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-rw-r--r--gn2/base/trait.py31
-rw-r--r--gn2/base/webqtlConfig.py4
-rw-r--r--gn2/default_settings.py6
-rw-r--r--gn2/gn2_main.py1
-rw-r--r--gn2/runserver.py4
-rw-r--r--gn2/wqflask/__init__.py55
-rw-r--r--gn2/wqflask/api/markdown.py8
-rw-r--r--gn2/wqflask/api/router.py33
-rw-r--r--gn2/wqflask/app_errors.py27
-rw-r--r--gn2/wqflask/collect.py2
-rw-r--r--gn2/wqflask/correlation/show_corr_results.py4
-rw-r--r--gn2/wqflask/do_search.py12
-rw-r--r--gn2/wqflask/gsearch.py10
-rw-r--r--gn2/wqflask/marker_regression/display_mapping_results.py27
-rw-r--r--gn2/wqflask/oauth2/checks.py8
-rw-r--r--gn2/wqflask/oauth2/client.py157
-rw-r--r--gn2/wqflask/oauth2/data.py8
-rw-r--r--gn2/wqflask/oauth2/groups.py32
-rw-r--r--gn2/wqflask/oauth2/jwks.py86
-rw-r--r--gn2/wqflask/oauth2/request_utils.py2
-rw-r--r--gn2/wqflask/oauth2/resources.py240
-rw-r--r--gn2/wqflask/oauth2/roles.py76
-rw-r--r--gn2/wqflask/oauth2/session.py25
-rw-r--r--gn2/wqflask/oauth2/toplevel.py35
-rw-r--r--gn2/wqflask/oauth2/ui.py19
-rw-r--r--gn2/wqflask/oauth2/users.py28
-rw-r--r--gn2/wqflask/parser.py2
-rw-r--r--gn2/wqflask/requests.py10
-rw-r--r--gn2/wqflask/search_results.py321
-rw-r--r--gn2/wqflask/show_trait/SampleList.py6
-rw-r--r--gn2/wqflask/static/new/css/pills.css25
-rw-r--r--gn2/wqflask/static/new/css/resource-roles.css5
-rw-r--r--gn2/wqflask/static/new/javascript/auth/search_phenotypes.js6
-rw-r--r--gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js2
-rw-r--r--gn2/wqflask/static/new/javascript/search_results.js49
-rw-r--r--gn2/wqflask/static/new/javascript/table_functions.js47
-rw-r--r--gn2/wqflask/templates/base.html2
-rw-r--r--gn2/wqflask/templates/collections/list.html8
-rw-r--r--gn2/wqflask/templates/collections/view.html4
-rw-r--r--gn2/wqflask/templates/correlation_page.html4
-rw-r--r--gn2/wqflask/templates/dataset.html27
-rw-r--r--gn2/wqflask/templates/gnqa.html4
-rw-r--r--gn2/wqflask/templates/gnqa_answer.html33
-rw-r--r--gn2/wqflask/templates/gnqa_search_history.html46
-rw-r--r--gn2/wqflask/templates/gsearch_gene.html8
-rw-r--r--gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html34
-rw-r--r--gn2/wqflask/templates/oauth2/create-role.html42
-rw-r--r--gn2/wqflask/templates/oauth2/data-list-mrna.html2
-rw-r--r--gn2/wqflask/templates/oauth2/data-list-phenotype.html3
-rw-r--r--gn2/wqflask/templates/oauth2/profile_nav.html7
-rw-r--r--gn2/wqflask/templates/oauth2/view-group-role.html102
-rw-r--r--gn2/wqflask/templates/oauth2/view-resource-role.html149
-rw-r--r--gn2/wqflask/templates/oauth2/view-resource.html56
-rw-r--r--gn2/wqflask/templates/search-syntax.html24
-rw-r--r--gn2/wqflask/templates/search_result_page.html22
-rw-r--r--gn2/wqflask/templates/show_trait_transform_and_filter.html4
-rw-r--r--gn2/wqflask/templates/tool_buttons.html4
-rw-r--r--gn2/wqflask/templates/tutorials.html11
-rw-r--r--gn2/wqflask/views.py110
59 files changed, 1393 insertions, 726 deletions
diff --git a/gn2/base/trait.py b/gn2/base/trait.py
index 701958d7..24288ba1 100644
--- a/gn2/base/trait.py
+++ b/gn2/base/trait.py
@@ -611,3 +611,34 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
f"{repr(trait.name)} information is not found in the database "
f"for dataset '{dataset.name}' with id '{dataset.id}'.")
return trait
+
+def fetch_symbols(trait_db_list):
+ """
+ Fetch list of trait symbols
+
+ From a list of traits and datasets (where each item has
+ the trait and dataset name separated by a colon), return
+
+ """
+
+ trimmed_trait_list = [trait_db for trait_db in trait_db_list
+ if 'Publish' not in trait_db and 'Geno' not in trait_db.split(":")[1]]
+
+ symbol_list = []
+ with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+ for trait_db in trimmed_trait_list:
+ symbol_query = """
+ SELECT ps.Symbol
+ FROM ProbeSet as ps
+ INNER JOIN ProbeSetXRef psx ON psx.ProbeSetId = ps.Id
+ INNER JOIN ProbeSetFreeze psf ON psx.ProbeSetFreezeId = psf.Id
+ WHERE
+ ps.Name = %(trait_name)s AND
+ psf.Name = %(db_name)s
+ """
+
+ cursor.execute(symbol_query, {'trait_name': trait_db.split(":")[0],
+ 'db_name': trait_db.split(":")[1]})
+ symbol_list.append(cursor.fetchone()[0])
+
+ return "+".join(symbol_list) \ No newline at end of file
diff --git a/gn2/base/webqtlConfig.py b/gn2/base/webqtlConfig.py
index 998c0efc..88f199f9 100644
--- a/gn2/base/webqtlConfig.py
+++ b/gn2/base/webqtlConfig.py
@@ -34,7 +34,7 @@ MAXLRS = 460.0
PUBLICTHRESH = 0
# Groups to treat as unique when drawing correlation dropdowns (not sure if this logic even makes sense or is necessary)
-BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD']
+BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD', 'BXD-JAX-OFS']
# EXTERNAL LINK ADDRESSES
PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
@@ -68,6 +68,8 @@ RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&
PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn7&section=geneEQTL"
RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
+GENE_CUP_URL = "https://genecup.org/progress?type=GWAS&type=addiction&type=drug&type=brain&type=stress&type=psychiatric&type=cell&type=function&query=%s"
+
# Temporary storage (note that this TMPDIR can be set as an
# environment variable - use utility.tools.TEMPDIR when you
diff --git a/gn2/default_settings.py b/gn2/default_settings.py
index e781f196..ab15dbe9 100644
--- a/gn2/default_settings.py
+++ b/gn2/default_settings.py
@@ -120,3 +120,9 @@ OAUTH2_CLIENT_SECRET="yadabadaboo"
SESSION_TYPE = "redis"
SESSION_PERMANENT = True
SESSION_USE_SIGNER = True
+
+
+# BEGIN: JSON WEB KEYS #####
+JWKS_ROTATION_AGE_DAYS = 7 # Days (from creation) to keep a JWK in use.
+JWKS_DELETION_AGE_DAYS = 14 # Days (from creation) to keep a JWK around before deleting it.
+# END: JSON WEB KEYS #####
diff --git a/gn2/gn2_main.py b/gn2/gn2_main.py
index 38444620..197eed83 100644
--- a/gn2/gn2_main.py
+++ b/gn2/gn2_main.py
@@ -15,5 +15,6 @@ from gn2.wqflask import search_results
from gn2.wqflask import resource_manager
from gn2.wqflask import update_search_results
+import gn2.wqflask.collect
import gn2.wqflask.views
import gn2.wqflask.partial_correlations_views
diff --git a/gn2/runserver.py b/gn2/runserver.py
index 0c95f715..dd176752 100644
--- a/gn2/runserver.py
+++ b/gn2/runserver.py
@@ -28,7 +28,7 @@ if WEBSERVER_MODE == 'DEBUG':
port=SERVER_PORT,
debug=True,
use_debugger=False,
- threaded=False,
+ threaded=True,
processes=0,
use_reloader=True)
elif WEBSERVER_MODE == 'DEV':
@@ -37,7 +37,7 @@ elif WEBSERVER_MODE == 'DEV':
port=SERVER_PORT,
debug=False,
use_debugger=False,
- threaded=False,
+ threaded=True,
processes=0,
use_reloader=True)
else: # staging/production modes
diff --git a/gn2/wqflask/__init__.py b/gn2/wqflask/__init__.py
index e3708b0b..00fe5127 100644
--- a/gn2/wqflask/__init__.py
+++ b/gn2/wqflask/__init__.py
@@ -33,6 +33,7 @@ from gn2.wqflask.api.markdown import environments_blueprint
from gn2.wqflask.api.markdown import facilities_blueprint
from gn2.wqflask.api.markdown import blogs_blueprint
from gn2.wqflask.api.markdown import news_blueprint
+from gn2.wqflask.api.markdown import xapian_syntax_blueprint
from gn2.wqflask.api.jobs import jobs as jobs_bp
from gn2.wqflask.oauth2.routes import oauth2
from gn2.wqflask.oauth2.client import user_logged_in
@@ -55,28 +56,17 @@ def numcoll():
return "ERROR"
-def parse_ssl_key(app: Flask, keyconfig: str):
- """Parse key file paths into objects"""
- keypath = app.config.get(keyconfig, "").strip()
- if not bool(keypath):
- app.logger.error("Expected configuration '%s'", keyconfig)
- return
-
- with open(keypath) as _sslkey:
- app.config[keyconfig] = JsonWebKey.import_key(_sslkey.read())
-
-
def dev_loggers(appl: Flask) -> None:
"""Default development logging."""
formatter = logging.Formatter(
- fmt="[%(asctime)s] %(levelname)s in %(module)s: %(message)s")
+ fmt="[%(asctime)s] %(levelname)s [%(thread)d -- %(threadName)s] in %(module)s: %(message)s")
stderr_handler = logging.StreamHandler(stream=sys.stderr)
stderr_handler.setFormatter(formatter)
appl.logger.addHandler(stderr_handler)
root_logger = logging.getLogger()
root_logger.addHandler(stderr_handler)
- root_logger.setLevel(appl.config.get("LOGLEVEL", "WARNING"))
+ root_logger.setLevel(appl.config.get("LOG_LEVEL", "WARNING"))
def gunicorn_loggers(appl: Flask) -> None:
@@ -93,12 +83,20 @@ def setup_logging(appl: Flask) -> None:
app = Flask(__name__)
-setup_logging(app)
-
+## BEGIN: Setup configurations ##
# See http://flask.pocoo.org/docs/config/#configuring-from-files
# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
app.config.from_object('gn2.default_settings')
app.config.from_envvar('GN2_SETTINGS')
+app.config["SESSION_REDIS"] = redis.from_url(app.config["REDIS_URL"])
+# BEGIN: SECRETS -- Should be the last of the settings to load
+secrets_file = Path(app.config.get("GN2_SECRETS", "")).absolute()
+if secrets_file.exists() and secrets_file.is_file():
+ app.config.from_pyfile(str(secrets_file))
+# END: SECRETS
+## END: Setup configurations ##
+setup_logging(app)
+### DO NOT USE logging BEFORE THIS POINT!!!! ###
app.jinja_env.globals.update(
undefined=jinja2.StrictUndefined,
@@ -109,14 +107,6 @@ app.jinja_env.globals.update(
num_collections=numcoll,
datetime=datetime)
-app.config["SESSION_REDIS"] = redis.from_url(app.config["REDIS_URL"])
-
-## BEGIN: SECRETS -- Should be the last of the settings to load
-secrets_file = Path(app.config.get("GN2_SECRETS", "")).absolute()
-if secrets_file.exists() and secrets_file.is_file():
- app.config.from_pyfile(str(secrets_file))
-## END: SECRETS
-
# Registering blueprints
app.register_blueprint(glossary_blueprint, url_prefix="/glossary")
@@ -127,6 +117,7 @@ app.register_blueprint(environments_blueprint, url_prefix="/environments")
app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
app.register_blueprint(blogs_blueprint, url_prefix="/blogs")
app.register_blueprint(news_blueprint, url_prefix="/news")
+app.register_blueprint(xapian_syntax_blueprint, url_prefix="/search-syntax")
app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks")
app.register_blueprint(resource_management, url_prefix="/resource-management")
@@ -148,29 +139,11 @@ except StartupError as serr:
server_session = Session(app)
-parse_ssl_key(app, "SSL_PRIVATE_KEY")
-parse_ssl_key(app, "AUTH_SERVER_SSL_PUBLIC_KEY")
-
@app.before_request
def before_request():
g.request_start_time = time.time()
g.request_time = lambda: "%.5fs" % (time.time() - g.request_start_time)
- token = session.get("oauth2_token", False)
- if token and not bool(session.get("user_details", False)):
- from gn2.wqflask.oauth2.client import oauth2_client
- config = current_app.config
- resp = oauth2_client().client.get(
- urljoin(config["GN_SERVER_URL"], "oauth2/user"))
- user_details = resp.json()
- session["user_details"] = user_details
-
- if user_details.get("error") == "invalid_token":
- flash(user_details["error_description"], "alert-danger")
- flash("You are now logged out.", "alert-info")
- session.pop("user_details", None)
- session.pop("oauth2_token", None)
-
@app.context_processor
def include_admin_role_class():
return {'AdminRole': AdminRole}
diff --git a/gn2/wqflask/api/markdown.py b/gn2/wqflask/api/markdown.py
index 580b9ac0..aa7dd3c4 100644
--- a/gn2/wqflask/api/markdown.py
+++ b/gn2/wqflask/api/markdown.py
@@ -24,6 +24,7 @@ links_blueprint = Blueprint("links_blueprint", __name__)
policies_blueprint = Blueprint("policies_blueprint", __name__)
facilities_blueprint = Blueprint("facilities_blueprint", __name__)
news_blueprint = Blueprint("news_blueprint", __name__)
+xapian_syntax_blueprint = Blueprint("xapian_syntax_blueprint", __name__)
blogs_blueprint = Blueprint("blogs_blueprint", __name__)
@@ -117,6 +118,13 @@ def news():
rendered_markdown=render_markdown("general/news/news.md")), 200
+@xapian_syntax_blueprint.route('/')
+def xapian():
+ return render_template(
+ "search-syntax.html",
+ rendered_markdown=render_markdown("general/search/xapian_syntax.md")), 200
+
+
@environments_blueprint.route("/")
def environments():
diff --git a/gn2/wqflask/api/router.py b/gn2/wqflask/api/router.py
index bcd08e8d..e9b70919 100644
--- a/gn2/wqflask/api/router.py
+++ b/gn2/wqflask/api/router.py
@@ -379,23 +379,28 @@ def fetch_traits(dataset_name, file_format="json"):
if len(trait_ids) > 0:
if data_type == "ProbeSet":
query = """
- SELECT
- ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
- ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2
- FROM
- ProbeSet, ProbeSetXRef, ProbeSetFreeze
+ SELECT DISTINCT
+ ProbeSet.`Id`, ProbeSet.`Name`, ProbeSet.`Symbol`, ProbeSet.`description`,
+ ProbeSet.`Chr`, ProbeSet.`Mb`, ProbeSet.`alias`, ProbeSetXRef.`mean`,
+ ProbeSetXRef.`se`, ProbeSetXRef.`Locus`, ProbeSetXRef.`LRS`,
+ ProbeSetXRef.`pValue`, ProbeSetXRef.`additive`, ProbeSetXRef.`h2`,
+ Geno.`Chr`, Geno.`Mb`
+ FROM
+ Species
+ INNER JOIN InbredSet ON InbredSet.`SpeciesId`= Species.`Id`
+ INNER JOIN ProbeFreeze ON ProbeFreeze.`InbredSetId` = InbredSet.`Id`
+ INNER JOIN Tissue ON ProbeFreeze.`TissueId` = Tissue.`Id`
+ INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.`ProbeFreezeId` = ProbeFreeze.`Id`
+ INNER JOIN ProbeSetXRef ON ProbeSetXRef.`ProbeSetFreezeId` = ProbeSetFreeze.`Id`
+ INNER JOIN ProbeSet ON ProbeSet.`Id` = ProbeSetXRef.`ProbeSetId`
+ LEFT JOIN Geno ON ProbeSetXRef.`Locus` = Geno.`Name` AND Geno.`SpeciesId` = Species.`Id`
WHERE
- ProbeSetXRef.ProbeSetFreezeId = "{0}" AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetFreeze.public > 0 AND
- ProbeSetFreeze.confidentiality < 1
+ ProbeSetXRef.ProbeSetFreezeId = "{0}"
ORDER BY
- ProbeSet.Id
- """
+ ProbeSet.Id"""
- field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb",
- "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
+ field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean",
+ "SE", "Locus", "LRS", "P-Value", "Additive", "h2", "Peak Chr", "Peak Mb"]
elif data_type == "Geno":
query = """
SELECT
diff --git a/gn2/wqflask/app_errors.py b/gn2/wqflask/app_errors.py
index 503f4e1c..b7b8527b 100644
--- a/gn2/wqflask/app_errors.py
+++ b/gn2/wqflask/app_errors.py
@@ -6,7 +6,8 @@ import traceback
from uuid import uuid4
from werkzeug.exceptions import InternalServerError
-from authlib.integrations.base_client.errors import InvalidTokenError
+from authlib.integrations.base_client.errors import (
+ OAuthError, InvalidTokenError)
from flask import (
flash, request, redirect, current_app, render_template, make_response)
@@ -46,13 +47,37 @@ def handle_authorisation_error(exc: AuthorisationError):
"authorisation_error.html", error_type=type(exc).__name__, error=exc)
def handle_invalid_token_error(exc: InvalidTokenError):
+ """Handle InvalidTokenError"""
flash("An invalid session token was detected. "
"You have been logged out of the system.",
"alert-danger")
+ current_app.logger.error("Invalid token detected. %s", request.url, exc_info=True)
+ session.clear_session_info()
+ return redirect("/")
+
+def __build_message__(exc: OAuthError) -> str:
+ """Build up the message to flash for any OAuthError"""
+ match exc.args[0]:
+ case "ForbiddenAccess: Token does not belong to client.":
+ return "An invalid token was used. The session has been cleared."
