From 9f7e3035d13b286238d878a0baa45cb4c1708cee Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 8 Nov 2021 16:19:40 +0300 Subject: Fix URL --- wqflask/wqflask/templates/base.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index ab8b644f..6e922f24 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -87,7 +87,7 @@
  • Systems Genetics PheWAS
  • Genome Browser
  • BXD Power Calculator
    • -
  • Jupyter Notebook Launcher
    • +
  • Jupyter Notebook Launcher
  • Interplanetary File System
    • -- cgit v1.2.3 From 14f3d5da0de60dea8b0a24f68c2e658d92268e3a Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 8 Nov 2021 16:40:22 +0300 Subject: Add some styling for the Jupyter links --- wqflask/wqflask/static/new/css/jupyter_notebooks.css | 12 ++++++++++++ wqflask/wqflask/templates/jupyter_notebooks.html | 4 ++++ 2 files changed, 16 insertions(+) create mode 100644 wqflask/wqflask/static/new/css/jupyter_notebooks.css diff --git a/wqflask/wqflask/static/new/css/jupyter_notebooks.css b/wqflask/wqflask/static/new/css/jupyter_notebooks.css new file mode 100644 index 00000000..b916f03b --- /dev/null +++ b/wqflask/wqflask/static/new/css/jupyter_notebooks.css @@ -0,0 +1,12 @@ +.jupyter-links .main-link:nth-of-type(2n) { + background: #EEEEEE; +} + +.jupyter-links .main-link { + font-size: larger; + display: block; +} + +.jupyter-links .src-link { + font-size: smaller; +} diff --git a/wqflask/wqflask/templates/jupyter_notebooks.html b/wqflask/wqflask/templates/jupyter_notebooks.html index 4dce0f27..da250b2a 100644 --- a/wqflask/wqflask/templates/jupyter_notebooks.html +++ b/wqflask/wqflask/templates/jupyter_notebooks.html @@ -4,6 +4,10 @@ Jupyter Notebooks {%endblock%} +{%block css%} + +{%endblock} + {%block content%}
    -- cgit v1.2.3 From c63d10c565f82413ae8b5e553b1f00485439530a Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 8 Nov 2021 16:43:50 +0300 Subject: Fix syntax error --- wqflask/wqflask/templates/jupyter_notebooks.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/jupyter_notebooks.html b/wqflask/wqflask/templates/jupyter_notebooks.html index da250b2a..afc95a15 100644 --- a/wqflask/wqflask/templates/jupyter_notebooks.html +++ b/wqflask/wqflask/templates/jupyter_notebooks.html @@ -6,7 +6,7 @@ Jupyter Notebooks {%block css%} -{%endblock} +{%endblock%} {%block content%} -- cgit v1.2.3 From 5a14bbc53dafd7b85c3e903a3dcb2dab87a6fed2 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 8 Nov 2021 16:45:05 +0300 Subject: Fix styling of divs --- wqflask/wqflask/static/new/css/jupyter_notebooks.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/static/new/css/jupyter_notebooks.css b/wqflask/wqflask/static/new/css/jupyter_notebooks.css index b916f03b..663d1746 100644 --- a/wqflask/wqflask/static/new/css/jupyter_notebooks.css +++ b/wqflask/wqflask/static/new/css/jupyter_notebooks.css @@ -1,4 +1,4 @@ -.jupyter-links .main-link:nth-of-type(2n) { +.jupyter-links:nth-of-type(2n) { background: #EEEEEE; } -- cgit v1.2.3 From a2f2d89a5fbe720d3c1f1ac9655adca8b2ff503d Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 8 Nov 2021 16:48:32 +0300 Subject: Add some padding --- wqflask/wqflask/static/new/css/jupyter_notebooks.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/wqflask/wqflask/static/new/css/jupyter_notebooks.css b/wqflask/wqflask/static/new/css/jupyter_notebooks.css index 663d1746..db972a17 100644 --- a/wqflask/wqflask/static/new/css/jupyter_notebooks.css +++ b/wqflask/wqflask/static/new/css/jupyter_notebooks.css @@ -1,3 +1,7 @@ +.jupyter-links { + padding: 1.5em; +} + .jupyter-links:nth-of-type(2n) { background: #EEEEEE; } -- cgit v1.2.3 From 2fcf4d0343244936d6b066e85a1a06ebb33adf26 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 9 Nov 2021 19:29:52 +0000 Subject: Temporary fix to get temp trait submission working again; maybe should be dealt with in GN3 in some way --- wqflask/wqflask/show_trait/show_trait.py | 10 ++++++---- wqflask/wqflask/templates/show_trait_details.html | 2 +- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 6020bc16..678e3132 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -40,10 +40,15 @@ ONE_YEAR = 60 * 60 * 24 * 365 class ShowTrait: def __init__(self, user_id, kw): + self.admin_status = None if 'trait_id' in kw and kw['dataset'] != "Temp": self.temp_trait = False self.trait_id = kw['trait_id'] helper_functions.get_species_dataset_trait(self, kw) + self.admin_status = get_highest_user_access_role( + user_id=user_id, + resource_id=(self.resource_id or ""), + gn_proxy_url=GN_PROXY_URL) elif 'group' in kw: self.temp_trait = True self.trait_id = "Temp_" + kw['species'] + "_" + kw['group'] + \ @@ -73,10 +78,7 @@ class ShowTrait: self.trait_vals = Redis.get(self.trait_id).split() self.resource_id = get_resource_id(self.dataset, self.trait_id) - self.admin_status = get_highest_user_access_role( - user_id=user_id, - resource_id=(self.resource_id or ""), - gn_proxy_url=GN_PROXY_URL) + # ZS: Get verify/rna-seq link URLs try: blatsequence = self.this_trait.blatseq diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 3e59a3ee..6b125221 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -234,7 +234,7 @@ {% endif %} {% endif %} - {% if admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} + {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} {% if this_trait.dataset.type == 'Publish' %} {% endif %} -- cgit v1.2.3 From fe549317a5e0996cec246a011eb044b065f7ed8c Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 9 Nov 2021 22:04:24 +0000 Subject: Fixed error mistakenly introduced by the last commit --- wqflask/wqflask/show_trait/show_trait.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 678e3132..93f95852 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -45,6 +45,8 @@ class ShowTrait: self.temp_trait = False self.trait_id = kw['trait_id'] helper_functions.get_species_dataset_trait(self, kw) + self.resource_id = get_resource_id(self.dataset, + self.trait_id) self.admin_status = get_highest_user_access_role( user_id=user_id, resource_id=(self.resource_id or ""), @@ -76,8 +78,6 @@ class ShowTrait: name=self.trait_id, cellid=None) self.trait_vals = Redis.get(self.trait_id).split() - self.resource_id = get_resource_id(self.dataset, - self.trait_id) # ZS: Get verify/rna-seq link URLs try: -- cgit v1.2.3 From 721a45006697830c5bf780133c03d909c35b63a3 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 08:55:02 +0300 Subject: Apply pep-8 to file --- wqflask/wqflask/__init__.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index fbf1c9f5..98416b41 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -10,8 +10,8 @@ from urllib.parse import urlparse from utility import formatting from gn3.authentication import DataRole, AdminRole -from wqflask.resource_manager import resource_management +from wqflask.group_manager import group_management from wqflask.metadata_edits import metadata_edit from wqflask.api.markdown import glossary_blueprint @@ -65,7 +65,6 @@ app.register_blueprint(news_blueprint, url_prefix="/news") app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks") app.register_blueprint(resource_management, url_prefix="/resource-management") - app.register_blueprint(metadata_edit, url_prefix="/datasets/") @app.before_request -- cgit v1.2.3 From d330150c71deb27c29c29bfce8f14856e49ca157 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 08:56:53 +0300 Subject: Delete all methods in group_manager.py --- wqflask/wqflask/group_manager.py | 175 --------------------------------------- 1 file changed, 175 deletions(-) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 04a100ba..e69de29b 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,175 +0,0 @@ -import random -import string - -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash) - -from wqflask import app -from wqflask.user_login import send_verification_email, send_invitation_email, basic_info, set_password - -from utility.redis_tools import get_user_groups, get_group_info, save_user, create_group, delete_group, add_users_to_group, remove_users_from_group, \ - change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info - -from utility.logger import getLogger -logger = getLogger(__name__) - - -@app.route("/groups/manage", methods=('GET', 'POST')) -def manage_groups(): - params = request.form if request.form else request.args - if "add_new_group" in params: - return redirect(url_for('add_group')) - else: - admin_groups, member_groups = get_user_groups(g.user_session.user_id) - return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups) - - -@app.route("/groups/view", methods=('GET', 'POST')) -def view_group(): - params = request.form if request.form else request.args - group_id = params['id'] - group_info = get_group_info(group_id) - admins_info = [] - user_is_admin = False - if g.user_session.user_id in group_info['admins']: - user_is_admin = True - for user_id in group_info['admins']: - if user_id: - user_info = get_user_by_unique_column("user_id", user_id) - admins_info.append(user_info) - members_info = [] - for user_id in group_info['members']: - if user_id: - user_info = get_user_by_unique_column("user_id", user_id) - members_info.append(user_info) - - # ZS: This whole part might not scale well with many resources - resources_info = [] - all_resources = get_resources() - for resource_id in all_resources: - resource_info = get_resource_info(resource_id) - group_masks = resource_info['group_masks'] - if group_id in group_masks: - this_resource = {} - privileges = group_masks[group_id] - this_resource['id'] = resource_id - this_resource['name'] = resource_info['name'] - this_resource['data'] = privileges['data'] - this_resource['metadata'] = privileges['metadata'] - this_resource['admin'] = privileges['admin'] - resources_info.append(this_resource) - - return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info) - - -@app.route("/groups/remove", methods=('POST',)) -def remove_groups(): - group_ids_to_remove = request.form['selected_group_ids'] - for group_id in group_ids_to_remove.split(":"): - delete_group(g.user_session.user_id, group_id) - - return redirect(url_for('manage_groups')) - - -@app.route("/groups/remove_users", methods=('POST',)) -def remove_users(): - group_id = request.form['group_id'] - admin_ids_to_remove = request.form['selected_admin_ids'] - member_ids_to_remove = request.form['selected_member_ids'] - - remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( - ":"), group_id, user_type="admins") - remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( - ":"), group_id, user_type="members") - - return redirect(url_for('view_group', id=group_id)) - - -@app.route("/groups/add_", methods=('POST',)) -def add_users(user_type='members'): - group_id = request.form['group_id'] - if user_type == "admins": - user_emails = request.form['admin_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, - user_emails, admins=True) - elif user_type == "members": - user_emails = request.form['member_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, - user_emails, admins=False) - - return redirect(url_for('view_group', id=group_id)) - - -@app.route("/groups/change_name", methods=('POST',)) -def change_name(): - group_id = request.form['group_id'] - new_name = request.form['new_name'] - group_info = change_group_name(g.user_session.user_id, group_id, new_name) - - return new_name - - -@app.route("/groups/create", methods=('GET', 'POST')) -def add_or_edit_group(): - params = request.form if request.form else request.args - if "group_name" in params: - member_user_ids = set() - admin_user_ids = set() - # ZS: Always add the user creating the group as an admin - admin_user_ids.add(g.user_session.user_id) - if "admin_emails_to_add" in params: - admin_emails = params['admin_emails_to_add'].split(",") - for email in admin_emails: - user_details = get_user_by_unique_column( - "email_address", email) - if user_details: - admin_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins") - if "member_emails_to_add" in params: - member_emails = params['member_emails_to_add'].split(",") - for email in member_emails: - user_details = get_user_by_unique_column( - "email_address", email) - if user_details: - member_user_ids.add(user_details['user_id']) - #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") - - create_group(list(admin_user_ids), list( - member_user_ids), params['group_name']) - return redirect(url_for('manage_groups')) - else: - return render_template("admin/create_group.html") - -# ZS: Will integrate this later, for now just letting users be added directly - - -def send_group_invites(group_id, user_email_list=[], user_type="members"): - for user_email in user_email_list: - user_details = get_user_by_unique_column("email_address", user_email) - if user_details: - group_info = get_group_info(group_id) - # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, - # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something - if group_info: - # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, - # but do add them if they're a regular user and are added as an admin - if (user_details['user_id'] in group_info['admins']) or \ - ((user_type == "members") and (user_details['user_id'] in group_info['members'])): - continue - else: - send_verification_email(user_details, template_name="email/group_verification.txt", - key_prefix="verification_code", subject="You've been invited to join a GeneNetwork user group") - else: - temp_password = ''.join(random.choice( - string.ascii_uppercase + string.digits) for _ in range(6)) - user_details = { - 'user_id': str(uuid.uuid4()), - 'email_address': user_email, - 'registration_info': basic_info(), - 'password': set_password(temp_password), - 'confirmed': 0 - } - save_user(user_details, user_details['user_id']) - send_invitation_email(user_email, temp_password) - -# @app.route() -- cgit v1.2.3 From 1184fa8b540b1fef205fd87e3a8f0a8a2c702d76 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 08:57:19 +0300 Subject: Register "group_management" blueprint --- wqflask/wqflask/__init__.py | 2 ++ wqflask/wqflask/group_manager.py | 31 +++++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 98416b41..05e040ed 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -12,6 +12,7 @@ from utility import formatting from gn3.authentication import DataRole, AdminRole from wqflask.group_manager import group_management +from wqflask.resource_manager import resource_management from wqflask.metadata_edits import metadata_edit from wqflask.api.markdown import glossary_blueprint @@ -66,6 +67,7 @@ app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks") app.register_blueprint(resource_management, url_prefix="/resource-management") app.register_blueprint(metadata_edit, url_prefix="/datasets/") +app.register_blueprint(group_management, url_prefix="/group-management") @app.before_request def before_request(): diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index e69de29b..4edafc66 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -0,0 +1,31 @@ +import redis + +from flask import current_app +from flask import Blueprint +from flask import g +from flask import render_template +from gn3.authentication import get_groups_by_user_uid +from wqflask.decorators import login_required + +group_management = Blueprint("group_management", __name__) + + +@group_management.route("/groups") +@login_required +def view_groups(): + groups = get_groups_by_user_uid( + user_uid=(g.user_session.record.get(b"user_id", + b"").decode("utf-8") or + g.user_session.record.get("user_id", "")), + conn=redis.from_url( + current_app.config["REDIS_URL"], + decode_responses=True)) + return render_template("admin/group_manager.html", + admin_groups=groups.get("admin"), + member_groups=groups.get("member")) + + +@group_management.route("/groups/create", methods=("GET",)) +@login_required +def view_create_group_page(): + return render_template("admin/create_group.html") -- cgit v1.2.3 From 8766b3104be9cdbe00f594c936442b76f3b9a83e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 08:57:57 +0300 Subject: Update "create_group" endpoint in template --- wqflask/wqflask/templates/admin/group_manager.html | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index 692a7abc..c5000869 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -12,7 +12,11 @@

