diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 22 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 12 |
2 files changed, 22 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index e1d7e2f9..41c5d8ba 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate, locate_ignore_error +from utility.tools import locate, locate_ignore_error, flat_files from maintenance import get_group_samplelists @@ -53,7 +53,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists from utility.logger import getLogger logger = getLogger(__name__ ) @@ -226,7 +226,7 @@ class Markers(object): class HumanMarkers(Markers): def __init__(self, name, specified_markers = []): - marker_data_fh = open(locate('genotype') + '/' + name + '.bim') + marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() @@ -299,11 +299,21 @@ class DatasetGroup(object): self.markers = HumanMarkers(self.name, markers) def get_markers(self): - #logger.debug("self.species is:", self.species) - if self.species == "human": + logger.debug("self.species is:", self.species) + + def check_plink_gemma(): + if flat_file_exists("mapping"): + MAPPING_PATH = flat_files("mapping")+"/" + if (os.path.isfile(MAPPING_PATH+self.name+".bed") and + (os.path.isfile(MAPPING_PATH+self.name+".map") or + os.path.isfile(MAPPING_PATH+self.name+".bim"))): + return True + return False + + if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers self.markers = marker_class(self.name) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index eb5b91c3..bf87e879 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -207,7 +207,7 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" - return formatted.capitalize() + return formatted @property def alias_fmt(self): @@ -379,7 +379,7 @@ def jsonable_table_row(trait, dataset_name, index): additive = "N/A" else: additive = "%.3f" % round(float(trait.additive), 2) - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.symbol, @@ -395,7 +395,7 @@ def jsonable_table_row(trait, dataset_name, index): else: additive = "%.2f" % round(float(trait.additive), 2) if trait.pubmed_id: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -405,7 +405,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] else: - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.description_display, @@ -415,7 +415,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] elif dataset.type == "Geno": - return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', index, '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', trait.location_repr] @@ -499,7 +499,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): for i, field in enumerate(dataset.display_fields): holder = trait_info[i] if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf8", "ignore") + holder = unicode(trait_info[i], "utf-8", "ignore") setattr(trait, field, holder) if dataset.type == 'Publish': |