+ case "ForbiddenAccess: Token is expired.":
+ return "The session has expired."
+ case "ForbiddenAccess: Token has previously been revoked.":
+ return "Revoked token was used. The session has been cleared."
+ case _:
+ return exc.args[0]
+
+def handle_oauth_error(exc: OAuthError):
+ """Handle generic OAuthError"""
+ flash((f"{type(exc).__name__}: {__build_message__(exc)} "
+ "Please log in again to continue."),
+ "alert-danger")
+ current_app.logger.error("Invalid token detected. %s", request.url, exc_info=True)
session.clear_session_info()
return redirect("/")
__handlers__ = {
+ OAuthError: handle_oauth_error,
AuthorisationError: handle_authorisation_error,
ExternalRequestError: lambda exc: render_error(exc),
InternalServerError: lambda exc: render_error(exc),
diff --git a/gn2/wqflask/collect.py b/gn2/wqflask/collect.py
index 9e0640a5..dd561a78 100644
--- a/gn2/wqflask/collect.py
+++ b/gn2/wqflask/collect.py
@@ -72,7 +72,7 @@ def store_traits_list():
return hash
-@app.route("/collections/add", methods=["POST"])
+@app.route("/collections/add", methods=('GET', 'POST'))
def collections_add():
anon_id = session_info()["anon_id"]
traits = request.args.get("traits", request.form.get("traits"))
diff --git a/gn2/wqflask/correlation/show_corr_results.py b/gn2/wqflask/correlation/show_corr_results.py
index c8625222..1abf1a28 100644
--- a/gn2/wqflask/correlation/show_corr_results.py
+++ b/gn2/wqflask/correlation/show_corr_results.py
@@ -91,6 +91,8 @@ def apply_filters(trait, target_trait, target_dataset, **filters):
min_location_mb, max_location_mb):
if target_dataset["type"] in ["ProbeSet", "Geno"] and location_type == "gene":
+ if not target_trait['mb'] or not target_trait['chr']:
+ return True
return (
((location_chr!=None) and (target_trait["chr"]!=location_chr))
or
@@ -154,7 +156,7 @@ def get_user_filters(start_vars):
if all(keys in start_vars for keys in ["loc_chr",
"min_loc_mb",
- "max_location_mb"]):
+ "max_loc_mb"]):
location_chr = get_string(start_vars, "loc_chr")
min_location_mb = get_int(start_vars, "min_loc_mb")
diff --git a/gn2/wqflask/do_search.py b/gn2/wqflask/do_search.py
index 3c81783d..b64c6fce 100644
--- a/gn2/wqflask/do_search.py
+++ b/gn2/wqflask/do_search.py
@@ -253,13 +253,15 @@ class PhenotypeSearch(DoSearch):
# Todo: Zach will figure out exactly what both these lines mean
# and comment here
- # if "'" not in self.search_term[0]:
- search_term = "%" + \
- self.handle_wildcard(self.search_term[0]) + "%"
+ search_term = self.search_term[0]
if "_" in self.search_term[0]:
if len(self.search_term[0].split("_")[0]) == 3:
- search_term = "%" + self.handle_wildcard(
- self.search_term[0].split("_")[1]) + "%"
+ search_term = self.search_term[0].split("_")[1]
+
+ if not search_term.isnumeric() or len(search_term) != 5: # To make sure phenotype trait IDs aren't included in a fulltext search
+ search_term = "%" + \
+ self.handle_wildcard(search_term) + "%"
+
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
diff --git a/gn2/wqflask/gsearch.py b/gn2/wqflask/gsearch.py
index cad6db94..2a214cf8 100644
--- a/gn2/wqflask/gsearch.py
+++ b/gn2/wqflask/gsearch.py
@@ -28,10 +28,16 @@ class GSearch:
hmac = curry(3, lambda trait_name, dataset, data_hmac: f"{trait_name}:{dataset}:{data_hmac}")
convert_lod = lambda x: x / 4.61
self.trait_list = []
- for i, trait in enumerate(requests.get(
+ response = requests.get(
urljoin(GN3_LOCAL_URL, "/api/search?" + urlencode({"query": self.terms,
"type": self.type,
- "per_page": MAX_SEARCH_RESULTS}))).json()):
+ "per_page": MAX_SEARCH_RESULTS})))
+ if response.status_code == 400 and "parsererror" in response.text.lower():
+ raise ValueError(f"Query `{self.terms}` has a problem: {response.json()}")
+ response.raise_for_status()
+ response_json = response.json()
+
+ for i, trait in enumerate(response_json):
trait = MonadicDict(trait)
trait["index"] = Just(i)
trait["location_repr"] = (Maybe.apply(chr_mb)
diff --git a/gn2/wqflask/marker_regression/display_mapping_results.py b/gn2/wqflask/marker_regression/display_mapping_results.py
index dec414c0..345751ad 100644
--- a/gn2/wqflask/marker_regression/display_mapping_results.py
+++ b/gn2/wqflask/marker_regression/display_mapping_results.py
@@ -773,8 +773,9 @@ class DisplayMappingResults:
pass
# draw position, no need to use a separate function
- self.drawProbeSetPosition(
- canvas, plotXScale, offset=newoffset, zoom=zoom)
+ if self.traitList[0].mb: # Only draw if position actually exists
+ self.drawProbeSetPosition(
+ canvas, plotXScale, offset=newoffset, zoom=zoom)
return gifmap
@@ -1130,7 +1131,7 @@ class DisplayMappingResults:
)
TEXT_Y_DISPLACEMENT = -8
im_drawer.text(
- text="Sequence Site",
+ text="Gene Location",
xy=(leftOffset + 20, startPosY + TEXT_Y_DISPLACEMENT), font=smallLabelFont,
fill=self.TOP_RIGHT_INFO_COLOR)
@@ -1170,20 +1171,20 @@ class DisplayMappingResults:
if self.haplotypeAnalystChecked:
im_drawer.line(
- xy=((startPosX - 34, startPosY), (startPosX - 17, startPosY)),
- fill=self.HAPLOTYPE_POSITIVE, width=4)
+ xy=((startPosX - 60, startPosY), (startPosX - 45, startPosY)),
+ fill=self.HAPLOTYPE_NEGATIVE, width=8)
im_drawer.line(
- xy=((startPosX - 17, startPosY), (startPosX, startPosY)),
- fill=self.HAPLOTYPE_NEGATIVE, width=4)
+ xy=((startPosX - 45, startPosY), (startPosX - 30, startPosY)),
+ fill=self.HAPLOTYPE_POSITIVE, width=8)
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX + 17, startPosY)),
- fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
+ xy=((startPosX - 30, startPosY), (startPosX - 15, startPosY)),
+ fill=self.HAPLOTYPE_HETEROZYGOUS, width=8)
im_drawer.line(
- xy=((startPosX + 17, startPosY), (startPosX + 34, startPosY)),
- fill=self.HAPLOTYPE_RECOMBINATION, width=4)
+ xy=((startPosX - 15, startPosY), (startPosX, startPosY)),
+ fill=self.HAPLOTYPE_RECOMBINATION, width=8)
im_drawer.text(
- text='Haplotypes (Pat, Mat, Het, Unk)',
- xy=(startPosX + 41, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ text='Haplotypes (Mat, Pat, Het, Unknown)',
+ xy=(startPosX + 10, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.permChecked and self.nperm > 0:
diff --git a/gn2/wqflask/oauth2/checks.py b/gn2/wqflask/oauth2/checks.py
index 7f33348e..4a5a117f 100644
--- a/gn2/wqflask/oauth2/checks.py
+++ b/gn2/wqflask/oauth2/checks.py
@@ -2,12 +2,10 @@
from functools import wraps
from urllib.parse import urljoin
+from flask import flash, request, redirect
from authlib.integrations.requests_client import OAuth2Session
-from flask import (
- flash, request, redirect, session as flask_session)
from . import session
-from .session import clear_session_info
from .client import (
oauth2_get,
oauth2_client,
@@ -24,8 +22,6 @@ def require_oauth2(func):
def __clear_session__(_no_token):
session.clear_session_info()
- flask_session.pop("oauth2_token", None)
- flask_session.pop("user_details", None)
flash("You need to be logged in.", "alert-warning")
return redirect("/")
@@ -36,7 +32,7 @@ def require_oauth2(func):
if not user_details.get("error", False):
return func(*args, **kwargs)
- return clear_session_info(token)
+ return __clear_session__(token)
return session.user_token().either(__clear_session__, __with_token__)
diff --git a/gn2/wqflask/oauth2/client.py b/gn2/wqflask/oauth2/client.py
index 75e438cc..a7d20f6b 100644
--- a/gn2/wqflask/oauth2/client.py
+++ b/gn2/wqflask/oauth2/client.py
@@ -1,12 +1,17 @@
"""Common oauth2 client utilities."""
import json
+import time
+import random
import requests
from typing import Optional
from urllib.parse import urljoin
+from datetime import datetime, timedelta
from flask import current_app as app
from pymonad.either import Left, Right, Either
-from authlib.jose import jwt
+from authlib.common.urls import url_decode
+from authlib.jose.errors import BadSignatureError
+from authlib.jose import KeySet, JsonWebKey, JsonWebToken
from authlib.integrations.requests_client import OAuth2Session
from gn2.wqflask.oauth2 import session
@@ -31,11 +36,76 @@ def oauth2_clientsecret():
def user_logged_in():
"""Check whether the user has logged in."""
suser = session.session_info()["user"]
- if suser["logged_in"]:
- if session.expired():
- session.clear_session_info()
- return False
- return suser["token"].is_right()
+ return suser["logged_in"] and suser["token"].is_right()
+
+
+def __make_token_validator__(keys: KeySet):
+ """Make a token validator function."""
+ def __validator__(token: dict):
+ for key in keys.keys:
+ try:
+ # Fixes CVE-2016-10555. See
+ # https://docs.authlib.org/en/latest/jose/jwt.html
+ jwt = JsonWebToken(["RS256"])
+ jwt.decode(token["access_token"], key)
+ return Right(token)
+ except BadSignatureError:
+ pass
+
+ return Left("INVALID-TOKEN")
+
+ return __validator__
+
+
+def auth_server_jwks() -> Optional[KeySet]:
+ """Fetch the auth-server JSON Web Keys information."""
+ _jwks = session.session_info().get("auth_server_jwks")
+ if bool(_jwks):
+ return {
+ "last-updated": _jwks["last-updated"],
+ "jwks": KeySet([
+ JsonWebKey.import_key(key) for key in _jwks.get(
+ "auth_server_jwks", {}).get(
+ "jwks", {"keys": []})["keys"]])}
+
+
+def __validate_token__(keys):
+ """Validate that the token is really from the auth server."""
+ def __index__(_sess):
+ return _sess
+ return session.user_token().then(__make_token_validator__(keys)).then(
+ session.set_user_token).either(__index__, __index__)
+
+
+def __update_auth_server_jwks__():
+ """Updates the JWKs every 2 hours or so."""
+ jwks = auth_server_jwks()
+ if bool(jwks):
+ last_updated = jwks.get("last-updated")
+ now = datetime.now().timestamp()
+ if bool(last_updated) and (now - last_updated) < timedelta(hours=2).seconds:
+ return __validate_token__(jwks["jwks"])
+
+ jwksuri = urljoin(authserver_uri(), "auth/public-jwks")
+ jwks = KeySet([
+ JsonWebKey.import_key(key)
+ for key in requests.get(jwksuri).json()["jwks"]])
+ return __validate_token__(jwks)
+
+
+def is_token_expired(token):
+ """Check whether the token has expired."""
+ __update_auth_server_jwks__()
+ jwks = auth_server_jwks()
+ if bool(jwks):
+ for jwk in jwks["jwks"].keys:
+ try:
+ jwt = JsonWebToken(["RS256"]).decode(
+ token["access_token"], key=jwk)
+ return datetime.now().timestamp() > jwt["exp"]
+ except BadSignatureError as _bse:
+ pass
+
return False
@@ -43,20 +113,56 @@ def oauth2_client():
def __update_token__(token, refresh_token=None, access_token=None):
"""Update the token when refreshed."""
session.set_user_token(token)
+ return token
+
+ def __delay__():
+ """Do a tiny delay."""
+ time.sleep(random.choice(tuple(i/1000.0 for i in range(0,100))))
+
+ def __refresh_token__(token):
+ """Synchronise token refresh."""
+ if is_token_expired(token):
+ __delay__()
+ if session.is_token_refreshing():
+ while session.is_token_refreshing():
+ __delay__()
+
+ _token = session.user_token().either(None, lambda _tok: _tok)
+ return _token
+
+ session.toggle_token_refreshing()
+ _client = __client__(token)
+ _client.get(urljoin(authserver_uri(), "auth/user/"))
+ session.toggle_token_refreshing()
+ return _client.token
+
+ return token
+
+ def __json_auth__(client, method, uri, headers, body):
+ return (
+ uri,
+ {**headers, "Content-Type": "application/json"},
+ json.dumps({
+ **dict(url_decode(body)),
+ "client_id": oauth2_clientid(),
+ "client_secret": oauth2_clientsecret()
+ }))
def __client__(token) -> OAuth2Session:
- _jwt = jwt.decode(token["access_token"],
- app.config["AUTH_SERVER_SSL_PUBLIC_KEY"])
client = OAuth2Session(
oauth2_clientid(),
oauth2_clientsecret(),
scope=SCOPE,
- token_endpoint=urljoin(authserver_uri(), "/auth/token"),
+ token_endpoint=urljoin(authserver_uri(), "auth/token"),
token_endpoint_auth_method="client_secret_post",
token=token,
update_token=__update_token__)
+ client.register_client_auth_method(
+ ("client_secret_post", __json_auth__))
return client
- return session.user_token().either(
+
+ __update_auth_server_jwks__()
+ return session.user_token().then(__refresh_token__).either(
lambda _notok: __client__(None),
lambda token: __client__(token))
@@ -70,12 +176,18 @@ def __no_token__(_err) -> Left:
resp.status_code = 400
return Left(resp)
-def oauth2_get(uri_path: str, data: dict = {},
- jsonify_p: bool = False, **kwargs) -> Either:
+def oauth2_get(
+ uri_path: str,
+ data: dict = {},
+ jsonify_p: bool = False,
+ headers: dict = {"Content-Type": "application/json"},
+ **kwargs
+) -> Either:
def __get__(token) -> Either:
resp = oauth2_client().get(
urljoin(authserver_uri(), uri_path),
data=data,
+ headers=headers,
**kwargs)
if resp.status_code == 200:
if jsonify_p:
@@ -87,11 +199,18 @@ def oauth2_get(uri_path: str, data: dict = {},
return session.user_token().either(__no_token__, __get__)
def oauth2_post(
- uri_path: str, data: Optional[dict] = None, json: Optional[dict] = None,
- **kwargs) -> Either:
+ uri_path: str,
+ data: Optional[dict] = None,
+ json: Optional[dict] = None,
+ headers: dict = {"Content-Type": "application/json"},
+ **kwargs
+) -> Either:
def __post__(token) -> Either:
resp = oauth2_client().post(
- urljoin(authserver_uri(), uri_path), data=data, json=json,
+ urljoin(authserver_uri(), uri_path),
+ data=data,
+ json=json,
+ headers=headers,
**kwargs)
if resp.status_code == 200:
return Right(resp.json())
@@ -100,10 +219,14 @@ def oauth2_post(
return session.user_token().either(__no_token__, __post__)
-def no_token_get(uri_path: str, **kwargs) -> Either:
+def no_token_get(
+ uri_path: str,
+ headers: dict = {"Content-Type": "application/json"},
+ **kwargs
+) -> Either:
uri = urljoin(authserver_uri(), uri_path)
try:
- resp = requests.get(uri, **kwargs)
+ resp = requests.get(uri, headers=headers, **kwargs)
if resp.status_code == 200:
return Right(resp.json())
return Left(resp)
diff --git a/gn2/wqflask/oauth2/data.py b/gn2/wqflask/oauth2/data.py
index 29d68be0..16e5f60c 100644
--- a/gn2/wqflask/oauth2/data.py
+++ b/gn2/wqflask/oauth2/data.py
@@ -69,8 +69,10 @@ def __search_phenotypes__(query, template, **kwargs):
template, traits=[], per_page=per_page, query=query,
selected_traits=selected_traits, search_results=search_results,
search_endpoint=urljoin(
- authserver_uri(), "auth/data/search"),
- gn_server_url = authserver_uri(),
+ request.host_url, "oauth2/data/phenotype/search"),
+ auth_server_url=authserver_uri(),
+ pheno_results_template=urljoin(
+ authserver_uri(), "auth/data/search/phenotype/<jobid>"),
results_endpoint=urljoin(
authserver_uri(),
f"auth/data/search/phenotype/{job_id}"),
@@ -122,6 +124,7 @@ def json_search_mrna() -> Response:
@data.route("/phenotype/search", methods=["POST"])
def json_search_phenotypes() -> Response:
"""Search for phenotypes."""