    Manage Groups

    {% if admin_groups|length != 0 or member_groups|length != 0 %}
    - + + +
    {% endif %} @@ -23,7 +27,11 @@ {% if admin_groups|length == 0 and member_groups|length == 0 %}

    You currently aren't a member or admin of any groups.


    - + + + {% else %}

    Admin Groups

    @@ -119,11 +127,6 @@ return $("#groups_form").submit(); }; - $("#create_group").on("click", function() { - url = $(this).data("url") - return submit_special(url) - }); - $("#remove_groups").on("click", function() { url = $(this).data("url") groups = [] -- cgit v1.2.3 From a70b6421221db391a1774ae1133a0a244f00f248 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 09:12:31 +0300 Subject: Replace "var" with "let" --- wqflask/wqflask/static/new/javascript/group_manager.js | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js index 4c172cbf..cd56133a 100644 --- a/wqflask/wqflask/static/new/javascript/group_manager.js +++ b/wqflask/wqflask/static/new/javascript/group_manager.js @@ -16,23 +16,22 @@ $('#clear_members').click(function(){ function add_emails(user_type){ - var email_address = $('input[name=user_email]').val(); - var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim() - console.log(email_list_string) + let email_address = $('input[name=user_email]').val(); + let email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim() if (email_list_string == ""){ - var email_set = new Set(); + let email_set = new Set(); } else { - var email_set = new Set(email_list_string.split(",")) + let email_set = new Set(email_list_string.split(",")) } email_set.add(email_address) $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) - var emails_display_string = Array.from(email_set).join('\n') + let emails_display_string = Array.from(email_set).join('\n') $('.added_' + user_type + 's').val(emails_display_string) } function clear_emails(user_type){ $('input[name=' + user_type + '_emails_to_add]').val("") $('.added_' + user_type + 's').val("") -} \ No newline at end of file +} -- cgit v1.2.3 From f8bdd6cabd97a66bd3e3f8eeff910a0a9a79cf55 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 09:12:51 +0300 Subject: Remove empty JavaScript script-block --- wqflask/wqflask/templates/admin/create_group.html | 6 ------ 1 file changed, 6 deletions(-) diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html index 21ef5653..7332ca77 100644 --- a/wqflask/wqflask/templates/admin/create_group.html +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -73,17 +73,11 @@
    - - - {% endblock %} {% block js %} - - {% endblock %} -- cgit v1.2.3 From 42a0bd960095e96b536a51249f2355e82b59fd30 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 15:41:00 +0300 Subject: group_manager.py: Add methods for creating and deleting groups --- wqflask/wqflask/group_manager.py | 59 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 4edafc66..3434eab9 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,10 +1,16 @@ +import json import redis from flask import current_app from flask import Blueprint from flask import g from flask import render_template +from flask import request +from flask import redirect +from flask import url_for from gn3.authentication import get_groups_by_user_uid +from gn3.authentication import get_user_info_by_key +from gn3.authentication import create_group from wqflask.decorators import login_required group_management = Blueprint("group_management", __name__) @@ -29,3 +35,56 @@ def view_groups(): @login_required def view_create_group_page(): return render_template("admin/create_group.html") + + +@group_management.route("/groups/create", methods=("POST",)) +@login_required +def create_new_group(): + conn = redis.from_url(current_app.config["REDIS_URL"], + decode_responses=True) + if group_name := request.form.get("group_name"): + members_uid, admins_uid = set(), set() + admins_uid.add(user_uid := ( + g.user_session.record.get( + b"user_id", + b"").decode("utf-8") or + g.user_session.record.get("user_id", ""))) + if admin_string := request.form.get("admin_emails_to_add"): + for email in admin_string.split(","): + user_info = get_user_info_by_key(key="email_address", + value=email, + conn=conn) + if user_uid := user_info.get("user_id"): + admins_uid.add(user_uid) + if member_string := request.form.get("member_emails_to_add"): + for email in member_string.split(","): + user_info = get_user_info_by_key(key="email_address", + value=email, + conn=conn) + if user_uid := user_info.get("user_id"): + members_uid.add(user_uid) + + # Create the new group: + create_group(conn=conn, + group_name=group_name, + member_user_uids=list(members_uid), + admin_user_uids=list(admins_uid)) + return redirect(url_for('group_management.view_groups')) + return redirect(url_for('group_management.create_groups')) + + +@group_management.route("/groups/delete", methods=("POST",)) +@login_required +def delete_groups(): + conn = redis.from_url(current_app.config["REDIS_URL"], + decode_responses=True) + user_uid = (g.user_session.record.get(b"user_id", b"").decode("utf-8") or + g.user_session.record.get("user_id", "")) + current_app.logger.info(request.form.get("selected_group_ids")) + for