diff options
| -rw-r--r-- | gn2/wqflask/external_tools/send_to_geneweaver.py | 2 | ||||
| -rw-r--r-- | gn2/wqflask/marker_regression/rqtl_mapping.py | 8 | ||||
| -rw-r--r-- | gn2/wqflask/oauth2/session.py | 7 | ||||
| -rw-r--r-- | gn2/wqflask/oauth2/toplevel.py | 1 | ||||
| -rw-r--r-- | gn2/wqflask/search_results.py | 5 | ||||
| -rw-r--r-- | gn2/wqflask/templates/gsearch_gene.html | 8 |
6 files changed, 23 insertions, 8 deletions
diff --git a/gn2/wqflask/external_tools/send_to_geneweaver.py b/gn2/wqflask/external_tools/send_to_geneweaver.py index 76ff7302..8faee78a 100644 --- a/gn2/wqflask/external_tools/send_to_geneweaver.py +++ b/gn2/wqflask/external_tools/send_to_geneweaver.py @@ -75,7 +75,7 @@ def test_chip(trait_list): (dataset.name,) ) - if result := cursor.fetchone: + if result := cursor.fetchone(): chip_name = result[0] if chip_name: if chip_name != final_chip_name: diff --git a/gn2/wqflask/marker_regression/rqtl_mapping.py b/gn2/wqflask/marker_regression/rqtl_mapping.py index 571935cb..c52add46 100644 --- a/gn2/wqflask/marker_regression/rqtl_mapping.py +++ b/gn2/wqflask/marker_regression/rqtl_mapping.py @@ -12,6 +12,8 @@ from urllib.parse import urljoin import numpy as np +from gn3.debug import __pk__ + from gn2.base.webqtlConfig import TMPDIR from gn2.base.trait import create_trait from gn2.utility.redis_tools import get_redis_conn @@ -55,8 +57,10 @@ def run_rqtl(trait_name, vals, samples, dataset, pair_scan, mapping_scale, model if perm_strata_list: post_data["pstrata"] = True - rqtl_output = requests.post(urljoin(GN3_LOCAL_URL, "api/rqtl/compute"), - data=post_data).json() + rqtl_output = __pk__( + "R/qtl or Pair-Scan results", + requests.post(urljoin(GN3_LOCAL_URL, "api/rqtl/compute"), + data=post_data).json()) if num_perm > 0: return rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'], rqtl_output['results'] else: diff --git a/gn2/wqflask/oauth2/session.py b/gn2/wqflask/oauth2/session.py index 78c766a8..883a3228 100644 --- a/gn2/wqflask/oauth2/session.py +++ b/gn2/wqflask/oauth2/session.py @@ -98,6 +98,7 @@ def set_masquerading(masq_info): "masquerading": orig_user }) + def unset_masquerading(): """Restore the original session.""" the_session = session_info() @@ -120,9 +121,15 @@ def is_token_refreshing(): """Returns whether the token is being refreshed or not.""" return session_info().get("token_refreshing", False) + def set_redirect_url(url): """Save the current endpoint object""" return save_session_info({ **session_info(), "redirect_url": url }) + + +def clear_redirect_url(): + """Clear the redirect url from Session""" + session_info().pop("redirect_url", None) diff --git a/gn2/wqflask/oauth2/toplevel.py b/gn2/wqflask/oauth2/toplevel.py index 425c598e..8dd57243 100644 --- a/gn2/wqflask/oauth2/toplevel.py +++ b/gn2/wqflask/oauth2/toplevel.py @@ -82,6 +82,7 @@ def authorisation_code(): "logged_in": True }) redirect_url = session.session_info().get("redirect_url", "/") + session.clear_redirect_url() return redirect(redirect_url) return no_token_post("auth/token", json=request_data).either( diff --git a/gn2/wqflask/search_results.py b/gn2/wqflask/search_results.py index 1d89e52a..e0138b5b 100644 --- a/gn2/wqflask/search_results.py +++ b/gn2/wqflask/search_results.py @@ -28,6 +28,7 @@ from gn2.utility.type_checking import is_str MAX_SEARCH_RESULTS = 50000 # Max number of search results, passed to Xapian search (this needs to match the value in GN3!) + class SearchResultPage: #maxReturn = 3000 @@ -137,7 +138,7 @@ class SearchResultPage: if self.dataset.type == "ProbeSet": trait["hmac"] = (Maybe.apply(hmac) - .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait['name']}:{trait['dataset']}")))) + .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait.data['name']}:{trait.data['dataset']}")))) elif self.dataset.type == "Publish": inbredsetcode = trait.pop("inbredsetcode") if inbredsetcode.map(len) == Just(3): @@ -146,7 +147,7 @@ class SearchResultPage: .to_arguments(inbredsetcode, trait["name"])) trait["hmac"] = (Maybe.apply(hmac) - .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait['name']}:{trait['dataset']}")))) + .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait.data['name']}:{trait.data['dataset']}")))) trait["authors"] = trait["authors_display"] = (trait.pop("authors").map( lambda authors: ", ".join(authors[:2] + ["et al."] if len(authors) >=2 else authors))) diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html index 6cd21e9a..33d12cfc 100644 --- a/gn2/wqflask/templates/gsearch_gene.html +++ b/gn2/wqflask/templates/gsearch_gene.html @@ -289,11 +289,13 @@ let header_length = 40; let max_header_length = 180; while (header_length <= search_result.length) { - let next_dot = search_result.indexOf(".", header_length+1); - + let next_dot = search_result.indexOf(".", header_length+1); + if (next_dot == -1) { + next_dot = search_result.length+1 + } if (next_dot > max_header_length) { let next_comma = search_result.indexOf(",", header_length+1); - if (next_comma > max_header_length) { + if (next_comma > max_header_length || next_comma == -1) { break; } header_length = next_comma; |