+ from gn2.utility.tools import GN_SERVER_URL
form = request.json
def __handle_error__(err):
error = process_error(err)
@@ -136,6 +139,7 @@ def json_search_phenotypes() -> Response:
"per_page": int(form.get("per_page", 50)),
"page": int(form.get("page", 1)),
"auth_server_uri": authserver_uri(),
+ "gn3_server_uri": GN_SERVER_URL,
"selected_traits": form.get("selected_traits", [])
}).either(__handle_error__, jsonify)
diff --git a/gn2/wqflask/oauth2/groups.py b/gn2/wqflask/oauth2/groups.py
index 3bc4bcb2..b3f1f54d 100644
--- a/gn2/wqflask/oauth2/groups.py
+++ b/gn2/wqflask/oauth2/groups.py
@@ -44,7 +44,7 @@ def create_group():
def __setup_group__(response):
session["user_details"]["group"] = response
- resp = oauth2_post("auth/group/create", data=dict(request.form))
+ resp = oauth2_post("auth/group/create", json=dict(request.form))
return resp.either(
handle_error("oauth2.group.join_or_create"),
handle_success(
@@ -116,7 +116,7 @@ def accept_join_request():
return redirect(url_for("oauth2.group.list_join_requests"))
return oauth2_post(
"auth/group/requests/join/accept",
- data=request.form).either(
+ json=dict(request.form)).either(
handle_error("oauth2.group.list_join_requests"),
__success__)
@@ -132,34 +132,10 @@ def reject_join_request():
return redirect(url_for("oauth2.group.list_join_requests"))
return oauth2_post(
"auth/group/requests/join/reject",
- data=request.form).either(
+ json=dict(request.form)).either(
handle_error("oauth2.group.list_join_requests"),
__success__)
-@groups.route("/role/<uuid:group_role_id>", methods=["GET"])
-@require_oauth2
-def group_role(group_role_id: uuid.UUID):
- """View the details of a particular role."""
- def __render_error__(**kwargs):
- return render_ui("oauth2/view-group-role.html", **kwargs)
-
- def __gprivs_success__(role, group_privileges):
- return render_ui(
- "oauth2/view-group-role.html", group_role=role,
- group_privileges=tuple(
- priv for priv in group_privileges
- if priv not in role["role"]["privileges"]))
-
- def __role_success__(role):
- return oauth2_get("auth/group/privileges").either(
- lambda err: __render_error__(
- group_role=group_role,
- group_privileges_error=process_error(err)),
- lambda privileges: __gprivs_success__(role, privileges))
-
- return oauth2_get(f"auth/group/role/{group_role_id}").either(
- lambda err: __render_error__(group_role_error=process_error(err)),
- __role_success__)
def add_delete_privilege_to_role(
group_role_id: uuid.UUID, direction: str) -> Response:
@@ -187,7 +163,7 @@ def add_delete_privilege_to_role(
}
return oauth2_post(
uris[direction],
- data={
+ json={
"group_role_id": group_role_id,
"privilege_id": privilege_id
}).either(__error__, __success__)
diff --git a/gn2/wqflask/oauth2/jwks.py b/gn2/wqflask/oauth2/jwks.py
new file mode 100644
index 00000000..efd04997
--- /dev/null
+++ b/gn2/wqflask/oauth2/jwks.py
@@ -0,0 +1,86 @@
+"""Utilities dealing with JSON Web Keys (JWK)"""
+import os
+from pathlib import Path
+from typing import Any, Union
+from datetime import datetime, timedelta
+
+from flask import Flask
+from authlib.jose import JsonWebKey
+from pymonad.either import Left, Right, Either
+
+def jwks_directory(app: Flask, configname: str) -> Path:
+ """Compute the directory where the JWKs are stored."""
+ appsecretsdir = Path(app.config[configname]).parent
+ if appsecretsdir.exists() and appsecretsdir.is_dir():
+ jwksdir = Path(appsecretsdir, "jwks/")
+ if not jwksdir.exists():
+ jwksdir.mkdir()
+ return jwksdir
+ raise ValueError(
+ "The `appsecretsdir` value should be a directory that actually exists.")
+
+
+def generate_and_save_private_key(
+ storagedir: Path,
+ kty: str = "RSA",
+ crv_or_size: Union[str, int] = 2048,
+ options: tuple[tuple[str, Any]] = (("iat", datetime.now().timestamp()),)
+) -> JsonWebKey:
+ """Generate a private key and save to `storagedir`."""
+ privatejwk = JsonWebKey.generate_key(
+ kty, crv_or_size, dict(options), is_private=True)
+ keyname = f"{privatejwk.thumbprint()}.private.pem"
+ with open(Path(storagedir, keyname), "wb") as pemfile:
+ pemfile.write(privatejwk.as_pem(is_private=True))
+
+ return privatejwk
+
+
+def pem_to_jwk(filepath: Path) -> JsonWebKey:
+ """Parse a PEM file into a JWK object."""
+ with open(filepath, "rb") as pemfile:
+ return JsonWebKey.import_key(pemfile.read())
+
+
+def __sorted_jwks_paths__(storagedir: Path) -> tuple[tuple[float, Path], ...]:
+ """A sorted list of the JWK file paths with their creation timestamps."""
+ return tuple(sorted(((os.stat(keypath).st_ctime, keypath)
+ for keypath in (Path(storagedir, keyfile)
+ for keyfile in os.listdir(storagedir)
+ if keyfile.endswith(".pem"))),
+ key=lambda tpl: tpl[0]))
+
+
+def list_jwks(storagedir: Path) -> tuple[JsonWebKey, ...]:
+ """
+ List all the JWKs in a particular directory in the order they were created.
+ """
+ return tuple(pem_to_jwk(keypath) for ctime,keypath in
+ __sorted_jwks_paths__(storagedir))
+
+
+def newest_jwk(storagedir: Path) -> Either:
+ """
+ Return an Either monad with the newest JWK or a message if none exists.
+ """
+ existingkeys = __sorted_jwks_paths__(storagedir)
+ if len(existingkeys) > 0:
+ return Right(pem_to_jwk(existingkeys[-1][1]))
+ return Left("No JWKs exist")
+
+
+def newest_jwk_with_rotation(jwksdir: Path, keyage: int) -> JsonWebKey:
+ """
+ Retrieve the latests JWK, creating a new one if older than `keyage` days.
+ """
+ def newer_than_days(jwkey):
+ filestat = os.stat(Path(
+ jwksdir, f"{jwkey.as_dict()['kid']}.private.pem"))
+ oldesttimeallowed = (datetime.now() - timedelta(days=keyage))
+ if filestat.st_ctime < (oldesttimeallowed.timestamp()):
+ return Left("JWK is too old!")
+ return jwkey
+
+ return newest_jwk(jwksdir).then(newer_than_days).either(
+ lambda _errmsg: generate_and_save_private_key(jwksdir),
+ lambda key: key)
diff --git a/gn2/wqflask/oauth2/request_utils.py b/gn2/wqflask/oauth2/request_utils.py
index 1cdc465f..456aba2b 100644
--- a/gn2/wqflask/oauth2/request_utils.py
+++ b/gn2/wqflask/oauth2/request_utils.py
@@ -36,7 +36,7 @@ def process_error(error: Response,
try:
err = error.json()
msg = err.get(
- "error", err.get("error_description", f"{error.reason}"))
+ "error_message", err.get("error_description", f"{error.reason}"))
except simplejson.errors.JSONDecodeError as _jde:
msg = message
return {
diff --git a/gn2/wqflask/oauth2/resources.py b/gn2/wqflask/oauth2/resources.py
index 32efbd2a..7ea7fe38 100644
--- a/gn2/wqflask/oauth2/resources.py
+++ b/gn2/wqflask/oauth2/resources.py
@@ -1,17 +1,25 @@
-import uuid
+from uuid import UUID
from flask import (
flash, request, url_for, redirect, Response, Blueprint)
from . import client
-from .ui import render_ui
+from . import session
+from .ui import render_ui as _render_ui
from .checks import require_oauth2
from .client import oauth2_get, oauth2_post
-from .request_utils import (
- flash_error, flash_success, request_error, process_error)
+from .request_utils import (flash_error,
+ flash_success,
+ request_error,
+ process_error,
+ with_flash_error,
+ with_flash_success)
resources = Blueprint("resource", __name__)
+def render_ui(template, **kwargs):
+ return _render_ui(template, uipages="resources", **kwargs)
+
@resources.route("/", methods=["GET"])
@require_oauth2
def user_resources():
@@ -51,7 +59,7 @@ def create_resource():
flash("Resource created successfully", "alert-success")
return redirect(url_for("oauth2.resource.user_resources"))
return oauth2_post(
- "auth/resource/create", data=request.form).either(
+ "auth/resource/create", json=dict(request.form)).either(
__perr__, __psuc__)
def __compute_page__(submit, current_page):
@@ -59,47 +67,48 @@ def __compute_page__(submit, current_page):
return current_page + 1
return (current_page - 1) or 1
-@resources.route("/view/<uuid:resource_id>", methods=["GET"])
+@resources.route("/<uuid:resource_id>/view", methods=["GET"])
@require_oauth2
-def view_resource(resource_id: uuid.UUID):
+def view_resource(resource_id: UUID):
"""View the given resource."""
page = __compute_page__(request.args.get("submit"),
int(request.args.get("page", "1"), base=10))
count_per_page = int(request.args.get("count_per_page", "100"), base=10)
def __users_success__(
- resource, unlinked_data, users_n_roles, this_user, group_roles,
+ resource, unlinked_data, users_n_roles, this_user, resource_roles,
users):
return render_ui(
"oauth2/view-resource.html", resource=resource,
unlinked_data=unlinked_data, users_n_roles=users_n_roles,
- this_user=this_user, group_roles=group_roles, users=users,
+ this_user=this_user, resource_roles=resource_roles, users=users,
page=page, count_per_page=count_per_page)
- def __group_roles_success__(
- resource, unlinked_data, users_n_roles, this_user, group_roles):
+ def __resource_roles_success__(
+ resource, unlinked_data, users_n_roles, this_user, resource_roles):
return oauth2_get("auth/user/list").either(
lambda err: render_ui(
"oauth2/view-resource.html", resource=resource,
unlinked_data=unlinked_data, users_n_roles=users_n_roles,
- this_user=this_user, group_roles=group_roles,
+ this_user=this_user, resource_roles=resource_roles,
users_error=process_error(err), count_per_page=count_per_page),
lambda users: __users_success__(
- resource, unlinked_data, users_n_roles, this_user, group_roles,
+ resource, unlinked_data, users_n_roles, this_user, resource_roles,
users))
def __this_user_success__(resource, unlinked_data, users_n_roles, this_user):
- return oauth2_get("auth/group/roles").either(
+ return oauth2_get(f"auth/resource/{resource_id}/roles").either(
lambda err: render_ui(
- "oauth2/view-resources.html", resource=resource,
+ "oauth2/view-resource.html", resource=resource,
unlinked_data=unlinked_data, users_n_roles=users_n_roles,
- this_user=this_user, group_roles_error=process_error(err)),
- lambda groles: __group_roles_success__(
- resource, unlinked_data, users_n_roles, this_user, groles))
+ this_user=this_user, resource_roles_error=process_error(err),
+ count_per_page=count_per_page),
+ lambda rroles: __resource_roles_success__(
+ resource, unlinked_data, users_n_roles, this_user, rroles))
def __users_n_roles_success__(resource, unlinked_data, users_n_roles):
return oauth2_get("auth/user/").either(
lambda err: render_ui(
- "oauth2/view-resources.html",
+ "oauth2/view-resource.html",
this_user_error=process_error(err)),
lambda usr_dets: __this_user_success__(
resource, unlinked_data, users_n_roles, usr_dets))
@@ -120,8 +129,10 @@ def view_resource(resource_id: uuid.UUID):
dataset_type = resource["resource_category"]["resource_category_key"]
return oauth2_get(f"auth/group/{dataset_type}/unlinked-data").either(
lambda err: render_ui(
- "oauth2/view-resource.html", resource=resource,
- unlinked_error=process_error(err)),
+ "oauth2/view-resource.html",
+ resource=resource,
+ unlinked_error=process_error(err),
+ count_per_page=count_per_page),
lambda unlinked: __unlinked_success__(resource, unlinked))
def __fetch_resource_data__(resource):
@@ -164,7 +175,7 @@ def link_data_to_resource():
flash(f"Data linked to resource successfully", "alert-success")
return redirect(url_for(
"oauth2.resource.view_resource", resource_id=resource_id))
- return oauth2_post("auth/resource/data/link", data=dict(form)).either(
+ return oauth2_post("auth/resource/data/link", json=dict(form)).either(
__error__,
__success__)
except AssertionError as aserr:
@@ -193,7 +204,7 @@ def unlink_data_from_resource():
return redirect(url_for(
"oauth2.resource.view_resource", resource_id=resource_id))
return oauth2_post(
- "auth/resource/data/unlink", data=dict(form)).either(
+ "auth/resource/data/unlink", json=dict(form)).either(
__error__, __success__)
except AssertionError as aserr:
flash(aserr.args[0], "alert-danger")
@@ -202,12 +213,12 @@ def unlink_data_from_resource():
@resources.route("<uuid:resource_id>/user/assign", methods=["POST"])
@require_oauth2
-def assign_role(resource_id: uuid.UUID) -> Response:
+def assign_role(resource_id: UUID) -> Response:
form = request.form
- group_role_id = form.get("group_role_id", "")
+ role_id = form.get("role_id", "")
user_email = form.get("user_email", "")
try:
- assert bool(group_role_id), "The role must be provided."
+ assert bool(role_id), "The role must be provided."
assert bool(user_email), "The user email must be provided."
def __assign_error__(error):
@@ -223,22 +234,22 @@ def assign_role(resource_id: uuid.UUID) -> Response:
return oauth2_post(
f"auth/resource/{resource_id}/user/assign",
- data={
- "group_role_id": group_role_id,
+ json={
+ "role_id": role_id,
"user_email": user_email
}).either(__assign_error__, __assign_success__)
except AssertionError as aserr:
flash(aserr.args[0], "alert-danger")
- return redirect(url_for("oauth2.resources.view_resource", resource_id=resource_id))
+ return redirect(url_for("oauth2.resource.view_resource", resource_id=resource_id))
@resources.route("<uuid:resource_id>/user/unassign", methods=["POST"])
@require_oauth2
-def unassign_role(resource_id: uuid.UUID) -> Response:
+def unassign_role(resource_id: UUID) -> Response:
form = request.form
- group_role_id = form.get("group_role_id", "")
+ role_id = form.get("role_id", "")
user_id = form.get("user_id", "")
try:
- assert bool(group_role_id), "The role must be provided."
+ assert bool(role_id), "The role must be provided."
assert bool(user_id), "The user id must be provided."
def __unassign_error__(error):
@@ -254,17 +265,17 @@ def unassign_role(resource_id: uuid.UUID) -> Response:
return oauth2_post(
f"auth/resource/{resource_id}/user/unassign",
- data={
- "group_role_id": group_role_id,
+ json={
+ "role_id": role_id,
"user_id": user_id
}).either(__unassign_error__, __unassign_success__)
except AssertionError as aserr:
flash(aserr.args[0], "alert-danger")
- return redirect(url_for("oauth2.resources.view_resource", resource_id=resource_id))
+ return redirect(url_for("oauth2.resource.view_resource", resource_id=resource_id))
@resources.route("/toggle/<uuid:resource_id>", methods=["POST"])
@require_oauth2
-def toggle_public(resource_id: uuid.UUID):
+def toggle_public(resource_id: UUID):
"""Toggle the given resource's public status."""
def __handle_error__(err):
flash_error(process_error(err))
@@ -277,18 +288,169 @@ def toggle_public(resource_id: uuid.UUID):
"oauth2.resource.view_resource", resource_id=resource_id))
return oauth2_post(
- f"auth/resource/{resource_id}/toggle-public", data={}).either(
+ f"auth/resource/{resource_id}/toggle-public").either(
lambda err: __handle_error__(err),
lambda suc: __handle_success__(suc))
@resources.route("/edit/<uuid:resource_id>", methods=["GET"])
@require_oauth2
-def edit_resource(resource_id: uuid.UUID):
+def edit_resource(resource_id: UUID):
"""Edit the given resource."""
return "WOULD Edit THE GIVEN RESOURCE'S DETAILS"
@resources.route("/delete/<uuid:resource_id>", methods=["GET"])
@require_oauth2
-def delete_resource(resource_id: uuid.UUID):
+def delete_resource(resource_id: UUID):
"""Delete the given resource."""
return "WOULD DELETE THE GIVEN RESOURCE"
+
+@resources.route("/<uuid:resource_id>/roles/<uuid:role_id>", methods=["GET"])
+@require_oauth2
+def view_resource_role(resource_id: UUID, role_id: UUID):
+ """View resource role page."""
