diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/trait.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 224 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 33 |
5 files changed, 134 insertions, 136 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index e6e1c6b3..37085448 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -7,7 +7,7 @@ from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset from utility.authentication_tools import check_resource_availability -from utility.tools import GN2_BASE_URL, GN_PROXY_URL +from utility.tools import GN2_BASE_URL from utility.redis_tools import get_redis_conn, get_resource_id from flask import g, request, url_for diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e958e78c..13e11ff2 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -37,17 +37,12 @@ ONE_YEAR = 60 * 60 * 24 * 365 class ShowTrait: def __init__(self, db_cursor, 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.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) elif 'group' in kw: self.temp_trait = True self.trait_id = "Temp_" + kw['species'] + "_" + kw['group'] + \ diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index b0390ace..bc5d75cd 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1,33 +1,38 @@ {% extends "base.html" %} +{%from "oauth2/display_error.html" import display_error%} + {% block title %}Trait Data and Analysis{% endblock %} + {% block css %} - <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" /> - <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> - <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" /> - <link href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" rel="stylesheet" type="text/css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" /> + <link href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" rel="stylesheet" type="text/css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} + {% block content %} <!-- Start of body --> + {{flash_me()}} + {%if "group:resource:view-resource" in trait_privileges%} <div class="container"> - <h2>Trait Data and Analysis for <b>{{ this_trait.display_name }}</b></h2> - {% if this_trait.dataset.type != 'Publish' %} - <h3>{{ this_trait.description_fmt[0]|upper }}{{ this_trait.description_fmt[1:]|safe }}</h3> - {% endif %} - </div> + <h2>Trait Data and Analysis for <b>{{ this_trait.display_name }}</b></h2> + {% if this_trait.dataset.type != 'Publish' %} + <h3>{{ this_trait.description_fmt[0]|upper }}{{ this_trait.description_fmt[1:]|safe }}</h3> + {% endif %} - <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form" class="form-horizontal"> - <div id="hidden_inputs"> - <input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}"> - {% for key in hddn %} + <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form" class="form-horizontal"> + <div id="hidden_inputs"> + <input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}"> + {% for key in hddn %} <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}"> - {% endfor %} + {% endfor %} </div> <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}"> @@ -40,100 +45,105 @@ <input type="hidden" name="sample_vals" value=""> <div class="container showtrait-main-div"> - <div class="panel-group" id="accordion"> - <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Details and Links - </h3> - </div> - <div id="collapseOne" class="panel-collapse collapse" aria-expanded="true"> - <div class="panel-body"> - {% include 'show_trait_details.html' %} - </div> - </div> - {% if metadata %} - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseMeta"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Data Set Group: {{ dataset.fullname }} - </h3> - </div> - <div id="collapseMeta" class="panel-collapse collapse in"> - <div class="panel-body"> - {% include 'show_metadata_details.html' %} - </div> - </div> - {% endif %} + <div class="panel-group" id="accordion"> + <div class="panel panel-default"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Details and Links + </h3> + </div> + <div id="collapseOne" class="panel-collapse collapse" aria-expanded="true"> + <div class="panel-body"> + {% include 'show_trait_details.html' %} </div> - <div class="panel panel-default"> - <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Statistics - </h3> - </div> - <div id="collapseTwo" class="panel-collapse collapse in"> - <div class="panel-body"> - {% include 'show_trait_statistics.html' %} - </div> - </div> + </div> + {% if metadata %} + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseMeta"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Data Set Group: {{ dataset.fullname }} + </h3> + </div> + <div id="collapseMeta" class="panel-collapse collapse in"> + <div class="panel-body"> + {% include 'show_metadata_details.html' %} + </div> + </div> + {% endif %} + </div> + <div class="panel panel-default"> + <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Statistics + </h3> + </div> + <div id="collapseTwo" class="panel-collapse collapse in"> + <div class="panel-body"> + {% include 'show_trait_statistics.html' %} </div> - <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Transform and Filter Data - </h3> - </div> - <div id="collapseThree" class="panel-collapse collapse in"> - <div class="panel-body"> - {% include 'show_trait_transform_and_filter.html' %} - </div> - <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a href="#" class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div> - </div> + </div> + </div> + <div class="panel panel-default"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Transform and Filter Data + </h3> + </div> + <div id="collapseThree" class="panel-collapse collapse in"> + <div class="panel-body"> + {% include 'show_trait_transform_and_filter.html' %} + </div> + <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a href="#" class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div> + </div> + </div> + <div