diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/__init__.py | 4 | ||||
| -rw-r--r-- | wqflask/utility/benchmark.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 6 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 4 | ||||
| -rw-r--r-- | wqflask/utility/helper_functions.py | 59 | ||||
| -rw-r--r-- | wqflask/utility/temp_data.py | 2 |
6 files changed, 39 insertions, 38 deletions
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 204ff59a..df926884 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -2,7 +2,7 @@ from pprint import pformat as pf # Todo: Move these out of __init__ -class Bunch(object): +class Bunch: """Like a dictionary but using object notation""" def __init__(self, **kw): self.__dict__ = kw @@ -11,7 +11,7 @@ class Bunch(object): return pf(self.__dict__) -class Struct(object): +class Struct: '''The recursive class for building and representing objects with. From http://stackoverflow.com/a/6573827/1175849 diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index ea5a0ab6..91ea91e8 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -6,7 +6,7 @@ from utility.tools import LOG_BENCH from utility.logger import getLogger logger = getLogger(__name__ ) -class Bench(object): +class Bench: entries = collections.OrderedDict() def __init__(self, name=None, write_output=LOG_BENCH): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 81085ffe..0a381c9b 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,7 +1,7 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) -class genotype(object): +class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure """ @@ -119,7 +119,7 @@ class genotype(object): self.chromosomes.append(chr_ob) -class Chr(object): +class Chr: def __init__(self, name, geno_ob): self.name = name self.loci = [] @@ -140,7 +140,7 @@ class Chr(object): def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) -class Locus(object): +class Locus: def __init__(self, geno_ob, marker_row = None): self.chr = None self.name = None diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 0b736176..f8e96d19 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -12,7 +12,7 @@ import simplejson as json from pprint import pformat as pf -class Marker(object): +class Marker: def __init__(self): self.name = None self.chr = None @@ -21,7 +21,7 @@ class Marker(object): self.genotypes = [] -class ConvertGenoFile(object): +class ConvertGenoFile: def __init__(self, input_file): self.mb_exists = False diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 46eeb35d..12fd6be5 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -4,20 +4,23 @@ from base.species import TheSpecies from utility import hmac -from flask import Flask, g +from flask import g import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) + def get_species_dataset_trait(self, start_vars): - #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" if "temp_trait" in list(start_vars.keys()): - if start_vars['temp_trait'] == "True": - self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) - else: - self.dataset = data_set.create_dataset(start_vars['dataset']) + if start_vars['temp_trait'] == "True": + self.dataset = data_set.create_dataset( + dataset_name="Temp", + dataset_type="Temp", + group_name=start_vars['group']) + else: + self.dataset = data_set.create_dataset(start_vars['dataset']) else: - self.dataset = data_set.create_dataset(start_vars['dataset']) + self.dataset = data_set.create_dataset(start_vars['dataset']) logger.debug("After creating dataset") self.species = TheSpecies(dataset=self.dataset) logger.debug("After creating species") @@ -27,9 +30,6 @@ def get_species_dataset_trait(self, start_vars): get_qtl_info=True) logger.debug("After creating trait") - #if read_genotype: - #self.dataset.group.read_genotype_file() - #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, str): @@ -42,28 +42,29 @@ def get_trait_db_obs(self, trait_db_list): assert hmac_string==hmac.hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":")[:2] if dataset_name == "Temp": - dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2]) + dataset_ob = data_set.create_dataset( + dataset_name=dataset_name, dataset_type="Temp", + group_name=trait_name.split("_")[2]) else: dataset_ob = data_set.create_dataset(dataset_name) trait_ob = create_trait(dataset=dataset_ob, - name=trait_name, - cellid=None) + name=trait_name, + cellid=None) if trait_ob: self.trait_list.append((trait_ob, dataset_ob)) -def get_species_groups(): - - species_query = "SELECT SpeciesId, MenuName FROM Species" - species_ids_and_names = g.db.execute(species_query).fetchall() - - species_and_groups = [] - for species_id, species_name in species_ids_and_names: - this_species_groups = {} - this_species_groups['species'] = species_name - groups_query = "SELECT InbredSetName FROM InbredSet WHERE SpeciesId = %s" % (species_id) - groups = [group[0] for group in g.db.execute(groups_query).fetchall()] - - this_species_groups['groups'] = groups - species_and_groups.append(this_species_groups) - return species_and_groups +def get_species_groups(): + """Group each species into a group""" + _menu = {} + for species, group_name in g.db.execute( + "SELECT s.MenuName, i.InbredSetName FROM InbredSet i " + "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId " + "ORDER BY i.SpeciesId ASC, i.Name ASC").fetchall(): + if _menu.get(species): + _menu = _menu[species].append(group_name) + else: + _menu[species] = [group_name] + return [{"species": key, + "groups": value} for key, value in + list(_menu.items())] diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 4144ae00..b2cbd458 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -2,7 +2,7 @@ from redis import Redis import simplejson as json -class TempData(object): +class TempData: def __init__(self, temp_uuid): self.temp_uuid = temp_uuid |