+ def __render_template__(**kwargs):
+ return render_ui("oauth2/view-resource-role.html", **kwargs)
+
+ def __fetch_users__(resource, role, unassigned_privileges):
+ return oauth2_get(
+ f"auth/resource/{resource_id}/role/{role_id}/users").either(
+ lambda error: __render_template__(
+ resource=resource,
+ role=role,
+ unassigned_privileges=unassigned_privileges,
+ user_error=process_error(error)),
+ lambda users: __render_template__(
+ resource=resource,
+ role=role,
+ unassigned_privileges=unassigned_privileges,
+ users=users))
+
+ def __fetch_all_roles__(resource, role):
+ return oauth2_get(f"auth/resource/{resource_id}/roles").either(
+ lambda error: __render_template__(
+ all_roles_error=process_error(error)),
+ lambda all_roles: __fetch_users__(
+ resource=resource,
+ role=role,
+ unassigned_privileges=[
+ priv for role in all_roles
+ for priv in role["privileges"]
+ if priv not in role["privileges"]
+ ]))
+
+ def __fetch_resource_role__(resource):
+ return oauth2_get(
+ f"auth/resource/{resource_id}/role/{role_id}").either(
+ lambda error: __render_template__(
+ resource=resource,
+ role_id=role_id,
+ role_error=process_error(error)),
+ lambda role: __fetch_all_roles__(resource, role))
+
+ return oauth2_get(
+ f"auth/resource/view/{resource_id}").either(
+ lambda error: __render_template__(
+ resource_error=process_error(error)),
+ lambda resource: __fetch_resource_role__(resource=resource))
+
+@resources.route("/<uuid:resource_id>/roles/<uuid:role_id>/unassign-privilege",
+ methods=["GET", "POST"])
+@require_oauth2
+def unassign_privilege_from_resource_role(resource_id: UUID, role_id: UUID):
+ """Remove a privilege from a resource role."""
+ form = request.form
+ returnto = redirect(url_for("oauth2.resource.view_resource_role",
+ resource_id=resource_id,
+ role_id=role_id))
+ privilege_id = (request.args.get("privilege_id")
+ or form.get("privilege_id"))
+ if not privilege_id:
+ flash("You need to specify a privilege to unassign.", "alert-danger")
+ return returnto
+
+ if request.method=="POST" and form.get("confirm") == "Unassign":
+ return oauth2_post(
+ f"auth/resource/{resource_id}/role/{role_id}/unassign-privilege",
+ json={
+ "privilege_id": form["privilege_id"]
+ }).either(with_flash_error(returnto), with_flash_success(returnto))
+
+ if form.get("confirm") == "Cancel":
+ flash("Cancelled the operation to unassign the privilege.",
+ "alert-info")
+ return returnto
+
+ def __fetch_privilege__(resource, role):
+ return oauth2_get(
+ f"auth/privileges/{privilege_id}/view").either(
+ with_flash_error(returnto),
+ lambda privilege: render_ui(
+ "oauth2/confirm-resource-role-unassign-privilege.html",
+ resource=resource,
+ role=role,
+ privilege=privilege))
+
+ def __fetch_resource_role__(resource):
+ return oauth2_get(
+ f"auth/resource/{resource_id}/role/{role_id}").either(
+ with_flash_error(returnto),
+ lambda role: __fetch_privilege__(resource, role))
+
+ return oauth2_get(
+ f"auth/resource/view/{resource_id}").either(
+ with_flash_error(returnto),
+ __fetch_resource_role__)
+
+
+@resources.route("/<uuid:resource_id>/roles/create-role",
+ methods=["GET", "POST"])
+@require_oauth2
+def create_resource_role(resource_id: UUID):
+ """Create new role for the resource."""
+ def __render__(**kwargs):
+ return render_ui("oauth2/create-role.html", **kwargs)
+
+ def __fetch_resource_roles__(resource):
+ user = session.session_info()["user"]
+ return oauth2_get(
+ f"auth/resource/{resource_id}/users/{user['user_id']}"
+ "/roles").either(
+ lambda error: {
+ "resource": resource,
+ "resource_role_error": process_error(error)
+ },
+ lambda roles: {"resource": resource, "roles": roles})
+
+ if request.method == "GET":
+ return oauth2_get(f"auth/resource/view/{resource_id}").map(
+ __fetch_resource_roles__).either(
+ lambda error: __render__(resource_error=error),
+ lambda kwargs: __render__(**kwargs))
+
+ formdata = request.form
+ privileges = formdata.getlist("privileges[]")
+ if not bool(privileges):
+ flash(
+ "You must provide at least one privilege for creation of the new "
+ "role.",
+ "alert-danger")
+ return redirect(url_for("oauth2.resource.create_resource_role",
+ resource_id=resource_id))
+
+ def __handle_error__(error):
+ flash_error(process_error(error))
+ return redirect(url_for(
+ "oauth2.resource.create_resource_role", resource_id=resource_id))
+
+ def __handle_success__(success):
+ flash("Role successfully created.", "alert-success")
+ return redirect(url_for(
+ "oauth2.resource.view_resource", resource_id=resource_id))
+
+ return oauth2_post(
+ f"auth/resource/{resource_id}/roles/create",
+ json={
+ "role_name": formdata["role_name"],
+ "privileges": privileges
+ }).either(
+ __handle_error__, __handle_success__)
diff --git a/gn2/wqflask/oauth2/roles.py b/gn2/wqflask/oauth2/roles.py
index 2fe35f9b..2a21670e 100644
--- a/gn2/wqflask/oauth2/roles.py
+++ b/gn2/wqflask/oauth2/roles.py
@@ -10,31 +10,6 @@ from .request_utils import request_error, process_error
roles = Blueprint("role", __name__)
-@roles.route("/user", methods=["GET"])
-@require_oauth2
-def user_roles():
- def __grerror__(roles, user_privileges, error):
- return render_ui(
- "oauth2/list_roles.html", roles=roles,
- user_privileges=user_privileges,
- group_roles_error=process_error(error))
-
- def __grsuccess__(roles, user_privileges, group_roles):
- return render_ui(
- "oauth2/list_roles.html", roles=roles,
- user_privileges=user_privileges, group_roles=group_roles)
-
- def __role_success__(roles):
- uprivs = tuple(
- privilege["privilege_id"] for role in roles
- for privilege in role["privileges"])
- return oauth2_get("auth/group/roles").either(
- lambda err: __grerror__(roles, uprivs, err),
- lambda groles: __grsuccess__(roles, uprivs, groles))
-
- return oauth2_get("auth/system/roles").either(
- request_error, __role_success__)
-
@roles.route("/role/<uuid:role_id>", methods=["GET"])
@require_oauth2
def role(role_id: uuid.UUID):
@@ -46,54 +21,3 @@ def role(role_id: uuid.UUID):
return oauth2_get(f"auth/role/view/{role_id}").either(
request_error, __success__)
-@roles.route("/create", methods=["GET", "POST"])
-@require_oauth2
-def create_role():
- """Create a new role."""
- def __roles_error__(error):
- return render_ui(
- "oauth2/create-role.html", roles_error=process_error(error))
-
- def __gprivs_error__(roles, error):
- return render_ui(
- "oauth2/create-role.html", roles=roles,
- group_privileges_error=process_error(error))
-
- def __success__(roles, gprivs):
- uprivs = tuple(
- privilege["privilege_id"] for role in roles
- for privilege in role["privileges"])
- return render_ui(
- "oauth2/create-role.html", roles=roles, user_privileges=uprivs,
- group_privileges=gprivs,
- prev_role_name=request.args.get("role_name"))
-
- def __fetch_gprivs__(roles):
- return oauth2_get("auth/group/privileges").either(
- lambda err: __gprivs_error__(roles, err),
- lambda gprivs: __success__(roles, gprivs))
-
- if request.method == "GET":
- return oauth2_get("auth/user/roles").either(
- __roles_error__, __fetch_gprivs__)
-
- form = request.form
- role_name = form.get("role_name")
- privileges = form.getlist("privileges[]")
- if len(privileges) == 0:
- flash("You must assign at least one privilege to the role",
- "alert-danger")
- return redirect(url_for(
- "oauth2.role.create_role", role_name=role_name))
- def __create_error__(error):
- err = process_error(error)
- flash(f"{err['error']}: {err['error_description']}",
- "alert-danger")
- return redirect(url_for("oauth2.role.create_role"))
- def __create_success__(*args):
- flash("Role created successfully.", "alert-success")
- return redirect(url_for("oauth2.role.user_roles"))
- return oauth2_post(
- "auth/group/role/create",data={
- "role_name": role_name, "privileges[]": privileges}).either(
- __create_error__,__create_success__)
diff --git a/gn2/wqflask/oauth2/session.py b/gn2/wqflask/oauth2/session.py
index 2ef534e2..b91534b0 100644
--- a/gn2/wqflask/oauth2/session.py
+++ b/gn2/wqflask/oauth2/session.py
@@ -22,6 +22,8 @@ class SessionInfo(TypedDict):
user_agent: str
ip_addr: str
masquerade: Optional[UserDetails]
+ refreshing_token: bool
+ auth_server_jwks: Optional[dict[str, Any]]
__SESSION_KEY__ = "GN::2::session_info" # Do not use this outside this module!!
@@ -61,16 +63,10 @@ def session_info() -> SessionInfo:
"user_agent": request.headers.get("User-Agent"),
"ip_addr": request.environ.get("HTTP_X_FORWARDED_FOR",
request.remote_addr),
- "masquerading": None
+ "masquerading": None,
+ "token_refreshing": False
}))
-def expired():
- the_session = session_info()
- def __expired__(token):
- return datetime.now() > datetime.fromtimestamp(token["expires_at"])
- return the_session["user"]["token"].either(
- lambda left: False,
- __expired__)
def set_user_token(token: str) -> SessionInfo:
"""Set the user's token."""
@@ -109,3 +105,16 @@ def unset_masquerading():
"user": the_session["masquerading"],
"masquerading": None
})
+
+
+def toggle_token_refreshing():
+ """Toggle the state of the token_refreshing variable."""
+ _session = session_info()
+ return save_session_info({
+ **_session,
+ "token_refreshing": not _session.get("token_refreshing", False)})
+
+
+def is_token_refreshing():
+ """Returns whether the token is being refreshed or not."""
+ return session_info().get("token_refreshing", False)
diff --git a/gn2/wqflask/oauth2/toplevel.py b/gn2/wqflask/oauth2/toplevel.py
index 23965cc1..24d60311 100644
--- a/gn2/wqflask/oauth2/toplevel.py
+++ b/gn2/wqflask/oauth2/toplevel.py
@@ -3,11 +3,17 @@ import uuid
import datetime
from urllib.parse import urljoin, urlparse, urlunparse
-from authlib.jose import jwt
-from flask import (
- flash, request, Blueprint, url_for, redirect, render_template,
- current_app as app)
+from authlib.jose import jwt, KeySet
+from flask import (flash,
+ request,
+ url_for,
+ jsonify,
+ redirect,
+ Blueprint,
+ render_template,
+ current_app as app)
+from . import jwks
from . import session
from .checks import require_oauth2
from .request_utils import user_details, process_error
@@ -29,7 +35,9 @@ def authorisation_code():
code = request.args.get("code", "")
if bool(code):
base_url = urlparse(request.base_url, scheme=request.scheme)
- jwtkey = app.config["SSL_PRIVATE_KEY"]
+ jwtkey = jwks.newest_jwk_with_rotation(
+ jwks.jwks_directory(app, "GN2_SECRETS"),
+ int(app.config["JWKS_ROTATION_AGE_DAYS"]))
issued = datetime.datetime.now()
request_data = {
"grant_type": "urn:ietf:params:oauth:grant-type:jwt-bearer",
@@ -47,7 +55,7 @@ def authorisation_code():
"iss": str(oauth2_clientid()),
"sub": request.args["user_id"],
"aud": urljoin(authserver_uri(), "auth/token"),
- "exp": (issued + datetime.timedelta(minutes=5)),
+ "exp": (issued + datetime.timedelta(minutes=5)).timestamp(),
"nbf": int(issued.timestamp()),
"iat": int(issued.timestamp()),
"jti": str(uuid.uuid4())},
@@ -75,8 +83,17 @@ def authorisation_code():
})
return redirect("/")
- return no_token_post(
- "auth/token", data=request_data).either(
- lambda err: __error__(process_error(err)), __success__)
+ return no_token_post("auth/token", json=request_data).either(
+ lambda err: __error__(process_error(err)), __success__)
flash("AuthorisationError: No code was provided.", "alert-danger")
return redirect("/")
+
+
+@toplevel.route("/public-jwks", methods=["GET"])
+def public_jwks():
+ """Provide endpoint that returns the public keys."""
+ return jsonify({
+ "documentation": "The keys are listed in order of creation.",
+ "jwks": KeySet(jwks.list_jwks(
+ jwks.jwks_directory(app, "GN2_SECRETS"))).as_dict().get("keys")
+ })
diff --git a/gn2/wqflask/oauth2/ui.py b/gn2/wqflask/oauth2/ui.py
index cf2e9af7..04095420 100644
--- a/gn2/wqflask/oauth2/ui.py
+++ b/gn2/wqflask/oauth2/ui.py
@@ -1,22 +1,17 @@
"""UI utilities"""
-from flask import session, render_template
+from flask import render_template
from .client import oauth2_get
-from .client import user_logged_in
-from .request_utils import process_error
def render_ui(templatepath: str, **kwargs):
"""Handle repetitive UI rendering stuff."""
