Paste or Type Multiple Values: You can enter data by pasting a series of numbers representing trait values into this area. diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 2c0ba586..c4b510d4 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -156,12 +156,6 @@ def index_page(): import_collections = params['import_collections'] if import_collections == "true": g.user_session.import_traits_to_user(params['anon_id']) - #if USE_GN_SERVER: - # # The menu is generated using GN_SERVER - # return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION) - #else: - - # Old style static menu (OBSOLETE) return render_template("index_page_orig.html", version=GN_VERSION) @@ -343,14 +337,10 @@ def intro(): @app.route("/tutorials") def tutorials(): - #doc = Docs("links", request.args) - #return render_template("docs.html", **doc.__dict__) return render_template("tutorials.html") @app.route("/credits") def credits(): - #doc = Docs("links", request.args) - #return render_template("docs.html", **doc.__dict__) return render_template("credits.html") @app.route("/update_text", methods=('POST',)) @@ -368,12 +358,9 @@ def submit_trait_form(): @app.route("/create_temp_trait", methods=('POST',)) def create_temp_trait(): logger.info(request.url) - - #template_vars = submit_trait.SubmitTrait(request.form) - doc = Docs("links") return render_template("links.html", **doc.__dict__) - #return render_template("show_trait.html", **template_vars.__dict__) + @app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): @@ -487,21 +474,17 @@ def export_perm_data(): mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): logger.info(request.url) template_vars = show_trait.ShowTrait(request.form) - #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") - # Sorting the keys messes up the ordered dictionary, so don't do that - #sort_keys=True) - - #logger.info("js_data after dump:", template_vars.js_data) - #logger.info("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) + @app.route("/show_trait") def show_trait_page(): logger.info(request.url) -- cgit v1.2.3 From 4534daa6fb07c23b90e024560ca64091fc330eed Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 19 Apr 2021 17:46:38 +0300 Subject: Move looped sql query into one statement in "get_species_groups" It's in-efficient to have a sql query executed in a loop. As data grows, the query becomes slower. It's better to let sql handle such queries. --- wqflask/utility/helper_functions.py | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 15d5b3ab..4ba92ed5 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -47,19 +47,18 @@ def get_trait_db_obs(self, trait_db_list): 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())] -- cgit v1.2.3 From d2e2046a3ce1af0ca97ea1b6d9ccb3a4c9aecf7c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 23 Apr 2021 17:21:12 +0300 Subject: Add full link to genetic data collected as part of WebQTL project --- wqflask/wqflask/templates/submit_trait.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html index 334a608d..2cc18240 100644 --- a/wqflask/wqflask/templates/submit_trait.html +++ b/wqflask/wqflask/templates/submit_trait.html @@ -14,7 +14,7 @@
The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.
-These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our full description of the genetic data collected as part of the WebQTL project.
+These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our full description of the genetic data collected as part of the WebQTL project.