Merge pull request #150 from usegalaxy-au/diann-form

Diann form
usegalaxy-au · Aug 26, 2024 · cb328d1 · cb328d1
2 parents 05d7135 + 568e013
commit cb328d1
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Showing 12 changed files with 298 additions and 45 deletions.
diff --git a/webapp/home/forms.py b/webapp/home/forms.py
@@ -1,6 +1,8 @@
 """User facing forms for making support requests (help/tools/data)."""
 
+import json
 import logging
+import bioblend
 from django_recaptcha import fields
 from django import forms
 from django.conf import settings
@@ -267,6 +269,7 @@ def clean_email(self):
     def action(self, request, resource):
         error = None
         actioned = False
+        is_registered_email = False
         email = self.cleaned_data['email']
         try:
             is_registered_email = galaxy.is_registered_email(email)
@@ -276,8 +279,12 @@ def action(self, request, resource):
                 f"{str(exc)[:1000]}\n")
             error = (
                 "Galaxy connection refused (could not check account"
-                " status)."
+                " status)"
             )
+            if isinstance(exc, bioblend.ConnectionError):
+                data = json.loads(exc.body)
+                if data.get('err_msg'):
+                    error += f": {data['err_msg']}"
             # Admins will have to action this manually
             actioned = self.dispatch(exception=error)
 
@@ -310,7 +317,7 @@ def action(self, request, resource):
             msg = f"Dispatching {resource} warning to {email}"
             logger.info(msg)
             records_logger.info(msg)
-            self.dispatch_warning(request)
+            self.dispatch_warning(request, error=error is not None)
 
         return actioned
 
@@ -355,12 +362,15 @@ def dispatch(self, exception=None, notify_user_success=True):
                 self.cleaned_data['email'],
                 self.RESOURCE_NAME,
             )
-        actioned = not exception and self.AUTO_ACTION
-        return actioned
+        return self.AUTO_ACTION
 
-    def dispatch_warning(self, request):
+    def dispatch_warning(self, request, error=False):
         """Dispatch warning email to let user know their email is invalid."""
-        template = 'home/requests/mail/invalid-institutional-email'
+        template = (
+            'home/requests/mail/error'
+            if error else
+            'home/requests/mail/invalid-institutional-email'
+        )
         dispatch_form_mail(
             to_address=self.cleaned_data['email'],
             subject=f"Access to {self.RESOURCE_NAME} could not be granted",
@@ -410,7 +420,7 @@ class FgeneshRequestForm(BaseAccessRequestForm):
     terms = {
         'button_text': 'View terms',
         'src': static('home/documents/fgenesh-biocommons-terms.html'),
-        'agreement_name': 'FGENESH++ Service Terms of Use and Policies',
+        'agreement_name': f'{RESOURCE_NAME} Service Terms of Use and Policies',
     }
 
     def render_matrix_field(self):
@@ -426,7 +436,7 @@ def dispatch(self, exception=None, notify_user_success=False):
 
 
 class CellRangerRequestForm(BaseAccessRequestForm):
-    """Form to request AlphaFold access."""
+    """Form to request Cell Ranger access."""
 
     RESOURCE_NAME = 'Cell Ranger'
     AUTO_ACTION = True
@@ -437,14 +447,34 @@ class CellRangerRequestForm(BaseAccessRequestForm):
     agree_usage = forms.BooleanField()
 
     terms = {
-        'button_text': 'View license agreement',
+        'button_text': 'View license',
         'src': static('home/documents/cellranger-end-user-license.html'),
-        'agreement_name': 'Cell Ranger End User Licence Agreement',
+        'agreement_name': f'{RESOURCE_NAME} End User Licence Agreement',
+    }
+
+
+class DiannRequestForm(BaseAccessRequestForm):
+    """Form to request Diann access."""
+
+    RESOURCE_NAME = 'DIA-NN'
+    AUTO_ACTION = True
+
+    name = forms.CharField()
+    email = forms.EmailField(validators=[validators.institutional_email])
+    research_description = forms.CharField(max_length=500, required=False)
+    research_topics = forms.CharField(max_length=200, required=False)
+    agree_terms = forms.BooleanField()
+
+    terms = {
+        'button_text': 'View license',
+        'src': static('home/documents/diann-1.8-license.txt'),
+        'agreement_name': f'{RESOURCE_NAME} End User Licence Agreement',
     }
 
