diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 37 |
1 files changed, 27 insertions, 10 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index c7dbc972..8476649f 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -22,12 +22,13 @@ class DoSearch(object): # Used to translate search phrases into classes search_types = dict() - def __init__(self, search_term, search_operator=None, dataset=None): + def __init__(self, search_term, search_operator=None, dataset=None, search_type=None): self.search_term = search_term # Make sure search_operator is something we expect assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset + self.search_type = search_type if self.dataset: logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) @@ -69,7 +70,7 @@ class DoSearch(object): logger.debug("search_types are:", pf(cls.search_types)) search_type_string = search_type['dataset_type'] - if 'key' in search_type: + if 'key' in search_type and search_type['key'] != None: search_type_string += '_' + search_type['key'] logger.debug("search_type_string is:", search_type_string) @@ -444,12 +445,13 @@ class LrsSearch(DoSearch): """ - DoSearch.search_types['LRS'] = 'LrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types[search_key] = "LrsSearch" def get_from_clause(self): #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats - if len(self.search_term) > 2 and "Chr" in self.search_term[2]: - chr_num = self.search_term[2].replace("Chr", "") + if len(self.search_term) > 2 and "chr" in self.search_term[2].lower(): + chr_num = self.search_term[2].lower().replace("chr", "") self.search_term[2] = chr_num self.search_term = [float(value) for value in self.search_term] @@ -465,6 +467,9 @@ class LrsSearch(DoSearch): if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) lrs_min, lrs_max = self.search_term[:2] + if self.search_type == "LOD": + lrs_min = lrs_min*4.61 + lrs_max = lrs_max*4.61 where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s """ % self.mescape(self.dataset.type, @@ -489,6 +494,10 @@ class LrsSearch(DoSearch): else: # Deal with >, <, >=, and <= logger.debug("self.search_term is:", self.search_term) + lrs_val = self.search_term[0] + if self.search_type == "LOD": + lrs_val = lrs_val*4.61 + where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) @@ -505,9 +514,11 @@ class LrsSearch(DoSearch): return self.execute(self.query) + class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): - DoSearch.search_types['ProbeSet_LRS'] = 'MrnaLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_' + search_key] = "MrnaLrsSearch" def run(self): @@ -520,7 +531,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): - DoSearch.search_types['Publish_LRS'] = 'PhenotypeLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['Publish_' + search_key] = "PhenotypeLrsSearch" def run(self): @@ -532,7 +544,6 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): return self.execute(self.query) - class CisTransLrsSearch(DoSearch): def get_from_clause(self): @@ -557,6 +568,10 @@ class CisTransLrsSearch(DoSearch): else: SomeError + if self.search_type == "CISLOD" or self.search_type == "TRANSLOD": + lrs_min = lrs_min * 4.61 + lrs_max = lrs_max * 4.61 + sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( escape(self.dataset.type), @@ -619,7 +634,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ - DoSearch.search_types['ProbeSet_CISLRS'] = 'CisLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "cis") @@ -648,7 +664,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ - DoSearch.search_types['ProbeSet_TRANSLRS'] = 'TransLrsSearch' + for search_key in ('LRS', 'LOD'): + DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "trans") |