class="panel panel-default"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations + </h3> + </div> + <div id="collapseFour" class="panel-collapse collapse in"> + <div class="panel-body"> + {% include 'show_trait_calculate_correlations.html' %} </div> - <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations - </h3> - </div> - <div id="collapseFour" class="panel-collapse collapse in"> - <div class="panel-body"> - {% include 'show_trait_calculate_correlations.html' %} - </div> - </div> - </div> - <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools - </h3> - </div> - <div id="collapseFive" class="panel-collapse collapse in"> - <div class="panel-body"> - {% include 'show_trait_mapping_tools.html' %} - </div> - <div id="outlier_alert_placeholder"></div> - </div> - </div> - <div class="panel panel-default" {% if (trait_table_width|int > 1100) %}style="min-width: {{ trait_table_width|int + 30 }}px;"{% endif %}> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseSix" aria-expanded="true"> - <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data - </h3> - </div> - <div id="collapseSix" class="panel-collapse collapse" aria-expanded="true"> - <div class="panel-body"> - {% include 'show_trait_edit_data.html' %} - </div> - </div> + </div> + </div> + <div class="panel panel-default"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools + </h3> + </div> + <div id="collapseFive" class="panel-collapse collapse in"> + <div class="panel-body"> + {% include 'show_trait_mapping_tools.html' %} </div> + <div id="outlier_alert_placeholder"></div> + </div> </div> - {% include 'show_trait_progress_bar.html' %} - + {%if "group:resource:edit-resource" in trait_privileges%} + <div class="panel panel-default" {%if (trait_table_width|int > 1100)%}style="min-width: {{trait_table_width|int + 30}}px;"{% endif %}> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseSix" aria-expanded="true"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data + </h3> + </div> + <div id="collapseSix" class="panel-collapse collapse" aria-expanded="true"> + <div class="panel-body"> + {% include 'show_trait_edit_data.html' %} + </div> + </div> + </div> + {%endif%} + </div> + {% include 'show_trait_progress_bar.html' %} </div> - </form> + </form> + </div> + {%else%} + {{display_error("Access Denied", {"error": "AuthorisationError", "error_description": "No read access for user '" + user.name + "'."})}} + {%endif%} - <!-- End of body --> + <!-- End of body --> {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 83ab1482..cce76082 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -235,7 +235,7 @@ {% endif %} {% endif %} <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> - {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} + {%if "group:resource:edit-resource" in trait_privileges%} {% if this_trait.dataset.type == 'Publish' %} <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/{{ this_trait.dataset.group.id }}/traits/{{ this_trait.name }}?resource-id={{ resource_id }}', '_blank')">Edit</button> {% endif %} @@ -245,9 +245,9 @@ {% endif %} {% endif %} </div> - {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} + {%if "group:resource:edit-resource" in trait_privileges%} <div class="btn-group"> - <button type="button" id="edit_resource" class="btn btn-success" title="Edit Privileges" onclick="window.open('/resource-management/resources/{{ resource_id }}', '_blank')">Edit Privileges</button> + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Privileges" onclick="window.open('{{url_for('oauth2.resource.view_resource', resource_id=resource_id)}}', '_blank')">Edit Privileges</button> </div> {% endif %} </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 164cf9ce..188dc27b 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -77,6 +77,7 @@ from wqflask.docs import Docs, update_text from wqflask.decorators import edit_access_required from wqflask.db_info import InfoPage +from wqflask.oauth2 import client from wqflask.oauth2.client import no_token_get from wqflask.oauth2.request_utils import process_error @@ -494,7 +495,10 @@ def show_temp_trait_page(): @app.route("/show_trait") def show_trait_page(): - def __show_trait__(): + def __show_trait__(privileges_data): + assert len(privileges_data) == 1 + privileges_data = privileges_data[0] + trait_privileges = tuple(item for item in privileges_data["privileges"]) with database_connection() as conn, conn.cursor() as cursor: user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") @@ -519,7 +523,12 @@ def show_trait_page(): return render_template( "show_trait.html", metadata=metadata, - **template_vars.__dict__) + **{ + **template_vars.__dict__, + "user": privileges_data["user"], + "trait_privileges": trait_privileges, + "resource_id": privileges_data["resource_id"] + }) dataset = request.args["dataset"] trait_id = request.args["trait_id"] def __failure__(err): @@ -527,27 +536,11 @@ def show_trait_page(): flash(f"{error['error']}: {error['error_description']}", "alert-error") return render_template("show_trait_error.html") - def __success__(auth_results): - trait_privileges = auth_results[0]["privileges"] - if ("group:resource:view-resource" in trait_privileges or - "system:resource:public-read" in trait_privileges): - return __show_trait__() - flash( - f"AuthorisationError: You do not have access to trait '{trait_id}' " - f"from the '{dataset}' dataset.", - "alert-danger") - return render_template("show_trait_error.html") - - return no_token_get( + return client.post( "oauth2/data/authorisation", - headers={ - "Content-Type": "application/json", - **({"Authorization": f"Bearer {session['token']}"} - if bool(session.get("token")) else {}) - }, json={ "traits": [f"{dataset}::{trait_id}"] - }).either(__failure__, __success__) + }).either(__failure__, __show_trait__) @app.route("/heatmap", methods=('POST',)) |