- roles = kwargs.get("roles", tuple()) # Get roles if already provided
- if user_logged_in() and not bool(roles): # If not, try fetching them
- roles_results = oauth2_get("auth/system/roles").either(
- lambda err: {"roles_error": process_error(err)},
- lambda roles: {"roles": roles})
- kwargs = {**kwargs, **roles_results}
+ roles = kwargs.get("roles", tuple()) # Get roles
+ if not roles:
+ roles = oauth2_get("auth/system/roles").either(
+ lambda _err: roles, lambda auth_roles: auth_roles)
user_privileges = tuple(
- privilege["privilege_id"] for role in roles
- for privilege in role["privileges"])
+ privilege["privilege_id"] for role in roles for privilege in role["privileges"])
kwargs = {
- **kwargs, "roles": roles, "user_privileges": user_privileges
+ **kwargs, "roles": roles, "user_privileges": user_privileges,
}
return render_template(templatepath, **kwargs)
diff --git a/gn2/wqflask/oauth2/users.py b/gn2/wqflask/oauth2/users.py
index 8a935170..7d9186ab 100644
--- a/gn2/wqflask/oauth2/users.py
+++ b/gn2/wqflask/oauth2/users.py
@@ -1,6 +1,6 @@
import requests
from uuid import UUID
-from urllib.parse import urljoin
+from urllib.parse import urljoin, urlparse
from authlib.integrations.base_client.errors import OAuthError
from flask import (
@@ -11,10 +11,16 @@ from . import client
from . import session
from .ui import render_ui
from .checks import require_oauth2
-from .client import (oauth2_get, oauth2_post, oauth2_client,
- authserver_uri, user_logged_in)
-from .request_utils import (
- user_details, request_error, process_error, with_flash_error)
+from .client import (oauth2_get,
+ oauth2_post,
+ oauth2_client,
+ authserver_uri,
+ user_logged_in)
+from .request_utils import (user_details,
+ request_error,
+ process_error,
+ with_flash_error,
+ authserver_authorise_uri)
users = Blueprint("user", __name__)
@@ -61,7 +67,7 @@ def request_add_to_group() -> Response:
return redirect(url_for("oauth2.user.user_profile"))
return oauth2_post(f"auth/group/requests/join/{group_id}",
- data=form).either(__error__, __success__)
+ json=form).either(__error__, __success__)
@users.route("/logout", methods=["GET", "POST"])
@@ -84,7 +90,8 @@ def logout():
f"{the_session['masquerading']['name']} "
f"({the_session['masquerading']['email']})",
"alert-success")
- return redirect("/")
+
+ return redirect("/")
@users.route("/register", methods=["GET", "POST"])
def register_user():
@@ -101,11 +108,14 @@ def register_user():
form = request.form
response = requests.post(
urljoin(authserver_uri(), "auth/user/register"),
- data = {
+ json = {
"user_name": form.get("user_name"),
"email": form.get("email_address"),
"password": form.get("password"),
- "confirm_password": form.get("confirm_password")})
+ "confirm_password": form.get("confirm_password"),
+ **dict(
+ item.split("=") for item in
+ urlparse(authserver_authorise_uri()).query.split("&"))})
results = response.json()
if "error" in results:
error_messages = tuple(
diff --git a/gn2/wqflask/parser.py b/gn2/wqflask/parser.py
index ddf48d90..fdd5d164 100644
--- a/gn2/wqflask/parser.py
+++ b/gn2/wqflask/parser.py
@@ -30,7 +30,7 @@ def parse(pstring):
pstring = re.split(r"""(?:(\w+\s*=\s*[\('"\[][^)'"]*[\)\]'"]) | # LRS=(1 2 3), cisLRS=[4 5 6], etc
(\w+\s*[=:\>\<][\w\*]+) | # wiki=bar, GO:foobar, etc
(".*?") | ('.*?') | # terms in quotes, i.e. "brain weight"
- ([\w\*\?\-]+)) # shh, brain, etc """, pstring,
+ ([\w\*\?\-]+\@\.)) # shh, brain, etc """, pstring,
flags=re.VERBOSE)
pstring = [item.strip() for item in pstring if item and item.strip()]
diff --git a/gn2/wqflask/requests.py b/gn2/wqflask/requests.py
index 43c8001f..182201a5 100644
--- a/gn2/wqflask/requests.py
+++ b/gn2/wqflask/requests.py
@@ -14,3 +14,13 @@ def get(url, params=None, **kwargs) -> Either:
def post(url, data=None, json=None, **kwargs) -> Either:
"""Wrap requests post method with Either monad"""
return __wrap_response__(requests.post(url, data=data, json=json, **kwargs))
+
+
+def put(url, data=None, json=None, **kwargs) -> Either:
+ """Wrap requests put method with Either monad"""
+ return __wrap_response__(requests.put(url, data=data, json=json, **kwargs))
+
+
+def delete(url, **kwargs) -> Either:
+ """Wrap requests delete method with Either monad"""
+ return __wrap_response__(requests.delete(url, **kwargs))
diff --git a/gn2/wqflask/search_results.py b/gn2/wqflask/search_results.py
index b0f08463..1d89e52a 100644
--- a/gn2/wqflask/search_results.py
+++ b/gn2/wqflask/search_results.py
@@ -2,12 +2,18 @@ import uuid
from math import *
import requests
import unicodedata
+from urllib.parse import urlencode, urljoin
import re
import json
+from pymonad.maybe import Just, Maybe
+from pymonad.tools import curry
+
from flask import g
+from gn3.monads import MonadicDict
+
from gn2.base.data_set import create_dataset
from gn2.base.webqtlConfig import PUBMEDLINK_URL
from gn2.wqflask import parser
@@ -15,11 +21,12 @@ from gn2.wqflask import do_search
from gn2.wqflask.database import database_connection
-from gn2.utility import hmac
from gn2.utility.authentication_tools import check_resource_availability
-from gn2.utility.tools import get_setting, GN2_BASE_URL
+from gn2.utility.hmac import hmac_creation
+from gn2.utility.tools import get_setting, GN2_BASE_URL, GN3_LOCAL_URL
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
@@ -36,6 +43,7 @@ class SearchResultPage:
self.uc_id = uuid.uuid4()
self.go_term = None
+ self.search_type = "sql" # Assume it's an SQL search by default, since all searches will work with SQL
if kw['search_terms_or']:
self.and_or = "or"
@@ -89,7 +97,6 @@ class SearchResultPage:
"""
trait_list = []
- json_trait_list = []
# result_set represents the results for each search term; a search of
# "shh grin2b" would have two sets of results, one for each term
@@ -105,97 +112,137 @@ class SearchResultPage:
if not result:
continue
- 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['symbol'] = "N/A" if result[3] is None else result[3].strip()
- description_text = ""
- if result[4] is not None and str(result[4]) != "":
- description_text = unicodedata.normalize("NFKD", result[4].decode('latin1'))
-
- target_string = result[5].decode('utf-8') if result[5] else ""
- 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[6] is not None) and (result[6] != "") and (result[6] != "Un") and (result[7] is not None) and (result[7] != 0):
- trait_dict['location'] = f"Chr{result[6]}: {float(result[7]):.6f}"
-
- trait_dict['mean'] = "N/A" if result[8] is None or result[8] == "" else f"{result[8]:.3f}"
- trait_dict['additive'] = "N/A" if result[12] is None or result[12] == "" else f"{result[12]:.3f}"
- trait_dict['lod_score'] = "N/A" if result[9] is None or result[9] == "" else f"{float(result[9]) / 4.61:.1f}"
- trait_dict['lrs_location'] = "N/A" if result[13] is None or result[13] == "" or result[14] is None else f"Chr{result[13]}: {float(result[14]):.6f}"
- elif self.dataset.type == "Geno":
- trait_dict['display_name'] = str(result[0])
- trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['display_name'], trait_dict['dataset']))
- trait_dict['location'] = "N/A"
- if (result[4] != "NULL" and result[4] != "") and (result[5] != 0):
- trait_dict['location'] = f"Chr{result[4]}: {float(result[5]):.6f}"
- 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']))
- 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"]):
- continue
-
- if result[10]:
- trait_dict['display_name'] = str(result[10]) + "_" + str(result[0])
- trait_dict['description'] = "N/A"
- trait_dict['pubmed_id'] = "N/A"
- trait_dict['pubmed_link'] = "N/A"
- trait_dict['pubmed_text'] = "N/A"
- trait_dict['mean'] = "N/A"
- trait_dict['additive'] = "N/A"
- pre_pub_description = "N/A" if result[1] is None else result[1].strip()
- post_pub_description = "N/A" if result[2] is None else result[2].strip()
- if result[5] != "NULL" and result[5] != None:
- trait_dict['pubmed_id'] = result[5]
- trait_dict['pubmed_link'] = PUBMEDLINK_URL % trait_dict['pubmed_id']
- trait_dict['description'] = post_pub_description
- else:
- trait_dict['description'] = pre_pub_description
+ if self.search_type == "xapian":
+ # These four lines are borrowed from gsearch.py; probably need to put them somewhere else to avoid duplicated code
+ chr_mb = curry(2, lambda chr, mb: f"Chr{chr}: {mb:.6f}")
+ format3f = lambda x: f"{x:.3f}"
+ hmac = curry(3, lambda trait_name, dataset, data_hmac: f"{trait_name}:{dataset}:{data_hmac}")
+ convert_lod = lambda x: x / 4.61
+
+ trait = MonadicDict(result)
+ trait["index"] = Just(index)
+ trait["display_name"] = trait["name"]
+ trait["location"] = (Maybe.apply(chr_mb)
+ .to_arguments(trait.pop("chr"), trait.pop("mb")))
+ trait["lod_score"] = trait.pop("lrs").map(convert_lod).map(format3f)
+ trait["additive"] = trait["additive"].map(format3f)
+ 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']}"))))
+ elif self.dataset.type == "Publish":
+ inbredsetcode = trait.pop("inbredsetcode")
+ if inbredsetcode.map(len) == Just(3):
+ trait["display_name"] = (Maybe.apply(
+ curry(2, lambda inbredsetcode, name: f"{inbredsetcode}_{name}"))
+ .to_arguments(inbredsetcode, trait["name"]))
+
+ trait["hmac"] = (Maybe.apply(hmac)
+ .to_arguments(trait['name'], trait['dataset'], Just(hmac_creation(f"{trait['name']}:{trait['dataset']}"))))
+ 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)
+ 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'] = f"{trait_dict['display_name']}:{trait_dict['dataset']}:{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]) != "":
+ description_text = unicodedata.normalize("NFKD", result[4].decode('latin1'))
+
+ target_string = result[5].decode('utf-8') if result[5] else ""
+ 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[6] is not None) and (result[6] != "") and (result[6] != "Un") and (result[7] is not None) and (result[7] != 0):
+ trait_dict['location'] = f"Chr{result[6]}: {float(result[7]):.6f}"
+
+ trait_dict['mean'] = "N/A" if result[8] is None or result[8] == "" else f"{result[8]:.3f}"
+ trait_dict['additive'] = "N/A" if result[12] is None or result[12] == "" else f"{result[12]:.3f}"
+ trait_dict['lod_score'] = "N/A" if result[9] is None or result[9] == "" else f"{float(result[9]) / 4.61:.1f}"
+ trait_dict['lrs_location'] = "N/A" if result[13] is None or result[13] == "" or result[14] is None else f"Chr{result[13]}: {float(result[14]):.6f}"
+ elif self.dataset.type == "Geno":
+ trait_dict['display_name'] = str(result[0])
+ trait_dict['hmac'] = f"{trait_dict['display_name']}:{trait_dict['dataset']}:{hmac_creation('{}:{}'.format(trait_dict['display_name'], trait_dict['dataset']))}"
+ trait_dict['location'] = "N/A"
+ if (result[4] != "NULL" and result[4] != "") and (result[5] != 0):
+ trait_dict['location'] = f"Chr{result[4]}: {float(result[5]):.6f}"
+ 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'] = f"{trait_dict['display_name']}:{trait_dict['dataset']}:{hmac_creation('{}:{}'.format(trait_dict['display_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"]):
+ continue
+
+ if result[10]:
+ trait_dict['display_name'] = str(result[10]) + "_" + str(result[0])
+ trait_dict['description'] = "N/A"
+ trait_dict['pubmed_id'] = "N/A"
+ trait_dict['pubmed_link'] = "N/A"
+ trait_dict['pubmed_text'] = "N/A"
+ trait_dict['mean'] = "N/A"
+ trait_dict['additive'] = "N/A"
+ pre_pub_description = "N/A" if result[1] is None else result[1].strip()
+ post_pub_description = "N/A" if result[2] is None else result[2].strip()
+ if result[5] != "NULL" and result[5] != None:
+ trait_dict['pubmed_id'] = result[5]
+ trait_dict['pubmed_link'] = PUBMEDLINK_URL % trait_dict['pubmed_id']
+ trait_dict['description'] = post_pub_description
+ else:
+ trait_dict['description'] = pre_pub_description
- if result[4].isdigit():
- trait_dict['pubmed_text'] = result[4]
+ if result[4].isdigit():
+ trait_dict['pubmed_text'] = result[4]
- trait_dict['authors'] = result[3]
- trait_dict['authors_display'] = trait_dict['authors']
- author_list = trait_dict['authors'].split(",")
- if len(author_list) >= 2:
- trait_dict['authors_display'] = (",").join(author_list[:2]) + ", et al."
+ trait_dict['authors'] = result[3]
+ trait_dict['authors_display'] = trait_dict['authors']
+ author_list = trait_dict['authors'].split(",")
+ if len(author_list) >= 2:
+ trait_dict['authors_display'] = (",").join(author_list[:2]) + ", et al."
- if result[6] != "" and result[6] != None:
- trait_dict['mean'] = f"{result[6]:.3f}"
+ if result[6] != "" and result[6] != None:
+ trait_dict['mean'] = f"{result[6]:.3f}"
- try:
- trait_dict['lod_score'] = f"{float(result[7]) / 4.61:.1f}"
- except:
- trait_dict['lod_score'] = "N/A"
+ try:
+ trait_dict['lod_score'] = f"{float(result[7]) / 4.61:.1f}"
+ except:
+ trait_dict['lod_score'] = "N/A"
- try:
- trait_dict['lrs_location'] = f"Chr{result[11]}: {float(result[12]):.6f}"
- except:
- trait_dict['lrs_location'] = "N/A"
+ try:
+ trait_dict['lrs_location'] = f"Chr{result[11]}: {float(result[12]):.6f}"
+ except:
+ trait_dict['lrs_location'] = "N/A"
- trait_dict['additive'] = "N/A" if not result[8] else f"{result[8]:.3f}"
+ trait_dict['additive'] = "N/A" if not result[8] else f"{result[8]:.3f}"
- trait_dict['trait_info_str'] = trait_info_str(trait_dict, self.dataset.type)
+ trait_dict['trait_info_str'] = trait_info_str(trait_dict, self.dataset.type)
- # Convert any bytes in dict to a normal utf-8 string
- for key in trait_dict.keys():
- if isinstance(trait_dict[key], bytes):
- try:
- trait_dict[key] = trait_dict[key].decode('utf-8')
- except UnicodeDecodeError:
- trait_dict[key] = trait_dict[key].decode('latin-1')
+ # Convert any bytes in dict to a normal utf-8 string
+ for key in trait_dict.keys():
+ if isinstance(trait_dict[key], bytes):
+ try:
+ trait_dict[key] = trait_dict[key].decode('utf-8')
+ except UnicodeDecodeError:
+ trait_dict[key] = trait_dict[key].decode('latin-1')
- trait_list.append(trait_dict)
+ trait_list.append(trait_dict)
if self.results:
self.max_widths = {}
@@ -229,6 +276,42 @@ class SearchResultPage:
"""
self.search_terms = parser.parse(self.search_terms)
+ # Set of terms compatible with Xapian currently (None is a search without a term)
+ xapian_terms = ["POSITION", "MEAN", "LRS", "LOD", "RIF", "WIKI"]
+
+ if all([(the_term['key'] in xapian_terms) or (not the_term['key'] and self.dataset.type != "Publish") for the_term in self.search_terms]):
+ self.search_type = "xapian"
+ self.results = requests.get(generate_xapian_request(self.dataset, self.search_terms, self.and_or)).json()
+ if not len(self.results) or 'error' in self.results:
+ self.results = []
+ self.sql_search()
+ else:
+ self.sql_search()
+
+ def get_search_ob(self, a_search):
+ search_term = a_search['search_term']
+ search_operator = a_search['separator']
+ search_type = {}
+ search_type['dataset_type'] = self.dataset.type
+ if a_search['key']:
+ search_type['key'] = a_search['key'].upper()
+ else:
+ search_type['key'] = None
+
+ search_ob = do_search.DoSearch.get_search(search_type)
+ if search_ob:
+ search_class = getattr(do_search, search_ob)
+ the_search = search_class(search_term,
+ search_operator,
+ self.dataset,
+ search_type['key']
+ )
+ return the_search
+ else:
+ return None
+
+ def sql_search(self):
+ self.search_type = "sql"
combined_from_clause = ""
combined_where_clause = ""
# The same table can't be referenced twice in the from clause
@@ -313,27 +396,6 @@ class SearchResultPage:
if the_search != None:
self.header_fields = the_search.header_fields
- def get_search_ob(self, a_search):
- search_term = a_search['search_term']
- search_operator = a_search['separator']
- search_type = {}
- search_type['dataset_type'] = self.dataset.type
- if a_search['key']:
- search_type['key'] = a_search['key'].upper()
- else:
- search_type['key'] = None
-
- search_ob = do_search.DoSearch.get_search(search_type)
- if search_ob:
- search_class = getattr(do_search, search_ob)
- the_search = search_class(search_term,
- search_operator,
- self.dataset,
- search_type['key']
- )
- return the_search
- else:
- return None
def trait_info_str(trait, dataset_type):
"""Provide a string representation for given trait"""
