) - print(" Confidential:", dataset.check_confidentiality()) - #print(" ---> self.datasets:", self.datasets) + logger.debug("\n Name:", dataset.name) + logger.debug(" Type:", dataset.type) + logger.debug(" ID:", dataset.id) + logger.debug(" Confidential:", dataset.check_confidentiality()) + #logger.debug(" ---> self.datasets:", self.datasets) class RegisterUser(object): @@ -215,7 +217,7 @@ class RegisterUser(object): if self.errors: return - print("No errors!") + logger.debug("No errors!") set_password(password, self.user) @@ -233,10 +235,10 @@ class RegisterUser(object): "Click the button above to sign in using an existing account.") return - print("Adding verification email to queue") + logger.debug("Adding verification email to queue") #self.send_email_verification() VerificationEmail(self.new_user) - print("Added verification email to queue") + logger.debug("Added verification email to queue") self.thank_you_mode = True @@ -259,8 +261,8 @@ def set_password(password, user): # One more check on password length assert len(password) >= 6, "Password shouldn't be so short here" - print("pwfields:", vars(pwfields)) - print("locals:", locals()) + logger.debug("pwfields:", vars(pwfields)) + logger.debug("locals:", locals()) enc_password = Password(password, pwfields.salt, @@ -324,14 +326,14 @@ class ForgotPasswordEmail(VerificationEmail): class Password(object): def __init__(self, unencrypted_password, salt, iterations, keylength, hashfunc): hashfunc = getattr(hashlib, hashfunc) - print("hashfunc is:", hashfunc) + logger.debug("hashfunc is:", hashfunc) # On our computer it takes around 1.4 seconds in 2013 start_time = time.time() salt = base64.b64decode(salt) self.password = pbkdf2.pbkdf2_hex(str(unencrypted_password), salt, iterations, keylength, hashfunc) self.encrypt_time = round(time.time() - start_time, 3) - print("Creating password took:", self.encrypt_time) + logger.debug("Creating password took:", self.encrypt_time) def basic_info(): @@ -355,7 +357,7 @@ def verify_email(): @app.route("/n/password_reset") def password_reset(): - print("in password_reset request.url is:", request.url) + logger.debug("in password_reset request.url is:", request.url) # We do this mainly just to assert that it's in proper form for displaying next page # Really not necessary but doesn't hurt @@ -365,7 +367,7 @@ def password_reset(): @app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): - print("in password_reset request.url is:", request.url) + logger.debug("in password_reset request.url is:", request.url) errors = [] @@ -373,13 +375,13 @@ def password_reset_step2(): verification_code, separator, hmac = user_encode.partition(':') hmac_verified = actual_hmac_creation(verification_code) - print("locals are:", locals()) + logger.debug("locals are:", locals()) assert hmac == hmac_verified, "Someone has been naughty" user = DecodeUser.actual_get_user(ForgotPasswordEmail.key_prefix, verification_code) - print("user is:", user) + logger.debug("user is:", user) password = request.form['password'] @@ -408,9 +410,9 @@ class DecodeUser(object): @staticmethod def actual_get_user(code_prefix, verification_code): data = Redis.get(code_prefix + ":" + verification_code) - print("in get_coded_user, data is:", data) + logger.debug("in get_coded_user, data is:", data) data = json.loads(data) - print("data is:", data) + logger.debug("data is:", data) return model.User.query.get(data['id']) @app.route("/n/login", methods=('GET', 'POST')) @@ -428,14 +430,14 @@ class LoginUser(object): def standard_login(self): """Login through the normal form""" params = request.form if request.form else request.args - print("in login params are:", params) + logger.debug("in login params are:", params) if not params: return render_template("new_security/login_user.html") else: try: user = model.User.query.filter_by(email_address=params['email_address']).one() except sqlalchemy.orm.exc.NoResultFound: - print("No account exists for that email address") + logger.debug("No account exists for that email address") valid = False user = None else: @@ -446,9 +448,9 @@ class LoginUser(object): pwfields.iterations, pwfields.keylength, pwfields.hashfunc) - print("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) + logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password) - print("valid is:", valid) + logger.debug("valid is:", valid) if valid and not user.confirmed: VerificationEmail(user) @@ -458,7 +460,7 @@ class LoginUser(object): if valid: if params.get('remember'): - print("I will remember you") + logger.debug("I will remember you") self.remember_me = True return self.actual_login(user) @@ -492,14 +494,14 @@ class LoginUser(object): #session_id = "session_id:{}".format(login_rec.session_id) session_id_signature = actual_hmac_creation(login_rec.session_id) session_id_signed = login_rec.session_id + ":" + session_id_signature - print("session_id_signed:", session_id_signed) + logger.debug("session_id_signed:", session_id_signed) session = dict(login_time = time.time(), user_id = user.id, user_email_address = user.email_address) key = UserSession.cookie_name + ":" + login_rec.session_id - print("Key when signing:", key) + logger.debug("Key when signing:", key) Redis.hmset(key, session) if self.remember_me: expire_time = self.remember_time @@ -518,7 +520,7 @@ class LoginUser(object): @app.route("/n/logout") def logout(): - print("Logging out...") + logger.debug("Logging out...") UserSession().delete_session() flash("You are now logged out. We hope you come back soon!") response = make_response(redirect(url_for('index_page'))) @@ -610,7 +612,7 @@ def register(): params = request.form if request.form else request.args if params: - print("Attempting to register the user...") + logger.debug("Attempting to register the user...") result = RegisterUser(params) errors = result.errors @@ -656,16 +658,16 @@ def data_hmac(stringy): def verify_url_hmac(url): """Pass in a url that was created with url_hmac and this assures it hasn't been tampered with""" - print("url passed in to verify is:", url) + logger.debug("url passed in to verify is:", url) # Verify parts are correct at the end - we expect to see &hm= or ?hm= followed by an hmac assert url[-23:-20] == "hm=", "Unexpected url (stage 1)" assert url[-24] in ["?", "&"], "Unexpected url (stage 2)" hmac = url[-20:] url = url[:-24] # Url without any of the hmac stuff - #print("before urlsplit, url is:", url) + #logger.debug("before urlsplit, url is:", url) #url = divide_up_url(url)[1] - #print("after urlsplit, url is:", url) + #logger.debug("after urlsplit, url is:", url) hm = actual_hmac_creation(url) @@ -706,4 +708,4 @@ class GroupsManager(object): class RolesManager(object): def __init__(self): self.roles = model.Role.query.all() - print("Roles are:", self.roles) + logger.debug("Roles are:", self.roles) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index c07e03ff..b6ce762f 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -132,7 +132,7 @@ def search_page(): return render_template("data_sharing.html", **template_vars.__dict__) else: key = "search_results:v1:" + json.dumps(request.args, sort_keys=True) - logger.info("key is:", pf(key)) + logger.debug("key is:", pf(key)) if USE_REDIS: with Bench("Trying Redis cache"): result = Redis.get(key) @@ -142,7 +142,7 @@ def search_page(): if result: logger.info("Cache hit on search results!!!") - logger.info("USE_REDIS=",USE_REDIS) + logger.debug("USE_REDIS=",USE_REDIS) with Bench("Loading results"): result = pickle.loads(result) else: @@ -151,7 +151,7 @@ def search_page(): the_search = search_results.SearchResultPage(request.args) result = the_search.__dict__ - logger.info("result: ", pf(result)) + logger.debug("result: ", pf(result)) if USE_REDIS: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) |