group_uid in request.form.get("selected_group_ids", "").split(":"): + if group_info := conn.hget("groups", group_uid): + group_info = json.loads(group_info) + # A user who is an admin can delete things + if user_uid in group_info.get("admins"): + conn.hdel("groups", group_uid) + return redirect(url_for('group_management.view_groups')) -- cgit v1.2.3 From 5763744f5044710066b3c94efed0413061412689 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 15:41:25 +0300 Subject: Update URL for removing groups in template --- wqflask/wqflask/templates/admin/group_manager.html | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index c5000869..c62cac20 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -17,7 +17,10 @@ Create Group - + {% endif %} -- cgit v1.2.3 From 965c25016c25256a1074131ac4c2c79b9ee97161 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 8 Nov 2021 15:41:45 +0300 Subject: Update URL for creating a new group --- wqflask/wqflask/templates/admin/create_group.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html index 7332ca77..b1d214ea 100644 --- a/wqflask/wqflask/templates/admin/create_group.html +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -6,7 +6,8 @@

    Create Group

    -
    +
    -- cgit v1.2.3 From c11ac641592da44a823fdf41c0b81cd7bc7971f1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:05:48 +0300 Subject: Update URL for viewing a particular group --- wqflask/wqflask/templates/admin/group_manager.html | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index c62cac20..eedfe138 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -58,11 +58,12 @@ {{ loop.index }} - {{ group.name }} + {% set group_url = url_for('group_management.view_group', group_id=group.uuid) %} + {{ group.name }} {{ group.admins|length + group.members|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }} - {{ group.id }} + {{ group.uuid }} {% endfor %} @@ -92,7 +93,8 @@ {{ loop.index }} - {{ group.name }} + {% set group_url = url_for('group_management.view_group', group_id=group.uuid) %} + {{ group.name }} {{ group.admins|length + group.members|length }} {{ group.created_timestamp }} {{ group.changed_timestamp }} -- cgit v1.2.3 From e0be9d3d6685b76a01c376655556295606ffea4e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:06:50 +0300 Subject: Rename "view_groups" to "display_groups" --- wqflask/wqflask/group_manager.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 3434eab9..0e1fa56e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -18,7 +18,7 @@ group_management = Blueprint("group_management", __name__) @group_management.route("/groups") @login_required -def view_groups(): +def display_groups(): groups = get_groups_by_user_uid( user_uid=(g.user_session.record.get(b"user_id", b"").decode("utf-8") or @@ -69,7 +69,7 @@ def create_new_group(): group_name=group_name, member_user_uids=list(members_uid), admin_user_uids=list(admins_uid)) - return redirect(url_for('group_management.view_groups')) + return redirect(url_for('group_management.display_groups')) return redirect(url_for('group_management.create_groups')) -- cgit v1.2.3 From e7fb408c3ab09b3aed5c862848f02d28d1a25f35 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:52:55 +0300 Subject: view_group.html: Remove redundant bool check --- wqflask/wqflask/templates/admin/view_group.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index 26692fe8..b14fd14e 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -14,7 +14,7 @@ - {% if user_is_admin == true %} + {% if is_admin %}
    @@ -51,7 +51,7 @@ {% endfor %} - {% if user_is_admin == true %} + {% if is_admin %}
    E-mail of user to add to admins (multiple e-mails can be added separated by commas): @@ -88,7 +88,7 @@ {% endfor %} - {% if user_is_admin == true %} + {% if is_admin %}
    E-mail of user to add to members (multiple e-mails can be added separated by commas): @@ -99,7 +99,7 @@ {% endif %} {% else %} There are currently no members in this group. - {% if user_is_admin == true %} + {% if is_admin %}
    E-mail of user to add to members (multiple e-mails can be added separated by commas): -- cgit v1.2.3 From 61270336f52d93eb1312fe27760962f927fc97c8 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:53:10 +0300 Subject: view_group.html: Add html indentation --- wqflask/wqflask/templates/admin/view_group.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index b14fd14e..abbdcf0e 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -1,9 +1,9 @@ {% extends "base.html" %} {% block title %}View and Edit Group{% endblock %} {% block css %} - - - + + + {% endblock %} {% block content %} -- cgit v1.2.3 From 1fe23d19c099305a7f3fe8afa1477964038e57a7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:54:05 +0300 Subject: view_group.html: Use GROUP_URL for adding admins and users --- wqflask/wqflask/templates/admin/view_group.html | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index abbdcf0e..a89ec54d 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -7,6 +7,7 @@ {% endblock %} {% block content %} +{% set GROUP_URL = url_for('group_management.view_group', group_id=guid) %}