@@ -431,3 +493,50 @@ def get_alias_terms(symbol, species):
alias_terms.append(the_search_term)
return alias_terms
+
+def generate_xapian_request(dataset, search_terms, and_or):
+ """ Generate the resquest to GN3 which queries Xapian """
+ match dataset.type:
+ case "ProbeSet":
+ search_type = "gene"
+ case "Publish":
+ search_type = "phenotype"
+ case "Geno":
+ search_type = "genotype"
+ case _: # This should never happen
+ raise ValueError(f"Dataset types should only be ProbeSet, Publish, or Geno, not '{dataset.type}'")
+
+ xapian_terms = f" {and_or.upper()} ".join([create_xapian_term(dataset, term) for term in search_terms])
+
+ return urljoin(GN3_LOCAL_URL, "/api/search?" + urlencode({"query": xapian_terms,
+ "type": search_type,
+ "per_page": MAX_SEARCH_RESULTS}))
+
+def create_xapian_term(dataset, term):
+ """ Create Xapian term for each search term """
+ search_term = term['search_term']
+ xapian_term = f"dataset:{dataset.name.lower()} AND "
+ match term['key']:
+ case 'MEAN':
+ return xapian_term + f"mean:{search_term[0]}..{search_term[1]}"
+ case 'POSITION':
+ return xapian_term + f"chr:{search_term[0].lower().replace('chr', '')} AND position:{int(search_term[1])*10**6}..{int(search_term[2])*10**6}"
+ case 'AUTHOR':
+ return xapian_term + f"author:{search_term[0]}"
+ case 'RIF':
+ return xapian_term + f"rif:{search_term[0]}"
+ case 'WIKI':
+ return xapian_term + f"wiki:{search_term[0]}"
+ case 'LRS':
+ xapian_term += f"peak:{search_term[0]}..{search_term[1]}"
+ if len(search_term) == 5:
+ xapian_term += f" AND peakchr:{search_term[2].lower().replace('chr', '')} AND peakmb:{float(search_term[3])}..{float(search_term[4])}"
+ return xapian_term
+ case 'LOD': # Basically just LRS search but all values are multiplied by 4.61
+ xapian_term += f"peak:{float(search_term[0]) * 4.61}..{float(search_term[1]) * 4.61}"
+ if len(search_term) == 5:
+ xapian_term += f" AND peakchr:{search_term[2].lower().replace('chr', '')}"
+ xapian_term += f" AND peakmb:{float(search_term[3])}..{float(search_term[4])}"
+ return xapian_term
+ case None:
+ return xapian_term + f"{search_term[0]}"
diff --git a/gn2/wqflask/show_trait/SampleList.py b/gn2/wqflask/show_trait/SampleList.py
index 64fc8fe6..200ff793 100644
--- a/gn2/wqflask/show_trait/SampleList.py
+++ b/gn2/wqflask/show_trait/SampleList.py
@@ -81,7 +81,8 @@ class SampleList:
sample.extra_attributes['36'].append(
webqtlConfig.RRID_MOUSE_URL % the_rrid)
elif self.dataset.group.species == "rat":
- if len(rrid_string):
+ # Check if it's a list just in case a parent/f1 strain also shows up in the .geno file, to avoid being added twice
+ if len(rrid_string) and not isinstance(sample.extra_attributes['36'], list):
the_rrid = rrid_string.split("_")[1]
sample.extra_attributes['36'] = [
rrid_string]
@@ -131,7 +132,8 @@ class SampleList:
"CaseAttribute, CaseAttributeXRefNew WHERE "
"CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.CaseAttributeId "
"AND CaseAttributeXRefNew.InbredSetId = %s "
- "ORDER BY CaseAttribute.CaseAttributeId", (str(self.dataset.group.id),)
+ "AND CaseAttribute.InbredSetId = %s "
+ "ORDER BY CaseAttribute.CaseAttributeId", (str(self.dataset.group.id),str(self.dataset.group.id))
)
self.attributes = {}
diff --git a/gn2/wqflask/static/new/css/pills.css b/gn2/wqflask/static/new/css/pills.css
new file mode 100644
index 00000000..57c84204
--- /dev/null
+++ b/gn2/wqflask/static/new/css/pills.css
@@ -0,0 +1,25 @@
+a.pill{
+ border: 1px;
+ color: #3071A9;
+ text-decoration: none;
+ border: 1px solid #3071A9;
+ border-radius: 5px;
+ padding: 0.3em;
+ box-shadow: 3px 3px #DEDEDE;
+ text-align: center;
+}
+
+a.pill:active {
+ box-shadow: 1px 1px aquamarine;
+ position: relative;
+ left: 2px;
+ top: 2px;
+}
+
+a.pill:hover {
+ text-decoration: none;
+}
+
+a.pill:focus {
+ text-decoration: none;
+}
diff --git a/gn2/wqflask/static/new/css/resource-roles.css b/gn2/wqflask/static/new/css/resource-roles.css
new file mode 100644
index 00000000..da8d60d3
--- /dev/null
+++ b/gn2/wqflask/static/new/css/resource-roles.css
@@ -0,0 +1,5 @@
+.resource_roles {
+ display: grid;
+ grid-template-columns: 1fr 1fr 1fr 1fr 1fr;
+ grid-gap: 5px;
+}
diff --git a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js
index 99ecb16e..8689af75 100644
--- a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js
+++ b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js
@@ -96,8 +96,8 @@ function display_search_results(data, textStatus, jqXHR) {
* @param {UUID}: The job id to fetch data for
*/
function fetch_search_results(job_id, success, error=default_error_fn) {
- host = $("#frm-search-traits").attr("data-gn-server-url");
- endpoint = host + "auth/data/search/phenotype/" + job_id
+ endpoint = $("#frm-search-traits").attr(
+ "data-pheno-results-template").replace("<jobid>", job_id);
$("#txt-search").prop("disabled", true);
$.ajax(
endpoint,
@@ -119,7 +119,7 @@ function search_phenotypes() {
per_page = document.getElementById("txt-per-page").value
search_table = new TableDataSource(
"#tbl-phenotypes", "data-traits", search_checkbox);
- endpoint = "/auth/data/phenotype/search"
+ endpoint = endpoint = $("#frm-search-traits").attr("data-search-endpoint");
$.ajax(
endpoint,
{
diff --git a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 44076c17..970a49a3 100644
--- a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -141,7 +141,7 @@ buildColumns = function() {
columnList.push(
{
'title': "<div title='" + js_data.attributes[attrKeys[i]].description + "' style='text-align: " + js_data.attributes[attrKeys[i]].alignment + "'>" + js_data.attributes[attrKeys[i]].name + "</div>",
- 'type': "natural",
+ 'type': "natural-minus-na",
'data': null,
'targets': attrStart + i,
'render': function(data, type, row, meta) {
diff --git a/gn2/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js
index c263ef49..c89b4ce3 100644
--- a/gn2/wqflask/static/new/javascript/search_results.js
+++ b/gn2/wqflask/static/new/javascript/search_results.js
@@ -309,7 +309,7 @@ $(function() {
return submit_special("/loading")
});
- $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() {
+ $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver, #send_to_genecup").on("click", function() {
traits = getTraitsFromTable()
$("#trait_list").val(traits)
url = $(this).data("url")
@@ -325,53 +325,6 @@ $(function() {
$("#export_traits").click(exportTraits);
$("#export_collection").click(exportCollection);
- let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
- let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
-
- let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
-
- function extractInnerText(the_string){
- var span = document.createElement('span');
- span.innerHTML = the_string;
- return span.textContent || span.innerText;
- }
-
- function sortNAs(a, b, sort_function){
- if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
- return 0;
- }
- if (na_equivalent_vals.includes(a)){
- return 1
- }
- if (na_equivalent_vals.includes(b)) {
- return -1;
- }
- return sort_function(a, b)
- }
-
- $.extend( $.fn.dataTableExt.oSort, {
- "natural-minus-na-asc": function (a, b) {
- return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc)
- },
- "natural-minus-na-desc": function (a, b) {
- return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc)
- }
- });
-
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
applyDefault = function() {
let default_collection_id = $.cookie('default_collection');
if (default_collection_id) {
diff --git a/gn2/wqflask/static/new/javascript/table_functions.js b/gn2/wqflask/static/new/javascript/table_functions.js
index 62888cd9..a648778e 100644
--- a/gn2/wqflask/static/new/javascript/table_functions.js
+++ b/gn2/wqflask/static/new/javascript/table_functions.js
@@ -88,3 +88,50 @@ function saveColumnSettings(tableId, traitTable) {
// Save (or update) the settings in localStorage
localStorage.setItem(tableId, JSON.stringify(userColumnDefs));
}
+
+let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
+let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
+
+let na_equivalent_vals = ["N/A", "--", "", "NULL"]; //ZS: Since there are multiple values that should be treated the same as N/A
+
+function extractInnerText(the_string){
+ var span = document.createElement('span');
+ span.innerHTML = the_string;
+ return span.textContent || span.innerText;
+}
+
+function sortNAs(a, b, sort_function){
+ if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
+ return 0;
+ }
+ if (na_equivalent_vals.includes(a)){
+ return 1
+ }
+ if (na_equivalent_vals.includes(b)) {
+ return -1;
+ }
+ return sort_function(a, b)
+}
+
+$.extend( $.fn.dataTableExt.oSort, {
+ "natural-minus-na-asc": function (a, b) {
+ return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc)
+ },
+ "natural-minus-na-desc": function (a, b) {
+ return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc)
+ }
+});
+
+$.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
+{
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $('input', td).prop('checked') ? '1' : '0';
+ } );
+};
+
+$.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
+{
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $(td).text();
+ } );
+} \ No newline at end of file
diff --git a/gn2/wqflask/templates/base.html b/gn2/wqflask/templates/base.html
index 26b75230..6c545646 100644
--- a/gn2/wqflask/templates/base.html
+++ b/gn2/wqflask/templates/base.html
@@ -188,7 +188,7 @@
</span>
<span style="padding: 5px;margin-left: 65px;" >
- <a style="text-decoration: none" target="_blank" href="https://issues.genenetwork.org/topics/xapian/xapian-search-queries">
+ <a style="text-decoration: none" target="_blank" href="/search-syntax">
<i style="text-align: center;color:#336699;;" class="fa fa-question-circle fa-2x" title="see more search hints" aria-hidden="true"></i>
</a>
</span>
diff --git a/gn2/wqflask/templates/collections/list.html b/gn2/wqflask/templates/collections/list.html
index c3d5d2a4..dc725fb6 100644
--- a/gn2/wqflask/templates/collections/list.html
+++ b/gn2/wqflask/templates/collections/list.html
@@ -57,8 +57,8 @@
<td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
<td align="right">{{ loop.index }}
<td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
- <td>{{ uc.created_timestamp }}</td>
- <td>{{ uc.changed_timestamp }}</td>
+ <td>{{ uc.created }}</td>
+ <td>{{ uc.changed }}</td>
<td align="right">{{ uc.num_members }}</td>
</tr>
{% endfor %}
@@ -88,8 +88,8 @@
<td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
<td align="right">{{ loop.index }}
<td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
- <td>{{ uc.created_timestamp }}</td>
- <td>{{ uc.changed_timestamp }}</td>
+ <td>{{ uc.created }}</td>
+ <td>{{ uc.changed }}</td>
<td align="right">{{ uc.num_members }}</td>
</tr>
{% endfor %}
diff --git a/gn2/wqflask/templates/collections/view.html b/gn2/wqflask/templates/collections/view.html
index 7e74442f..55669f09 100644
--- a/gn2/wqflask/templates/collections/view.html
+++ b/gn2/wqflask/templates/collections/view.html
@@ -214,9 +214,9 @@
'render': function(data) {
if (Object.hasOwn(data, 'description')){
try {
- return decodeURIComponent(escape(data.description))
+ return decodeURIComponent(data.description)
} catch(err){
- return escape(data.description)
+ return data.description
}
} else if (Object.hasOwn(data, 'location')){
return data.location
diff --git a/gn2/wqflask/templates/correlation_page.html b/gn2/wqflask/templates/correlation_page.html
index 24eaff1f..07118145 100644
--- a/gn2/wqflask/templates/correlation_page.html
+++ b/gn2/wqflask/templates/correlation_page.html
@@ -69,8 +69,8 @@
<input type="text" name="r_less_select" value="1.0" size="6" maxlength="10">, with mean >
<input type="text" name="mean_greater_select" value="0" size="6" maxlength="10">
<select id="mean_and_or" size="1">
- <option value="and" selected>AND</option>
- <option value="or">OR</option>
+ <option value="and">AND</option>
+ <option value="or" selected>OR</option>
</select>
mean <
<input type="text" name="mean_less_select" value="100" size="6" maxlength="10">
diff --git a/gn2/wqflask/templates/dataset.html b/gn2/wqflask/templates/dataset.html
index 096a3724..62fac650 100644
--- a/gn2/wqflask/templates/dataset.html
+++ b/gn2/wqflask/templates/dataset.html
@@ -40,31 +40,6 @@
.panel-metadata dt::after {
content: ":";
}
-
- .search {
- width: 50%;
- margin: 1em auto;
- }
- .has-search .form-control-feedback {
- right: initial;
- left: 0;
- color: #ccc;
- }
-
- .has-search .form-control {
- padding-right: 12px;
- padding-left: 34px;
- }
-
- .search {
- transform: scale(1.5, 1.5);
- }
- .search input {
- min-width: 17em;
- }
- .dataset-search {
- padding: 0 17%;
- }
</style>
{% endblock %}
@@ -348,7 +323,7 @@
</div>
{% else %}
-<div class="container dataset-search">
+<div class="container">
<p class="lead">We appreciate your interest, but unfortunately, we don't have any additional information available for: <strong>{{ name }}</strong>. If you have other inquiries or need assistance with something else, please don't hesitate to get in touch with us.
</div>
diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html
index 8b50fe43..b3bc74fd 100644
--- a/gn2/wqflask/templates/gnqa.html
+++ b/gn2/wqflask/templates/gnqa.html
@@ -93,7 +93,7 @@
AI Search
<small>
<sup>
- <button class="search-hist-btn" hx-get="/gnqna/hist/" hx-target="#swap" hx-swap="innerHTML" >
+ <button class="search-hist-btn" hx-get="/gnqna/hist" hx-target="#swap" hx-swap="innerHTML">
[Search History]
</button>
</sup>
@@ -107,7 +107,7 @@
<button class="btn btn-default btn-sm col-xs-1 col-sm-1 col-sm-offset-3"
hx-post="/gnqna"
hx-target="#swap"
- hx-swap="innerHTML"
+ hx-swap="innerHTML"
hx-indicator="#indicator">
<i class="fa fa-search fa-3x" aria-hidden="true" title="Search"></i>
<img id="indicator" class="htmx-indicator" src="/static/gif/loader.gif"/>
diff --git a/gn2/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html
index 0ddcfde7..41c1b338 100644
--- a/gn2/wqflask/templates/gnqa_answer.html
+++ b/gn2/wqflask/templates/gnqa_answer.html
@@ -3,10 +3,10 @@
<div class="row container gnqa-answer" style="margin-bottom: 1em">
<p class="row lead">
<mark style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;"><b><i>{{ query }}</i></b></mark><br/>
- {{ answer }}
+ {{ answer|safe }}
</p>
<div class="rating row" data-doc-id="{{query}}">
- <button class="btn" id="upvote" data-toggle="tooltip" data-placement="top" title="Vote Up"><i class="fa fa-thumbs-up fa-sm fa-1x" aria-hidden="true"></i></button>
+ <button class="btn" id="upvote" data-toggle="tooltip" data-placement="top" title="Vote Up"><i class="fa fa-thumbs-up fa-sm fa-1x" aria-hidden="true"></i></button>
<button class="btn" id="downvote" data-toggle="tooltip" data-placement="top" title="Vote Down"><i class="fa fa-thumbs-down fa-sm fa-1x" aria-hidden="true"></i></button>
<sub id="rate" class="text-info">
</sub>
@@ -32,7 +32,7 @@
</div>
<div id="collapse{{reference.doc_id}}" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading{{reference.doc_id}}">
<div class="panel-body">
- <p class="node-references">{{ reference.comboTxt }}</p>
+ <p class="node-references">{{ reference.comboTxt|safe }}</p>
<div>
{% if reference.pubmed %}
<details open>
@@ -60,7 +60,7 @@
</div>
<div id="collapse{{reference.doc_id}}" class="panel-collapse collapse" role="tabpanel" aria-labelledby="heading{{reference.doc_id}}">
<div class="panel-body">
- <p class="node-references">{{reference.comboTxt}}</p>
+ <p class="node-references">{{ reference.comboTxt|safe }}</p>
<div>
{% if reference.pubmed %}
<details >
@@ -93,20 +93,27 @@
{% block js %}
<script>
+ function updateRatingHandler(target, responseObj, args){
+ let {status, response} = responseObj.xhr
+ if (status==200 && args == "upvote"){
+ htmx.toggleClass(htmx.find('#upvote'), 'btn-success');
+ htmx.removeClass(htmx.find("#downvote"), "btn-danger");
+ }
+ else if(status == 200 && args == "downvote") {
+ htmx.toggleClass(htmx.find('#downvote'), 'btn-danger');
+ htmx.removeClass(htmx.find("#upvote"), "btn-success");
+ }
+ else {
