diff options
Diffstat (limited to 'gn2/wqflask')
| -rw-r--r-- | gn2/wqflask/search_results.py | 37 |
1 files changed, 14 insertions, 23 deletions
diff --git a/gn2/wqflask/search_results.py b/gn2/wqflask/search_results.py index 9558ffa8..accc3a53 100644 --- a/gn2/wqflask/search_results.py +++ b/gn2/wqflask/search_results.py @@ -129,6 +129,12 @@ class SearchResultPage: trait["mean"] = trait["mean"].map(format3f) trait["lrs_location"] = (Maybe.apply(chr_mb) .to_arguments(trait.pop("geno_chr"), trait.pop("geno_mb"))) + + description_text = trait['description'].maybe("N/A", lambda a: a) + if len(description_text) > 200: + description_text = description_text[:200] + "..." + trait['description'] = Just(description_text) + if self.dataset.type == "ProbeSet": trait["hmac"] = (Maybe.apply(hmac) .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait['name']}:{trait['dataset']}")))) @@ -141,37 +147,18 @@ class SearchResultPage: trait["hmac"] = (Maybe.apply(hmac) .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait['name']}:{trait['dataset']}")))) - trait["authors_display"] = (trait.pop("authors").map( + trait["authors"] = trait["authors_display"] = (trait.pop("authors").map( lambda authors: ", ".join(authors[:2] + ["et al."] if len(authors) >=2 else authors))) trait["pubmed_text"] = trait["year"].map(str) trait_list.append(trait.data) -# if self.dataset.type == "ProbeSet": -# trait_dict['display_name'] = result['name'] -# trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['display_name'], trait_dict['dataset'])) -# trait_dict['symbol'] = "N/A" if not result['symbol'] else result['symbol'].strip() -# description_text = "" -# if result['description']: -# description_text = unicodedata.normalize("NFKD", result['description'].decode('latin1')) -# -# target_string = None # Will change this one the probe_target_description values are indexed -# -# description_display = description_text if target_string is None or str(target_string) == "" else description_text + "; " + str(target_string).strip() -# trait_dict['description'] = description_display -# -# trait_dict['location'] = "N/A" -# if result['chr'] and result['chr'] != "" and result['chr'] != "Un" and result['mb'] and result['mb'] != 0: -# trait_dict['location'] = f"Chr{result['chr']}: {float(result['mb']):.6f}" -# -# trait_dict['mean'] = "N/A" if not result['mean'] else f"{result['mean']:.3f}" -# trait_dict['additive'] = "N/A" if not result['additive'] else: trait_dict = {} trait_dict['index'] = index + 1 trait_dict['dataset'] = self.dataset.name if self.dataset.type == "ProbeSet": trait_dict['display_name'] = result[2] - trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['display_name'], trait_dict['dataset'])) + trait_dict['hmac'] = hmac_creation('{}:{}'.format(trait_dict['display_name'], trait_dict['dataset'])) trait_dict['symbol'] = "N/A" if result[3] is None else result[3].strip() description_text = "" if result[4] is not None and str(result[4]) != "": @@ -198,7 +185,7 @@ class SearchResultPage: elif self.dataset.type == "Publish": # Check permissions on a trait-by-trait basis for phenotype traits trait_dict['name'] = trait_dict['display_name'] = str(result[0]) - trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['name'], trait_dict['dataset'])) + trait_dict['hmac'] = hmac_creation('{}:{}'.format(trait_dict['name'], trait_dict['dataset'])) permissions = check_resource_availability( self.dataset, g.user_session.user_id, trait_dict['display_name']) if not any(x in permissions['data'] for x in ["view", "edit"]): @@ -289,9 +276,13 @@ class SearchResultPage: """ self.search_terms = parser.parse(self.search_terms) - if self.search_type == "xapian": + # Set of terms compatible with Xapian currently (None is a search without a term) + xapian_terms = ["POSITION", "MEAN", "LRS", "LOD"] + + if self.search_type == "xapian" and all([(the_term['key'] in xapian_terms) or not the_term['key'] for the_term in self.search_terms]): self.results = requests.get(generate_xapian_request(self.dataset, self.search_terms, self.and_or)).json() else: + self.search_type = "sql" combined_from_clause = "" combined_where_clause = "" # The same table can't be referenced twice in the from clause |