 
 ACCESS_FORMS = {
     'alphafold': AlphafoldRequestForm,
-    'fgenesh': FgeneshRequestForm,
     'cellranger': CellRangerRequestForm,
+    'diann': DiannRequestForm,
+    'fgenesh': FgeneshRequestForm,
 }
diff --git a/webapp/home/static/home/css/main.css b/webapp/home/static/home/css/main.css
@@ -186,6 +186,12 @@ textarea.invalid {
   border-radius: .25rem;
   transition-duration: .25s;
 }
+.ga-btn:focus {
+  box-shadow: var(--color) 0 0 5px 2px;
+}
+.ga-btn:focus-visible {
+  outline: 0;
+}
 .ga-btn.sm {
   margin: .5rem;
   padding: .15rem .35rem;

diff --git a/webapp/home/static/home/documents/diann-1.8-license.txt b/webapp/home/static/home/documents/diann-1.8-license.txt
@@ -0,0 +1,46 @@
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, 
+OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, 
+OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+1. General. The DIA-NN software is licensed to you for use only under the terms of this License, 
+and all rights not expressly granted to you are reserved. The rights granted herein are limited to Vadim Demichev’s intellectual
+property rights in the DIA-NN software and do not include any other patents or intellectual property rights.
+
+2. Permitted License Uses and Restrictions. This License allows you to install and use the DIA-NN software.
+You may make one copy of the DIA-NN Software in machine-readable form for backup purposes only; 
+provided that the backup copy must include all copyright or other proprietary notices contained on the original.
+Except as and only to the extent expressly permitted in this License or by applicable law, you may not copy, decompile, 
+reverse engineer, disassemble, attempt to derive the source code of, modify, or create derivative works of the DIA-NN software or any part thereof. 
+
+3. Transfer. You may not rent, lease, lend or sublicense the DIA-NN software. You may, however, make a one-time permanent transfer 
+of all of your license rights to the DIA-NN software to another party, provided that: (a) the transfer must include all of the DIA-NN software, 
+including all its component parts, original media, printed materials and this License; (b) you do not retain any copies of the DIA-NN software, 
+full or partial, including copies stored on a computer or other storage device; and (c) the party receiving the DIA-NN software reads 
+and agrees to accept the terms and conditions of this License.
+
+4. Attribution. If you share, distribute or publish any materials that were produced using the DIA-NN software ("Derived Materials"), you must indicate 
+within these Derived Materials that they were produced using the DIA-NN software. You may satisfy this condition in any reasonable manner 
+based on the medium, means, and context in which you share the Derived Materials. For example, the required attribution can be expressed by including
+one of the statements "Processed using DIA-NN", "Generated using DIA-NN" or "Produced using DIA-NN" in the Derived Materials.
+
+5. All third-party software included in this DIA-NN software distribution retains its original license (see below).
+For the inclusion in this DIA-NN software distribution, the source code of MSToolkit and MiniDNN was modified.
+
+MiniDNN
+ - folder within this distribution: /MiniDNN
+ - URL: https://github.com/yixuan/MiniDNN
+ - License information: /MiniDNN/LICENSE.txt
+
+MSToolkit
+ - folder within this distribution: /mstoolkit
+ - URL: https://github.com/mhoopmann/mstoolkit
+ - License information: /mstoolkit/LICENSE.txt
+
+Eigen
+ - folder within this distribution: /eigen
+ - URL: http://eigen.tuxfamily.org/
+ - License information: eigen/COPYING.README
diff --git a/webapp/home/templates/home/requests/access/alphafold.html b/webapp/home/templates/home/requests/access/alphafold.html
@@ -130,15 +130,7 @@ <h2> Galaxy Australia AlphaFold 2 Access Request </h2>
     </div>
 