    @@ -57,7 +58,7 @@

    - +
    {% endif %}
    @@ -94,7 +95,7 @@
    - +
    {% endif %} {% else %} @@ -230,7 +231,7 @@ new_name = $('input[name=new_group_name]').val() $.ajax({ type: "POST", - url: "/groups/change_name", + url: "{{ GROUP_URL }} ", data: { group_id: $('input[name=group_id]').val(), new_name: new_name -- cgit v1.2.3 From c2ca2dc66ec1b6be726eafde187eee561f074ad4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:54:53 +0300 Subject: view_group.html: Display the group's UID if the user is an admin --- wqflask/wqflask/templates/admin/view_group.html | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index a89ec54d..a7d80388 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -38,6 +38,9 @@ Name Email Address Organization + {% if is_admin %} + UID + {% endif %} @@ -48,6 +51,9 @@ {% if 'full_name' in admin %}{{ admin.full_name }}{% elif 'name' in admin %}{{ admin.name }}{% else %}N/A{% endif %} {% if 'email_address' in admin %}{{ admin.email_address }}{% else %}N/A{% endif %} {% if 'organization' in admin %}{{ admin.organization }}{% else %}N/A{% endif %} + {% if is_admin %} + {{admin.user_id}} + {% endif %} {% endfor %} @@ -75,6 +81,9 @@ Name Email Address Organization + {% if is_admin %} + UID + {% endif %} @@ -85,6 +94,10 @@ {% if 'full_name' in member %}{{ member.full_name }}{% elif 'name' in admin %}{{ admin.name }}{% else %}N/A{% endif %} {% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %} {% if 'organization' in member %}{{ member.organization }}{% else %}N/A{% endif %} + {% if is_admin %} + {{ member }} + {% endif %} + {% endfor %} -- cgit v1.2.3 From b4ed3cb7beca79b89ee05117daae264487d442cb Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:55:41 +0300 Subject: view_group.html: Prepend "Name" before the group name --- wqflask/wqflask/templates/admin/view_group.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index a7d80388..b4bac7d2 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -11,8 +11,8 @@

    - {{ group_info.name }} + Name: {{ group_info.name }}

    {% if is_admin %} -- cgit v1.2.3 From 511d3450e4301173a1c0c8af371b6c9354b5bff1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:56:36 +0300 Subject: view_group.html: Hide the "Change Group Name" button for non-admins --- wqflask/wqflask/templates/admin/view_group.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index b4bac7d2..4a3ecede 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -11,9 +11,11 @@

    - Name: {{ group_info.name }} + + {% if is_admin %} + {% endif %}

    {% if is_admin %}
    -- cgit v1.2.3 From d545936f3eb8dd491c2f691da0fcdc89722e2c64 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 9 Nov 2021 12:57:14 +0300 Subject: view_group.html: Hide checkbox for non-users --- wqflask/wqflask/templates/admin/view_group.html | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index 4a3ecede..4a20c0dd 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -91,7 +91,12 @@ {% for member in members %} - + + + {% if is_admin %} + + {% endif %} + {{ loop.index }} {% if 'full_name' in member %}{{ member.full_name }}{% elif 'name' in admin %}{{ admin.name }}{% else %}N/A{% endif %} {% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %} -- cgit v1.2.3 From 17b91bc55a502fc90bd0e6b4275253880e99f7c1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 11 Nov 2021 09:28:26 +0300 Subject: Add new group endpoints --- wqflask/wqflask/group_manager.py | 69 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 68 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 0e1fa56e..3936e36e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,5 +1,6 @@ import json import redis +import datetime from flask import current_app from flask import Blueprint @@ -87,4 +88,70 @@ def delete_groups(): # A user who is an admin can delete things if user_uid in group_info.get("admins"): conn.hdel("groups", group_uid) - return redirect(url_for('group_management.view_groups')) + return redirect(url_for('group_management.display_groups')) + + +@group_management.route("/groups/") +@login_required +def view_group(group_id: str): + conn = redis.from_url(current_app.config["REDIS_URL"], + decode_responses=True) + user_uid = (g.user_session.record.get(b"user_id", b"").decode("utf-8") or + g.user_session.record.get("user_id", "")) + + resource_info = [] + for resource_uid, resource in conn.hgetall("resources").items(): + resource = json.loads(resource) + if group_id in (group_mask := resource.get("group_masks")): + __dict = {} + for val in group_mask.values(): + __dict.update(val) + __dict.update({ + "id": resource_uid, + "name": resource.get("name"), + }) + resource_info.append(__dict) + group_info = json.loads(conn.hget("groups", + group_id)) + group_info["guid"] = group_id + + return render_template( + "admin/view_group.html", + group_info=group_info, + admins=[get_user_info_by_key(key="user_id", + value=user_id, + conn=conn) + for user_id in group_info.get("admins")], + members=[get_user_info_by_key(key="user_id", + value=user_id, + conn=conn) + for user_id in group_info.get("members")], + is_admin = (True if user_uid in group_info.get("admins") else False), + resources=resource_info) + + +@group_management.route("/groups/", methods=("POST",)) +def update_group(group_id: str): + conn = redis.from_url(current_app.config["REDIS_URL"], + decode_responses=True) + user_uid = (g.user_session.record.get(b"user_id", b"").decode("utf-8") or + g.user_session.record.get("user_id", "")) + group = json.loads(conn.hget("groups", group_id)) + timestamp = group["changed_timestamp"] + timestamp_ = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + if user_uid in group.get("admins"): + if name := request.form.get("new_name"): + group["name"] = name + group["changed_timestamp"] = timestamp_ + if admins := request.form.get("admin_emails_to_add"): + group["admins"] = list(set(admins.split(":") + + group.get("admins"))) + group["changed_timestamp"] = timestamp_ + if members := request.form.get("member_emails_to_add"): + print(f"\n+++++\n{members}\n+++++\n") + group["members"] = list(set(members.split(":") + + group.get("members"))) + group["changed_timestamp"] = timestamp_ + conn.hset("groups", group_id, json.dumps(group)) + return redirect(url_for('group_management.view_group', + group_id=group_id)) -- cgit v1.2.3 From 166bca11dee1a09d346c4bd72edbf51832f13820 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 11 Nov 2021 09:28:45 +0300 Subject: Update links for updating groups --- wqflask/wqflask/templates/admin/view_group.html | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index 4a20c0dd..c88ce0e7 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -7,8 +7,9 @@ {% endblock %} {% block content %} -{% set GROUP_URL = url_for('group_management.view_group', group_id=guid) %} -
    +{% set GROUP_URL = url_for('group_management.view_group', group_id=group_info.guid) %} +{% set UPDATE_GROUP_URL = url_for('group_management.update_group', group_id=group_info.guid) %} +