+ alert(`Error occurred with status ${status} and Error ${response}` )
+}}
var query = {{ query|tojson }};
var answer = {{ answer|tojson }}
var {task_id} = {{ task_id|tojson }}
- htmx.on("#upvote", "click", function(evt){
+htmx.on("#upvote", "click", function(evt){
vote_count = htmx.find(".btn-success") ? 0 : 1
- htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", swap:"innerHTML",values: {'query': query, 'answer': answer}}).then(()=>{
- htmx.toggleClass(htmx.find('#upvote'), 'btn-success');
- htmx.removeClass(htmx.find("#downvote"), "btn-danger");
-})});
+ htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", handler: (target,obj)=> updateRatingHandler(target,obj,"upvote"), swap:"innerHTML",values: {'query': query, 'answer': answer}})});
htmx.on("#downvote", "click", function(evt){
vote_count = htmx.find(".btn-danger") ? 0 : -1
- htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", swap:"innerHTML",values: {'query': query, 'answer': answer}}).then(()=>{
- htmx.toggleClass(htmx.find('#downvote'), 'btn-danger');
- htmx.removeClass(htmx.find("#upvote"), "btn-success")
- })});
+ htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate",handler: (target,obj)=> updateRatingHandler(target,obj,"downvote") , swap:"innerHTML",values: {'query': query, 'answer': answer}})});
</script>
{% endblock %}
diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html
index 2c07b8c0..976fd7fd 100644
--- a/gn2/wqflask/templates/gnqa_search_history.html
+++ b/gn2/wqflask/templates/gnqa_search_history.html
@@ -1,42 +1,52 @@
-<section class="container-fluid gnqa-copy">
+<section class="container-fluid gnqa-copy" id="search-hist">
<header class="row">
-
<div class="panel panel default col-sm-6 col-sm-offset-3">
<div class="panel panel-default">
<div class="panel-heading">
<div>
- <h4 class="text-primary">You search History </h4>
+ <h4 class="text-secondary" style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;font-size:2.3rem">Your AI search History </h4>
</div>
</div>
</div>
</div>
</header>
<div class="container row">
- <div class="panel panel-default col-sm-6 col-sm-offset-3 ">
- {% for record in prev_queries %}
- <div class="panel-body">
- <div class="row">
- <input name="" type="checkbox" value="" class="col-sm-1">
+ <div>
+ <div class="col-sm-6 col-sm-offset-3" style="margin-bottom:10px">
+ <button type="button" class="btn btn-danger" id="delete-btn">Delete Selected </button>
+ </div>
+ <div >
+ <div class="panel panel-default col-sm-6 col-sm-offset-3 ">
+ <div>
+ <ul class="list-group list-group-flush" style="overflow-y:scroll">
+ {% for item in prev_queries %}
+ <li class="row list-group-item">
+ <input name="" type="checkbox" value="{{item['task_id']}}" class="col-sm-1" style="height: 20px;
+ width: 20px;">
<div class="col-sm-10">
- {% for id,val in record.items() %}
<button
- hx-get="/gnqna/hist/search/{{id}}"
+ hx-get="/gnqna/hist?query={{item['query']}}&search_term={{item['task_id']}}"
hx-target="#swap"
hx-swap="innerHTML"
hx-trigger= "click"
data-bs-toggle="tooltip"
data-bs-placement="left"
- title="/gnqna/hist/search?{{id}}"
+ title="/gnqna/hist?query={{item['query']}}&search_term={{item['task_id']}}"
style="background:transparent;border:none;cursor:pointer"
>
- <b class="text-info">{{val}} </b>
+ <p class="text-info">{{item.get('query')}} </p>
</button>
- {% endfor %}
- </div>
- </div>
- </div>
- {% endfor %}
+ </div>
+ </li>
+ {% endfor %}
+ </ul>
</div>
</div>
</div>
- </section>
+</section>
+<script>
+ htmx.on("#delete-btn", "click", function(evt){
+ htmx.ajax("DELETE","/gnqna/hist", {target: "#search-hist","swap" :"outerHTML",
+ values: Array.from(htmx.findAll("input[type=checkbox]:checked"), e => e.value)})
+ })
+</script>
diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html
index 50b48401..3432662d 100644
--- a/gn2/wqflask/templates/gsearch_gene.html
+++ b/gn2/wqflask/templates/gsearch_gene.html
@@ -258,8 +258,12 @@
"scroller": true
{% endif %}
}
-
- create_table(tableId, traitsJson, columnDefs, tableSettings);
+
+ if (traitsJson.length > 0) {
+ create_table(tableId, traitsJson, columnDefs, tableSettings);
+ } else {
+ $("#" + tableId +" td").replaceWith("<td>No data</td>")
+ }
});
diff --git a/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html b/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html
new file mode 100644
index 00000000..988cf3b4
--- /dev/null
+++ b/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html
@@ -0,0 +1,34 @@
+{%extends "base.html"%}
+{%from "oauth2/profile_nav.html" import profile_nav%}
+{%from "oauth2/display_error.html" import display_error%}
+{%block title%}View User{%endblock%}
+{%block content%}
+<div class="container">
+ {{profile_nav(uipages, user_privileges)}}
+ {{flash_me()}}
+
+ <form id="frm_confirm_resource_role_unassign_privilege"
+ method="POST"
+ action="{{url_for('oauth2.resource.unassign_privilege_from_resource_role',
+ resource_id=resource.resource_id,
+ role_id=role.role_id)}}">
+ <p>
+ Are you sure you want to unassign the privilege to
+ '{{privilege.privilege_description}}' from the role '{{role.role_name}}'
+ on resource '{{resource.resource_name}}'?</p>
+ <input type="hidden"
+ name="privilege_id"
+ value="{{privilege.privilege_id}}" />
+
+ <input type="submit"
+ name="confirm"
+ value="Cancel"
+ class="btn btn-success" />
+
+ <input type="submit"
+ name="confirm"
+ value="Unassign"
+ class="btn btn-danger" />
+ </form>
+</div>
+{%endblock%}
diff --git a/gn2/wqflask/templates/oauth2/create-role.html b/gn2/wqflask/templates/oauth2/create-role.html
index f2bff7b4..6cf0bb78 100644
--- a/gn2/wqflask/templates/oauth2/create-role.html
+++ b/gn2/wqflask/templates/oauth2/create-role.html
@@ -7,31 +7,43 @@
{{profile_nav("roles", user_privileges)}}
<h3>Create Role</h3>
- {{flash_me()}}
+ <p>Create a new role to act on resource "{{resource.resource_name}}"</p>
- {%if group_privileges_error is defined%}
- {{display_error("Group Privileges", group_privileges_error)}}
+ {%if resource_role_error is defined%}
+ {{display_error("Resource Role", resource_role_error)}}
{%else%}
- {%if "group:role:create-role" in user_privileges%}
- <form method="POST" action="{{url_for('oauth2.role.create_role')}}">
- <legend>Create Group Role</legend>
+ {%if "resource:role:create-role" in (user_privileges|map(attribute="privilege_id")) %}
+ <form method="POST" action="{{url_for('oauth2.resource.create_resource_role',
+ resource_id=resource.resource_id)}}">
+ <legend>create resource role</legend>
+
+ {{flash_me()}}
+
<div class="form-group">
<label for="role_name" class="form-label">Name</label>
- <input type="text" id="role_name" name="role_name" required="required"
- class="form-control"
- {%if prev_role_name is defined and prev_role_name is not none%}
- value="{{prev_role_name}}"
- {%endif%} />
+ <div class="input-group">
+ <span class="input-group-addon">
+ {{resource.resource_name|replace(" ", "_")}}::
+ </span>
+ <input type="text" id="role_name" name="role_name" required="required"
+ class="form-control"
+ {%if prev_role_name is defined and prev_role_name is not none%}
+ value="{{prev_role_name}}"
+ {%endif%} />
+ </div>
+ <span class="form-text text-muted">
+ The name of the role will have the resource's name appended.
+ </span>
</div>
<label class="form-label">Privileges</label>
- {%for priv in group_privileges%}
+ {%for priv in user_privileges%}
<div class="checkbox">
- <label for="chk:{{priv.privilege_id}}">
- <input type="checkbox" id="chk:{{priv.privilege_id}}"
+ <label for="chk-{{priv.privilege_id}}">
+ <input type="checkbox" id="chk-{{priv.privilege_id}}"
name="privileges[]" value={{priv.privilege_id}} />
<span style="text-transform: capitalize;">
{{priv.privilege_description}}
- </span> ({{priv.privilege_id}})
+ </span>
</label>
</div>
{%endfor%}
diff --git a/gn2/wqflask/templates/oauth2/data-list-mrna.html b/gn2/wqflask/templates/oauth2/data-list-mrna.html
index 728e95d4..c5c1c27e 100644
--- a/gn2/wqflask/templates/oauth2/data-list-mrna.html
+++ b/gn2/wqflask/templates/oauth2/data-list-mrna.html
@@ -92,7 +92,7 @@
<div class="row">
<span id="search-messages" class="alert-danger" style="display:none"></span>
<form id="frm-search"
- action="{{search_uri}}"
+ action="{{url_for('oauth2.data.json_search_mrna')}}"
method="POST">
<legend>Search: mRNA Assay</legend>
<input type="hidden" value="{{species_name}}" name="species"
diff --git a/gn2/wqflask/templates/oauth2/data-list-phenotype.html b/gn2/wqflask/templates/oauth2/data-list-phenotype.html
index e5172c70..d355f3f9 100644
--- a/gn2/wqflask/templates/oauth2/data-list-phenotype.html
+++ b/gn2/wqflask/templates/oauth2/data-list-phenotype.html
@@ -113,7 +113,8 @@
<form id="frm-search-traits"
action="#"
method="POST"
- data-gn-server-url="{{gn_server_url}}">
+ data-search-endpoint="{{search_endpoint}}"
+ data-pheno-results-template="{{pheno_results_template}}">
{%if dataset_type == "mrna"%}
<legend>mRNA: Search</legend>
{%else%}
diff --git a/gn2/wqflask/templates/oauth2/profile_nav.html b/gn2/wqflask/templates/oauth2/profile_nav.html
index aa752905..c79bccbc 100644
--- a/gn2/wqflask/templates/oauth2/profile_nav.html
+++ b/gn2/wqflask/templates/oauth2/profile_nav.html
@@ -17,13 +17,6 @@
</li>
<li role="presentation"
- {%if calling_page == "roles"%}
- class="active"
- {%endif%}>
- <a href="{{url_for('oauth2.role.user_roles')}}">Roles</a>
- </li>
-
- <li role="presentation"
{%if calling_page == "resources"%}
class="active"
{%endif%}>
diff --git a/gn2/wqflask/templates/oauth2/view-group-role.html b/gn2/wqflask/templates/oauth2/view-group-role.html
deleted file mode 100644
index 5da023bf..00000000
--- a/gn2/wqflask/templates/oauth2/view-group-role.html
+++ /dev/null
@@ -1,102 +0,0 @@
-{%extends "base.html"%}
-{%from "oauth2/profile_nav.html" import profile_nav%}
-{%from "oauth2/display_error.html" import display_error%}
-{%block title%}View User{%endblock%}
-{%block content%}
-<div class="container" style="min-width: 1250px;">
- {{profile_nav("roles", user_privileges)}}
- <h3>View Group Role</h3>
-
- {{flash_me()}}
-
- <div class="container-fluid">
- <div class="row">
- <h3>Role Details</h3>
- {%if group_role_error is defined%}
- {{display_error("Group Role", group_role_error)}}
- {%else%}
- <table class="table">
- <caption>Details for '{{group_role.role.role_name}}' Role</caption>
- <thead>
- <tr>
- <th>Privilege</th>
- <th>Description</th>
- <th>Action</th>
- </tr>
- </thead>
- <tbody>
- {%for privilege in group_role.role.privileges%}
- <tr>
- <td>{{privilege.privilege_id}}</td>
- <td>{{privilege.privilege_description}}</td>
- <td>
- <form action="{{url_for(
- 'oauth2.group.delete_privilege_from_role',
- group_role_id=group_role.group_role_id)}}"
- method="POST">
- <input type="hidden" name="privilege_id"
- value="{{privilege.privilege_id}}" />
- <input type="submit" class="btn btn-danger"
- value="Remove"
- {%if not group_role.role.user_editable%}
- disabled="disabled"
- {%endif%} />
- </form>
- </td>
- </tr>
- {%endfor%}
- </tbody>
- </table>
- {%endif%}
- </div>
-
- <div class="row">
- <h3>Other Privileges</h3>
- <table class="table">
- <caption>Other Privileges not Assigned to this Role</caption>
- <thead>
- <tr>
- <th>Privilege</th>
- <th>Description</th>
- <th>Action</th>
- </tr>
- </thead>
-
- <tbody>
- {%for priv in group_privileges%}
- <tr>
- <td>{{priv.privilege_id}}</td>
- <td>{{priv.privilege_description}}</td>
- <td>
- <form action="{{url_for(
- 'oauth2.group.add_privilege_to_role',
- group_role_id=group_role.group_role_id)}}"
- method="POST">
- <input type="hidden" name="privilege_id"
- value="{{priv.privilege_id}}" />
- <input type="submit" class="btn btn-warning"
- value="Add to Role"
- {%if not group_role.role.user_editable%}
- disabled="disabled"
- {%endif%} />
- </form>
- </td>
- </tr>
- {%else%}
- <tr>
- <td colspan="3">
- <span class="glyphicon glyphicon-info-sign text-info">
- </span>
- &nbsp;
- <span class="text-info">All privileges assigned!</span>
- </td>
- </tr>
- {%endfor%}
- </tbody>
- </table>
- </div>
-
- </div>
-
-</div>
-{%endblock%}
diff --git a/gn2/wqflask/templates/oauth2/view-resource-role.html b/gn2/wqflask/templates/oauth2/view-resource-role.html
new file mode 100644
index 00000000..4bd0ab45
--- /dev/null
+++ b/gn2/wqflask/templates/oauth2/view-resource-role.html
@@ -0,0 +1,149 @@
+{%extends "base.html"%}
+{%from "oauth2/profile_nav.html" import profile_nav%}
+{%from "oauth2/display_error.html" import display_error%}
+{%block title%}View User{%endblock%}
+{%block content%}
+
+{%macro unassign_button(resource_id, role_id, privilege_id)%}
+<form method="GET"
+ action="{{url_for('oauth2.resource.unassign_privilege_from_resource_role',
+ resource_id=resource_id,
+ role_id=role_id)}}"
+ id="frm_unlink_privilege_{{privilege_id}}">
+ <input type="hidden" name="resource_id" value="{{resource_id}}" />
+ <input type="hidden" name="role_id" value="{{role_id}}" />
+ <input type="hidden" name="privilege_id" value="{{privilege_id}}" />
+ <input type="submit" value="Unassign" class="btn btn-danger" />
+</form>
+{%endmacro%}
+
+<div class="container">
+ <div class="row">
+ {{profile_nav(uipages, user_privileges)}}
+ {{flash_me()}}
+ {%if resource_error is defined%}
+ {{display_error("Resource", resource_error)}}
+ {%else%}
+ <h3>Role for Resource '{{resource.resource_name}}'</h3>
+ {%if role_error is defined%}
+ {{display_error("Role", role_error)}}
+ {%else%}
+ <table class="table">
+ <caption>Role '{{role.role_name}}' for resource '{{resource.resource_name}}'</caption>
+ <thead>
+ <tr>
+ <th>Role Name</th>
+ <th>Privilege</th>
+ <th>Action</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for priv in role.privileges%}
+ {%if loop.index0 == 0%}
+ <tr>
+ <td rowspan="{{role.privileges | length}}"
+ style="text-align: center;vertical-align: middle;">
+ {{role.role_name}}</td>
+ <td>{{priv.privilege_description}}</td>
+ <td>{{unassign_button(resource.resource_id, role.role_id, priv.privilege_id)}}</td>
+ </tr>
+ {%else%}
+ <tr>
+ <td>{{priv.privilege_description}}</td>
+ <td>{{unassign_button(resource.resource_id, role.role_id, priv.privilege_id)}}</td>
+ </tr>
+ {%endif%}
+ {%else%}
+ <tr>
+ <td colspan="3">
+ <p class="text-info">
+ <span class="glyphicon glyphicon-info-sign text-info"></span>
+ &nbsp;
+ This role has no privileges.
+ </p>
+ </td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+ </div>
+
+ <div class="row">
+ <form id="frm_assign_privileges" method="POST" action="#">
+ <input type="hidden" name="resource_id" value="{{resource_id}}" />
+ <input type="hidden" name="role_id" value="{{role_id}}" />
+ {%if unassigned_privileges | length == 0%}
+ <p class="text-info">
+ <strong>{{title}}</strong>:
+ <span class="glyphicon glyphicon-info-sign text-info"></span>
+ &nbsp;
+ There are no more privileges left to assign.
+ </p>
+ {%else%}
+ <fieldset>
+ <legend>Select privileges to assign to this role</legend>
+ {%for priv in unassigned_privileges%}
+ <div class="checkbox">
+ <label for="rdo_{{priv.privilege_id}}">
+ <input type="checkbox" value="{{priv.privilege_id}}" />
+ {{priv.privilege_description}}
+ </label>
+ </div>
+ {%endfor%}
+ </fieldset>
+
+ <input type="submit" class="btn btn-primary" value="Assign" />
+ {%endif%}
+ </form>
+ </div>
+
+ {%if user_error is defined%}
+ {{display_error("Users", user_error)}}
+ {%endif%}
+
+ {%if users is defined and users | length > 0%}
+ <div class="row">
+ <h3>Users</h3>
+
+ <table class="table">
+ <caption>
+ Users assigned role '{{role.role_name}}' on resource
+ '{{resource.resource_name}}'
+ </caption>
+
+ <thead>
+ <tr>
+ <th>Email</th>
+ <th>Name</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for user in users%}
+ <tr>
+ <td>{{user.email}}</td>
+ <td>{{user.name}}</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+ </div>
+ {%endif%}
+
+ {%if users is defined and users | length == 0%}
+ <div class="row">
+ <h3>Delete this role</h3>
+ <p class="text-danger">
+ <strong>Delete Role</strong>:
+ <span class="glyphicon glyphicon-exclamation-sign text-danger"></span>
+ &nbsp;
+ This will delete this role, and you will no longer have access to it.
