diff options
| -rw-r--r-- | wqflask/base/data_set.py | 34 | ||||
| -rw-r--r-- | wqflask/db/call.py | 12 | ||||
| -rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 5 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 7 |
4 files changed, 35 insertions, 23 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index c70738f7..ec3750dd 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -466,14 +466,20 @@ class DataSet(object): Weve_Renamed_This_As_Group def retrieve_other_names(self): - """ - If the data set name parameter is not found in the 'Name' field of the data set table, - check if it is actually the FullName or ShortName instead. + """This method fetches the the dataset names in search_result. + + If the data set name parameter is not found in the 'Name' field of + the data set table, check if it is actually the FullName or + ShortName instead. - This is not meant to retrieve the data set info if no name at all is passed. + This is not meant to retrieve the data set info if no name at + all is passed. """ + def helper(r): + return r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"] + try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( @@ -482,14 +488,18 @@ class DataSet(object): self.name, self.name)) - self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetchone(""" - SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name - FROM ProbeSetFreeze, ProbeFreeze, Tissue - WHERE ProbeSetFreeze.public > %s AND - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND - ProbeFreeze.TissueId = Tissue.Id AND - (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') - """ % (query_args)) + # self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = + result = fetch1(""" +SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name +FROM ProbeSetFreeze, ProbeFreeze, Tissue +WHERE ProbeSetFreeze.public > %s +AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id +AND ProbeFreeze.TissueId = Tissue.Id +AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') + """ % (query_args), + "/dataset/"+self.name+".json",helper) + self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = result + logger.debug("retrieve_other_names result:",result) else: query_args = tuple(escape(x) for x in ( (self.type + "Freeze"), diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 194a7650..6c195afa 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -14,17 +14,19 @@ logger = getLogger(__name__ ) # from inspect import stack def fetch1(query, path=None, func=None): - """Fetch one result using either a SQL query or the URI path to -GN_SERVER (when USE_GN_SERVER is True). Apply func to GN_SERVER result -when set. + """Fetch one result as a Tuple using either a SQL query or the URI +path to GN_SERVER (when USE_GN_SERVER is True). Apply func to +GN_SERVER result when set (which should return a Tuple) """ if USE_GN_SERVER and path: result = gn_server(path) if func != None: - return [func(result)] + res2 = func(result) else: - return [result] + res2 = result, + logger.debug(path,query,res2) + return res2 else: return fetchone(query) diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 7fc096a9..ba998e91 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -21,6 +21,7 @@ # This module is used by GeneNetwork project (www.genenetwork.org) from db.call import fetch1 +from utility.tools import USE_GN_SERVER from utility.logger import getLogger logger = getLogger(__name__ ) @@ -42,13 +43,13 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: r["species"])[0] + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0] logger.debug("retrieve_species result:",result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: r["species_id"])[0] + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0] logger.debug("retrieve_species_id result:",result) return result diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 86ee1c52..ddc0ea82 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -48,13 +48,12 @@ class GNLogger: """Set the undelying log level""" self.logger.setLevel(value) - def debug(self,level=0,*args): + def debug(self,*args): """Call logging.debug for multiple args. Use level=num to filter on -LOG_LEVEL_DEBUG. +LOG_LEVEL_DEBUG (NYI). """ - if level <= LOG_LEVEL_DEBUG: - self.collect(self.logger.debug,*args) + self.collect(self.logger.debug,*args) def info(self,*args): """Call logging.info for multiple args""" |