    Name: {{ group_info.name }} @@ -23,7 +24,7 @@

    {% endif %}
    - + @@ -66,7 +67,7 @@
    - +
    {% endif %}
    @@ -126,7 +127,7 @@
    - +
    {% endif %} {% endif %} @@ -240,6 +241,7 @@ $("#add_admins, #add_members").on("click", function() { url = $(this).data("url"); + console.log(url) return submit_special(url) }); -- cgit v1.2.3 From 50580bf1d8114c8cc0fafb429232fa29fab10415 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 12 Nov 2021 06:59:28 +0000 Subject: Added check for too_many_results before writing the table JS --- wqflask/wqflask/templates/search_result_page.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 95842316..dade6ba5 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -176,7 +176,7 @@ return params; }; - {% if results|count > 0 %} + {% if results|count > 0 and not too_many_results %} var tableId = "trait_table"; var width_change = 0; //ZS: For storing the change in width so overall table width can be adjusted by that amount -- cgit v1.2.3 From d6398ea7db0072694b0d8f79d909c276fae75bdd Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 12 Nov 2021 07:08:12 +0000 Subject: Change the max results to display depending upon data type, since ProbeSet results can be displayed in larger numbers more easily --- wqflask/wqflask/search_results.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 5ca1f9ca..33f9319c 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -62,8 +62,10 @@ class SearchResultPage: self.search_term_exists = True self.results = [] + max_result_count = 100000 # max number of results to display type = kw.get('type') if type == "Phenotypes": # split datatype on type field + max_result_count = 50000 dataset_type = "Publish" elif type == "Genotypes": dataset_type = "Geno" @@ -81,7 +83,7 @@ class SearchResultPage: self.too_many_results = False if self.search_term_exists: - if len(self.results) > 50000: + if len(self.results) > max_result_count: self.trait_list = [] self.too_many_results = True else: -- cgit v1.2.3 From b983afd6be0b8fc5ae8065a1b0745296645da593 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 12 Nov 2021 12:47:37 +0300 Subject: bugfix:cases where trait symbol is none --- wqflask/wqflask/correlation/correlation_gn3_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 1e3a40f2..20c0d99a 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -290,7 +290,7 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict): """Gets tissue expression values for the primary trait and target tissues values""" primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=[this_trait.symbol]) - if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: + if this_trait.symbol and this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( )] corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( -- cgit v1.2.3 From e2647916b051f5d46ccb24e08a6c97cbb8f668f2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 12 Nov 2021 16:27:03 +0000 Subject: This change prevents an error caused by trying to export mapping results for a ProbeSet trait when there is no gene symbol --- wqflask/wqflask/marker_regression/run_mapping.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 769b9240..9d70bb15 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -556,7 +556,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_method transform_text = "" output_file.write(transform_text + "\n") if dataset.type == "ProbeSet": - output_file.write("Gene Symbol: " + trait.symbol + "\n") + if trait.symbol: + output_file.write("Gene Symbol: " + trait.symbol + "\n") output_file.write("Location: " + str(trait.chr) + \ " @ " + str(trait.mb) + " Mb\n") if len(covariates) > 0: -- cgit v1.2.3 From cddae6a6593a3f65cdb9565207a9a58c338e9024 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 17 Nov 2021 01:19:00 +0300 Subject: temp disable query caching --- wqflask/base/data_set.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 70c58136..768ad49b 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -754,8 +754,8 @@ class DataSet: # Postgres doesn't have that limit, so we can get rid of this after we transition chunk_size = 50 number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) - cached_results = fetch_cached_results(self.name, self.type) - # cached_results = None + # cached_results = fetch_cached_results(self.name, self.type) + cached_results = None if cached_results is None: trait_sample_data = [] for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): @@ -800,8 +800,6 @@ class DataSet: results = g.db.execute(query).fetchall() trait_sample_data.append([list(result) for result in results]) - cache_dataset_results( - self.name, self.type, trait_sample_data) else: trait_sample_data = cached_results -- cgit v1.2.3 From f5dd4b9f6b02ebe20733df0e8bd5e1b5e89f9e93 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 17 Nov 2021 01:31:38 +0300 Subject: temp disable traits metadata cache --- wqflask/wqflask/correlation/show_corr_results.py | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 42010a1e..55915a74 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -86,30 +86,17 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe corr_results = correlation_data['correlation_results'] results_list = [] - file_name = f"{target_dataset['name']}_metadata.json" - - file_path = os.path.join(TMPDIR, file_name) - new_traits_metadata = {} - - try: - with open(file_path,"r+") as file_handler: - dataset_metadata = json.load(file_handler) - - except FileNotFoundError: - Path(file_path).touch(exist_ok=True) - dataset_metadata = {} for i, trait_dict in enumerate(corr_results): trait_name = list(trait_dict.keys())[0] trait = trait_dict[trait_name] - target_trait = dataset_metadata.get(trait_name) + target_trait = None if target_trait is None: target_trait_ob = create_trait(dataset=target_dataset_ob, name=trait_name, get_qtl_info=True) target_trait = jsonable(target_trait_ob, target_dataset_ob) - new_traits_metadata[trait_name] = target_trait if target_trait['view'] == False: continue results_dict = {} @@ -184,12 +171,6 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe results_list.append(results_dict) - - if bool(new_traits_metadata): - # that means new traits exists - dataset_metadata.update(new_traits_metadata) - with open(file_path,"w+") as file_handler: - json.dump(dataset_metadata, file_handler) return json.dumps(results_list) -- cgit v1.2.3 From 9577152dfed7ae3fab2fb677a89b78ed88b9e127 Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 17 Nov 2021 02:37:17 -0500 Subject: update jupyter notebook link name This does not point to the launcher app but to the curated notebooks. --- wqflask/wqflask/templates/base.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 6e922f24..a3bd1b63 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -87,7 +87,7 @@