+ </p>
+ </div>
+ {%endif%}
+ {%endif%}
+ {%endif%}
+</div>
+
+{%endblock%}
diff --git a/gn2/wqflask/templates/oauth2/view-resource.html b/gn2/wqflask/templates/oauth2/view-resource.html
index 275fcb24..0788e30c 100644
--- a/gn2/wqflask/templates/oauth2/view-resource.html
+++ b/gn2/wqflask/templates/oauth2/view-resource.html
@@ -2,6 +2,10 @@
{%from "oauth2/profile_nav.html" import profile_nav%}
{%from "oauth2/display_error.html" import display_error%}
{%block title%}View User{%endblock%}
+{%block css%}
+<link rel="stylesheet" href="/static/new/css/pills.css" />
+<link rel="stylesheet" href="/static/new/css/resource-roles.css" />
+{%endblock%}
{%block content%}
<div class="container" style="min-width: 1250px;">
{{profile_nav("resources", user_privileges)}}
@@ -230,7 +234,27 @@
</div>
<div class="row">
- <h3>User Roles</h3>
+ <h3>Available Resource Roles</h3>
+ <div class="resource_roles">
+ {%for role in resource_roles%}
+ <a class="pill"
+ href="{{url_for('oauth2.resource.view_resource_role',
+ resource_id=resource.resource_id,
+ role_id=role.role_id)}}"
+ title="Role page for role named '{{role.role_name}}'">
+ {{role.role_name}}
+ </a>
+ {%endfor%}
+ </div>
+ <hr />
+ <a title="create a new role for this resource"
+ href="{{url_for('oauth2.resource.create_resource_role',
+ resource_id=resource.resource_id)}}"
+ class="btn btn-info">New Role</a>
+ </div>
+
+ <div class="row">
+ <h3>Users: Assigned Roles</h3>
{%if users_n_roles_error is defined%}
{{display_error("Users and Roles", users_n_roles_error)}}
{%else%}
@@ -254,14 +278,14 @@
<th>Role</th>
<th>Action</th>
</tr>
- {%for grole in user_row.roles%}
+ {%for role in user_row.roles%}
<tr>
<td>
<a href="{{url_for(
'oauth2.role.role',
- role_id=grole.role_id)}}"
- title="Details for '{{grole.role_name}}' role">
- {{grole.role_name}}
+ role_id=role.role_id)}}"
+ title="Details for '{{role.role_name}}' role">
+ {{role.role_name}}
</a>
</td>
<td>
@@ -270,8 +294,8 @@
method="POST">
<input type="hidden" name="user_id"
value="{{user_row.user.user_id}}" />
- <input type="hidden" name="group_role_id"
- value="{{grole.group_role_id}}">
+ <input type="hidden" name="role_id"
+ value="{{role.role_id}}">
<input type="submit"
value="Unassign"
class="btn btn-danger"
@@ -301,8 +325,8 @@
<div class="row">
<h3>Assign</h3>
- {%if group_roles_error is defined%}
- {{display_error("Group Roles", group_roles_error)}}
+ {%if resource_roles_error is defined%}
+ {{display_error("Resource Roles", resource_roles_error)}}
{%elif users_error is defined%}
{{display_error("Users", users_error)}}
{%else%}
@@ -312,13 +336,13 @@
method="POST" autocomplete="off">
<input type="hidden" name="resource_id" value="{{resource_id}}" />
<div class="form-group">
- <label for="group_role_id" class="form-label">Role</label>
- <select class="form-control" name="group_role_id"
- id="group_role_id" required="required">
- <option value="">Select role</option>
- {%for grole in group_roles%}
- <option value="{{grole.group_role_id}}">
- {{grole.role.role_name}}
+ <label for="role_id" class="form-label">Role</label>
+ <select class="form-control" name="role_id"
+ id="role_id" required="required">
+ <option value="">Select role</option>>
+ {%for rrole in resource_roles%}
+ <option value="{{rrole.role_id}}">
+ {{rrole.role_name}}
</option>
{%endfor%}
</select>
diff --git a/gn2/wqflask/templates/search-syntax.html b/gn2/wqflask/templates/search-syntax.html
new file mode 100644
index 00000000..52538826
--- /dev/null
+++ b/gn2/wqflask/templates/search-syntax.html
@@ -0,0 +1,24 @@
+{% extends "base.html" %}
+
+{% block title %}Global Search Syntax{% endblock %}
+
+{% block css %}
+<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
+{% endblock %}
+
+{% block content %}
+
+ <div class="github-btn-container">
+ <div class="github-btn">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/search/xapian_syntax.md">
+ Edit Text
+ <img src="/static/images/edit.png">
+ </a>
+ </div>
+</div>
+<div id="markdown" class="container">
+ {{ rendered_markdown|safe }}
+
+</div>
+
+{% endblock %} \ No newline at end of file
diff --git a/gn2/wqflask/templates/search_result_page.html b/gn2/wqflask/templates/search_result_page.html
index 934b6a9d..fccda1ae 100644
--- a/gn2/wqflask/templates/search_result_page.html
+++ b/gn2/wqflask/templates/search_result_page.html
@@ -224,7 +224,8 @@
'type': "natural",
'width': "{{ max_widths.symbol * 8 }}px",
'targets': 3,
- 'data': "symbol"
+ 'data': "symbol",
+ 'defaultContent': "N/A"
},
{
'title': "Description",
@@ -237,9 +238,9 @@
description = data.description.slice(0, 200) + '...'
}
try {
- return decodeURIComponent(escape(description))
+ return decodeURIComponent(description)
} catch(err){
- return escape(description)
+ return description
}
}
},
@@ -248,14 +249,16 @@
'type': "natural-minus-na",
'width': "130px",
'targets': 5,
- 'data': "location"
+ 'data': "location",
+ 'defaultContent': "N/A"
},
{
'title': "<div style='text-align: right;'>Mean</div>",
'type': "natural-minus-na",
'width': "40px",
- 'data': "mean",
'targets': 6,
+ 'data': "mean",
+ 'defaultContent': "N/A",
'orderSequence': [ "desc", "asc"]
},
{
@@ -279,6 +282,7 @@
'data': "additive",
'width': "65px",
'targets': 9,
+ 'defaultContent': "N/A",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Publish' %},
{
@@ -294,6 +298,7 @@
{
'title': "Description",
'type': "natural",
+ 'width': "500px",
'data': null,
'targets': 3,
'render': function(data) {
@@ -302,9 +307,9 @@
description = data.description.slice(0, 200) + '...'
}
try {
- return decodeURIComponent(escape(description))
+ return decodeURIComponent(description)
} catch(err){
- return escape(description)
+ return description
}
}
},
@@ -312,8 +317,9 @@
'title': "<div style='text-align: right;'>Mean</div>",
'type': "natural-minus-na",
'width': "60px",
- 'data': "mean",
'targets': 4,
+ 'data': "mean",
+ 'defaultContent': "N/A",
'orderSequence': [ "desc", "asc"]
},
{
diff --git a/gn2/wqflask/templates/show_trait_transform_and_filter.html b/gn2/wqflask/templates/show_trait_transform_and_filter.html
index e61e1248..8a7cd8a5 100644
--- a/gn2/wqflask/templates/show_trait_transform_and_filter.html
+++ b/gn2/wqflask/templates/show_trait_transform_and_filter.html
@@ -5,7 +5,7 @@
needed.
</p>
<div id="blockMenuSpan" class="input-append block-div">
- <label for="remove_samples_field">Block samples by index:</label>
+ <label for="remove_samples_field">Filter samples by index:</label>
<input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
<select id="block_group" size="1">
<option value="primary">
@@ -23,7 +23,7 @@
</div>
{% if categorical_attr_exists == "true" %}
<div class="input-append block-div-2">
- <label for="exclude_column">Block samples by group:</label>
+ <label for="exclude_column">Filter samples by group:</label>
<select id="exclude_column" size=1>
{% for attribute in sample_groups[0].attributes %}
{% if sample_groups[0].attributes[attribute].distinct_values|length <= 500 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %}
diff --git a/gn2/wqflask/templates/tool_buttons.html b/gn2/wqflask/templates/tool_buttons.html
index c6d1476c..3e716d70 100644
--- a/gn2/wqflask/templates/tool_buttons.html
+++ b/gn2/wqflask/templates/tool_buttons.html
@@ -18,6 +18,10 @@
BNW
</button>
+<button id="send_to_genecup" class="btn btn-primary submit_special" data-url="/genecup" >
+ GeneCup
+</button>
+
<button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
WGCNA
</button>
diff --git a/gn2/wqflask/templates/tutorials.html b/gn2/wqflask/templates/tutorials.html
index 870dba1a..6281291f 100644
--- a/gn2/wqflask/templates/tutorials.html
+++ b/gn2/wqflask/templates/tutorials.html
@@ -221,11 +221,12 @@ $('#myTable3').dataTable( {
</tr>
</thead>
<tbody>
- <tr><td><a href="https://www.biorxiv.org/content/10.1101/2020.12.23.424047v1">GeneNetwork: a continuously updated tool for systems genetics analyses</a></td></tr>
- <tr><td><a href="https://doi.org/10.3390/genes13040614">New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork</a></td>
- <tr><td><a href="https://www.opar.io/pdf/Rat_HRDP_Brain_Proteomics_Wang_WIlliams_08Oct2021.pdf">A Primer on Brain Proteomics and protein-QTL Analysis for Substance Use Disorders</a></td></tr>
-
- </tbody>
+ <tr><td><a href="https://www.opar.io/pdf/Ashbrook_ExperimentalPrecisionMedicineMouseModels_2023.pdf">Experimental precision medicine: Mouse models in which to test precision medicine</a></td>
+ <tr><td><a href="https://www.opar.io/pdf/Williams_ResourcesForSystemsGenetics_2017.pdf">Systems Genetics. Methods and Protocols</a></td></tr>
+ <tr><td><a href="https://www.biorxiv.org/content/10.1101/2020.12.23.424047v1">GeneNetwork: a continuously updated tool for systems genetics analyses</a></td></tr>
+ <tr><td><a href="https://doi.org/10.3390/genes13040614">New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork</a></td>
+ <tr><td><a href="https://www.opar.io/pdf/Rat_HRDP_Brain_Proteomics_Wang_WIlliams_08Oct2021.pdf">A Primer on Brain Proteomics and protein-QTL Analysis for Substance Use Disorders</a></td></tr>
+ </tbody>
</table>
<script>
$('#myTable4').dataTable( {
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py
index 843ed07a..993c6f0c 100644
--- a/gn2/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -46,12 +46,12 @@ from gn2.wqflask import search_results
from gn2.wqflask import server_side
# Used by YAML in marker_regression
from gn2.base.data_set import create_dataset
+from gn2.base.trait import fetch_symbols
from gn2.wqflask.show_trait import show_trait
from gn2.wqflask.show_trait import export_trait_data
from gn2.wqflask.show_trait.show_trait import get_diff_of_vals
from gn2.wqflask.heatmap import heatmap
-from gn2.wqflask.external_tools import send_to_bnw
-from gn2.wqflask.external_tools import send_to_webgestalt
+from gn2.wqflask.external_tools import send_to_bnw, send_to_webgestalt
from gn2.wqflask.external_tools import send_to_geneweaver
from gn2.wqflask.comparison_bar_chart import comparison_bar_chart
from gn2.wqflask.marker_regression import run_mapping
@@ -88,8 +88,8 @@ from gn2.utility.redis_tools import get_redis_conn
import gn2.utility.hmac as hmac
-from gn2.base.webqtlConfig import TMPDIR
-from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
+from gn2.base.webqtlConfig import TMPDIR, GENERATED_IMAGE_DIR
+from gn2.base.webqtlConfig import GENE_CUP_URL
from gn2.wqflask.database import database_connection
@@ -137,6 +137,10 @@ def handle_generic_exceptions(e):
stack={formatted_lines},
error_image=animation,
version=current_app.config.get("GN_VERSION")))
+ try:
+ resp.status_code = exc_type.code
+ except AttributeError:
+ resp.status_code = 500
resp.set_cookie(err_msg[:32], animation)
return resp
@@ -258,28 +262,19 @@ def gsearchtable():
@app.route("/gnqna", methods=["POST", "GET"])
@require_oauth2
def gnqna():
-
if request.method == "POST":
try:
- def __error__(resp):
- return resp.json()
-
def error_page(resp):
return render_template("gnqa_errors.html",
**{"status_code": resp.status_code, **resp.json()})
def __success__(resp):
return render_template("gnqa_answer.html", **{"gn_server_url": GN3_LOCAL_URL, **(resp.json())})
- """
- disable gn-auth currently not stable
- if not user_logged_in():
- return error_page("Please Login/Register to Genenetwork to access this Service")
- """
token = session_info()["user"]["token"].either(
lambda err: err, lambda tok: tok["access_token"])
- return monad_requests.post(
+ return monad_requests.put(
urljoin(GN3_LOCAL_URL,
- "/api/llm/gnqna"),
+ "/api/llm/search"),
json=dict(request.form),
headers={
"Authorization": f"Bearer {token}"
@@ -290,44 +285,39 @@ def gnqna():
error_page, __success__)
except Exception as error:
return flask.jsonify({"error": str(error)})
- prev_queries = (monad_requests.get(
- urljoin(GN3_LOCAL_URL,
- "/api/llm/get_hist_names")
- ).then(
- lambda resp: resp
- ).either(lambda x: [], lambda x: x.json()["prev_queries"]))
-
- return render_template("gnqa.html", prev_queries=prev_queries)
+ return render_template("gnqa.html")
-@app.route("/gnqna/hist/", methods=["GET"])
-@require_oauth2
-def get_hist_titles():
- token = session_info()["user"]["token"].either(
- lambda err: err, lambda tok: tok["access_token"])
- response = monad_requests.get(urljoin(GN3_LOCAL_URL,
- "/api/llm/hist/titles"),
- headers={
- "Authorization": f"Bearer {token}"
- }
- ).then(lambda resp: resp).either(
- lambda x: x.json(), lambda x: x.json())
- return render_template("gnqa_search_history.html", **response)
-
-@app.route("/gnqna/hist/search/<search_term>", methods=["GET"])
+@app.route("/gnqna/hist", methods=["GET", "DELETE"])
@require_oauth2
-def fetch_hist_records(search_term):
+def get_gnqa_history():
+ def _error_(resp):
+ return render_template("gnqa_errors.html",
+ **{"status_code": resp.status_code,
+ **resp.json()})
token = session_info()["user"]["token"].either(
lambda err: err, lambda tok: tok["access_token"])
+ if request.method == "DELETE":
+ monad_requests.delete(urljoin(GN3_LOCAL_URL, "/api/llm/history"),
+ json=dict(request.form),
+ headers={
+ "Authorization": f"Bearer {token}"
+ }
+ ).either(
+ _error_, lambda x: x.json())
response = monad_requests.get(urljoin(GN3_LOCAL_URL,
- f"/api/llm/history/{search_term}"),
+ (f"/api/llm/history?search_term={request.args.get('search_term')}"
+ if request.args.get("search_term") else "/api/llm/history")),
headers={
"Authorization": f"Bearer {token}"
}
).then(lambda resp: resp).either(
- lambda x: x.json(), lambda x: x.json())
- return render_template("gnqa_answer.html", **response)
+ _error_, lambda x: x.json())
+ if request.args.get("search_term"):
+ return render_template("gnqa_answer.html", **response)
+ return render_template("gnqa_search_history.html",
+ prev_queries=response)
@app.route("/gnqna/rating/<task_id>/<int(signed=True):weight>",
@@ -741,6 +731,22 @@ def geneweaver_page():
return rendered_template
+@app.route("/genecup", methods=('POST',))
+def genecup_page():
+ start_vars = request.form
+
+ traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+
+ if traits[0] != "":
+ symbol_string = fetch_symbols(traits)
+ return redirect(GENE_CUP_URL % symbol_string)
+ else:
+ rendered_template = render_template(
+ "empty_collection.html", **{'tool': 'GeneWeaver'})
+
+ return rendered_template
+
+
@app.route("/comparison_bar_chart", methods=('POST',))
def comp_bar_chart_page():
start_vars = request.form
@@ -1230,8 +1236,8 @@ def get_dataset(name):
lambda err: {"roles": []},
lambda val: val
)
-
- metadata["editable"] = "group:resource:edit-resource" in result["roles"]
+ if metadata:
+ metadata["editable"] = "group:resource:edit-resource" in result["roles"]
return render_template(
"dataset.html",
name=name,
@@ -1346,7 +1352,7 @@ def edit_case_attributes(inbredset_id: int) -> Response:
return monad_requests.post(
urljoin(
current_app.config["GN_SERVER_URL"],
- f"/api/case-attribute/{inbredset_id}/edit"),
+ f"case-attribute/{inbredset_id}/edit"),
json={
"edit-data": reduce(__process_data__, form.items(), {})
},
@@ -1358,29 +1364,33 @@ def edit_case_attributes(inbredset_id: int) -> Response:
def __fetch_strains__(inbredset_group):
return monad_requests.get(urljoin(
current_app.config["GN_SERVER_URL"],
- f"/api/case-attribute/{inbredset_id}/strains")).then(
+ f"case-attribute/{inbredset_id}/strains")).then(
lambda resp: {**inbredset_group, "strains": resp.json()})
def __fetch_names__(strains):
return monad_requests.get(urljoin(
current_app.config["GN_SERVER_URL"],
- f"/api/case-attribute/{inbredset_id}/names")).then(
+ f"case-attribute/{inbredset_id}/names")).then(
lambda resp: {**strains, "case_attribute_names": resp.json()})
def __fetch_values__(canames):
return monad_requests.get(urljoin(
current_app.config["GN_SERVER_URL"],
- f"/api/case-attribute/{inbredset_id}/values")).then(
+ f"case-attribute/{inbredset_id}/values")).then(
lambda resp: {**canames, "case_attribute_values": {
value["StrainName"]: value for value in resp.json()}})
+ def __view_error__(err):
+ current_app.logger.error("%s", err)
+ return "We experienced an error"
+
return monad_requests.get(urljoin(
current_app.config["GN_SERVER_URL"],
- f"/api/case-attribute/{inbredset_id}")).then(
+ f"case-attribute/{inbredset_id}")).then(
lambda resp: {"inbredset_group": resp.json()}).then(
__fetch_strains__).then(__fetch_names__).then(
__fetch_values__).either(
- lambda err: err, # TODO: Handle error better
+ __view_error__,
lambda values: render_template(
"edit_case_attributes.html", inbredset_id=inbredset_id, **values))