  • Systems Genetics PheWAS
  • Genome Browser
  • BXD Power Calculator
    • -
  • Jupyter Notebook Launcher
    • +
  • Jupyter Notebooks
  • Interplanetary File System
    • -- cgit v1.2.3 From ea2ce4c05f9b367510ba60a9adc5da9e8337f032 Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 17 Nov 2021 02:47:52 -0500 Subject: update live jupyter notebooks --- wqflask/wqflask/jupyter_notebooks.py | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/wqflask/wqflask/jupyter_notebooks.py b/wqflask/wqflask/jupyter_notebooks.py index dbea04dd..7d76828e 100644 --- a/wqflask/wqflask/jupyter_notebooks.py +++ b/wqflask/wqflask/jupyter_notebooks.py @@ -6,16 +6,12 @@ jupyter_notebooks = Blueprint('jupyter_notebooks', __name__) def launcher(): links = ( { - "main_url": "http://notebook.genenetwork.org/51091/tree?", - "notebook_name": "COVID-19 in mybinder.org federation", - "src_link_url": "https://github.com/jgarte/covid19_in_binder"}, + "main_url": "http://notebook.genenetwork.org/34301/notebooks/genenetwork-api-using-r.ipynb", + "notebook_name": "R notebook showing how to query the GeneNetwork API.", + "src_link_url": "https://github.com/jgarte/genenetwork-api-r-jupyter-notebook"}, { - "main_url": "http://notebook.genenetwork.org/35639/tree?", - "notebook_name": "Simple requirements.txt based example", - "src_link_url": "https://github.com/jgarte/requirements"}, - { - "main_url": "http://notebook.genenetwork.org/40733/tree?", - "notebook_name": "Guile Jupyter Notebook Querying GeneNetwork API", - "src_link_url": "https://github.com/jgarte/guile-notebook-genenetwork-api"}) + "main_url": "http://notebook.genenetwork.org/57675/notebooks/genenetwork.ipynb", + "notebook_name": "Querying the GeneNetwork API declaratively with python.", + "src_link_url": "https://github.com/jgarte/genenetwork-jupyter-notebook-example"}) return render_template("jupyter_notebooks.html", links=links) -- cgit v1.2.3 From 9c17856e0aa047408d91b0fe0bd6591d305cca42 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 17 Nov 2021 04:07:08 -0600 Subject: Moven GN API doc to gn-docs repo --- doc/API_readme.md | 168 +----------------------------------------------------- 1 file changed, 1 insertion(+), 167 deletions(-) diff --git a/doc/API_readme.md b/doc/API_readme.md index be6668dc..17d10e44 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -1,169 +1,3 @@ # API Query Documentation # ---- -# Fetching Dataset/Trait info/data # ---- -## Fetch Species List ## -To get a list of species with data available in GN (and their associated names and ids): -``` -curl http://genenetwork.org/api/v_pre1/species -[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] -``` - -Or to get a single species info: -``` -curl http://genenetwork.org/api/v_pre1/species/mouse -``` -OR -``` -curl http://genenetwork.org/api/v_pre1/species/mouse.json -``` - -*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* - -## Fetch Groups/RISets ## - -This query can optionally filter by species: - -``` -curl http://genenetwork.org/api/v_pre1/groups (for all species) -``` -OR -``` -curl http://genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets) -[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] -``` - -## Fetch Genotypes for Group/RISet ## -``` -curl http://genenetwork.org/api/v_pre1/genotypes/bimbam/BXD -curl http://genenetwork.org/api/v_pre1/genotypes/BXD.bimbam -``` -Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes) - -Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example: -``` -curl http://genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip -``` - -## Fetch Datasets ## -``` -curl http://genenetwork.org/api/v_pre1/datasets/bxd -``` -OR -``` -curl http://genenetwork.org/api/v_pre1/datasets/mouse/bxd -[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] -``` -(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) - -## Fetch Individual Dataset Info ## -### For mRNA Assay/"ProbeSet" ### - -``` -curl http://genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P -``` -OR -``` -curl http://genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` -{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } -``` -(This also has the option to specify group/riset) - -### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### -For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: -``` -curl http://genenetwork.org/api/v_pre1/dataset/bxd/10001 -{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } -``` - -## Fetch Sample Data for Dataset ## -``` -curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv -``` - -Returns a CSV file with sample/strain names as the columns and trait IDs as rows - -## Fetch Sample Data for Single Trait ## -``` -curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at -[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] -``` - -## Fetch Trait List for Dataset ## -``` -curl http://genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json -[ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] -``` - -Both JSON and CSV formats can be specified, with JSON as default. There is also an optional "ids_only" and "names_only" parameter that will only return a list of trait IDs or names, respectively. - -## Fetch Trait Info (Name, Description, Location, etc) ## -### For mRNA Expression/"ProbeSet" ### -``` -curl http://genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at -{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } -``` - -### For "Phenotypes" ### -For phenotypes this just gets the max LRS, its location, and additive effect (as calculated by qtlreaper) - -Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input -``` -curl http://genenetwork.org/api/v_pre1/trait/BXD/10001 -{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } -``` - ---- - -# Analyses # ---- -## Mapping ## -Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper - -Each method's query takes the following parameters respectively (more will be added): -### GEMMA ### -* trait_id (*required*) - ID for trait being mapped -* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) -* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) -* maf - minor allele frequency (default = 0.01) - -Example query: -``` -curl http://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true -``` - -### R/qtl ### -(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) -* trait_id (*required*) - ID for trait being mapped -* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) -* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. -* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function -* num_perm - number of permutations; 0 by default -* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate -* interval_mapping - Whether to use interval mapping; "false" by default -* pair_scan - *NYI* - -Example query: -``` -curl http://genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 -``` - -Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) - -## Calculate Correlation ## -Currently only Sample and Tissue correlations are implemented - -This query currently takes the following parameters (though more will be added): -* trait_id (*required*) - ID for trait used for correlation -* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) -* target_db (*required*) - Target DB name to be correlated against -* type - sample (default) | tissue -* method - pearson (default) | spearman -* return - Number of results to return (default = 500) - -Example query: -``` -curl http://genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 -[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] -``` +This document has moved to [gn-docs](https://github.com/genenetwork/gn-docs/blob/master/api/GN2-REST-API.md)! -- cgit v1.2.3 From 83719648e505747f16281d7e8e14f1003297be5c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 17 Nov 2021 13:42:26 +0300 Subject: README.org: Replace broken link with environments page --- doc/README.org | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/README.org b/doc/README.org index 8839aefc..e1c6b614 100644 --- a/doc/README.org +++ b/doc/README.org @@ -26,7 +26,7 @@ * Introduction -Large system deployments can get very [[http://biogems.info/contrib/genenetwork/gn2.svg ][complex]]. In this document we +Large system deployments can get very [[http://genenetwork.org/environments/][complex]]. In this document we explain the GeneNetwork version 2 (GN2) reproducible deployment system which is based on GNU Guix (see also [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install GN with all its files and dependencies. -- cgit v1.2.3 From 747544906c4d331a8d46ed692070e0f9d335191b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 18:31:59 +0000 Subject: Fixes gene global search error caused by some genes not having a symbol (not sure why this is in the DB; seems to have only happened recently) --- wqflask/wqflask/gsearch.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 2516e4fb..bf44408e 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -82,12 +82,13 @@ class GSearch: this_trait['species'] = line[0] this_trait['group'] = line[1] this_trait['tissue'] = line[2] - this_trait['symbol'] = line[6] + this_trait['symbol'] = "N/A" + if line[6]: + this_trait['symbol'] = line[6] + this_trait['description'] = "N/A" if line[7]: this_trait['description'] = line[7].decode( 'utf-8', 'replace') - else: - this_trait['description'] = "N/A" this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % ( -- cgit v1.2.3 From 3325440faef1161da90d51444543d8d847fb9cdd Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 18:27:56 +0000 Subject: Fix issue where gene global search throws an error due to some traits not having a gene symbol (not sure why they don't in the DB, but the code defaults it to N/A now) --- wqflask/wqflask/gsearch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index bf44408e..31f3305c 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -89,7 +89,7 @@ class GSearch: if line[7]: this_trait['description'] = line[7].decode( 'utf-8', 'replace') - this_trait['location_repr'] = 'N/A' + this_trait['location_repr'] = "N/A" if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % ( line[8], float(line[9])) -- cgit v1.2.3 From dea1afa01025026a0754de60615b974a5cb3fd24 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 21:53:20 +0000 Subject: Changed the URL for editing trait metadata to use the dataset group ID instead of the PublishFreezeId --- wqflask/wqflask/templates/show_trait_details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 6b125221..4e9ea0fb 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -236,7 +236,7 @@ {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} {% if this_trait.dataset.type == 'Publish' %} - + {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} -- cgit v1.2.3 From 42eee3a5f5d4055210e971db02e94e33b66d0b71 Mon Sep 17 00:00:00 2001 From: Arthur Centeno Date: Thu, 18 Nov 2021 17:53:11 +0000 Subject: AC Updating base, index_page and tutorials on 11-18-21 --- wqflask/wqflask/templates/base.html | 9 +++++- wqflask/wqflask/templates/index_page.html | 52 ++++++++++++++++++++++++++++--- wqflask/wqflask/templates/tutorials.html | 27 +++++++--------- 3 files changed, 67 insertions(+), 21 deletions(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 6e922f24..a231c48c 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -22,6 +22,12 @@ + + + + + + {% block css %} @@ -87,7 +93,7 @@
  • Systems Genetics PheWAS
  • Genome Browser
  • BXD Power Calculator
    • -
  • Jupyter Notebook Launcher
    • +
  • Jupyter Notebook Launcher
  • Interplanetary File System
    • @@ -227,6 +233,7 @@ Registered with Nif +
    diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 7b103305..cfb1bed4 100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -193,10 +193,40 @@
    +
    -
    -
    +
    +
    +

    Tutorials

    + +
    +
    + Webinars & Courses +

    In-person courses, live webinars and webinar recordings +

    + +

    +
    + +
    + Tutorials +

    Tutorials: Training materials in HTML, PDF and video formats +

    +
    + +
    + Documentation +

    Online manuals, handbooks, fact sheets and FAQs +

    +
    + +
    +
    + +
    @@ -241,8 +271,22 @@
  • Time Machine: Full GN versions from 2009 to 2016 (mm9)
    • Cloud (EC2) - +
    +
    +
    +

    Affiliates

    + +
    + +
    diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html index 8f3447e3..edec803c 100644 --- a/wqflask/wqflask/templates/tutorials.html +++ b/wqflask/wqflask/templates/tutorials.html @@ -56,9 +56,7 @@ -

    Webinar #01 - Introduction to Quantitative Trait Loci (QTL) Analysis

    -

    Friday, May 8th, 2020
    - 10am PDT/ 11am MDT/ 12pm CDT/ 1pm EDT

    +

    Introduction to Quantitative Trait Loci (QTL) Analysis

    Goals of this webinar (trait variance to QTL):