     <div class="container mb-10">
-      Privacy Collection Notice By completing this form you agree that your
-      responses will be provided to the Australian BioCommons and Galaxy
-      Australia and will be used solely for the purposes of determining
-      suitability for access to the Australian AlphaFold Service. Your
-      responses will be protected against unauthorised access and use; providing
-      your name is required to enable any follow ups. For more information,
-      please see the
-      <a href="https://www.biocommons.org.au/privacy/">
-        BioCommons Privacy Statement</a>.
+      {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
     </div>
 
     <div class="row mb-10">

diff --git a/webapp/home/templates/home/requests/access/cellranger.html b/webapp/home/templates/home/requests/access/cellranger.html
@@ -93,15 +93,7 @@ <h2> Galaxy Australia Cell Ranger Access Request </h2>
     </div>
 
     <div class="container mb-10">
-      <b>Privacy Collection Notice</b>: by completing this form you agree that your
-      responses will be provided to the Australian BioCommons and Galaxy
-      Australia and will be used solely for the purposes of determining
-      suitability for access to the Australian Cell Ranger Service. Your
-      responses will be protected against unauthorised access and use; providing
-      your name is required to enable any follow ups. For more information,
-      please see the
-      <a href="https://www.biocommons.org.au/privacy/">
-        BioCommons Privacy Statement</a>.
+      {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
     </div>
 
     <div class="row mb-10">

diff --git a/webapp/home/templates/home/requests/access/diann.html b/webapp/home/templates/home/requests/access/diann.html
@@ -0,0 +1,116 @@
+{% extends 'home/header.html' %}
+
+{% load static %}
+
+
+{% block head %}
+<link rel="stylesheet" href="{% static 'home/css/requests.css' %}">
+<link rel="stylesheet" href="{% static 'home/css/request-form.css' %}">
+{% endblock %}
+
+
+{% block content %}
+<main class="container mt-4">
+
+  <div class="mb-10">
+    <h2> Galaxy Australia DIA-NN Access Request </h2>
+    <small>
+      <a href="/request/access">
+        <span class="material-icons">arrow_back</span>
+        Back to tool access menu
+      </a>
+    </small>
+  </div>
+
+  <p class="lead">
+    DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing by the Demichev, Ralser and Lilley labs.
+  </p>
+
+  <p>
+    DIA-NN (v1.8.1) is available on Galaxy Australia for Australian researchers undertaking publicly funded research (i.e. using DIA-NN for academic research purposes).
+  </p>
+
+  <p>
+    Please apply for access, using your institutional email. The following sign up form is to confirm eligibility for access to DIA-NN on Galaxy Australia.
+  </p>
+
+  <form class="mt-10" method="post">
+
+    {% csrf_token %}
+
+    {{ form.non_field_errors }}
+
+    {% include 'home/requests/access/snippets/personal-details-fields.html' %}
+
+    <hr>
+
+    <div class="mb-10">
+      <h3 class="mb-3">Your research (optional)</h3>
+      <div class="form-group mb-3">
+        <label class="form-label" for="researchDescription">Please provide a brief description of your research</label>
+        <input
+          class="form-control"
+          id="researchDescription"
+          name="research_description"
+          type="text"
+          value="{{ form.research_description.value|default_if_none:'' }}"
+        />
+      </div>
+      <div class="form-group mb-3">
+        <label class="form-label" for="researchTopics">Which broad topics best describe your research?</label>
+        <input
+          class="form-control"
+          id="researchTopics"
+          name="research_topics"
+          type="text"
+          value="{{ form.research_topics.value|default_if_none:'' }}"
+        />
+      </div>
+    </div>
+
+    <hr>
+
+    <div class="row mb-10">
+      <div class="col-sm-12">
+        <h3 class="mb-3">License acknowledgement statement</h3>
+        <p>
+          The {{ form.RESOURCE_NAME }} DIA-NN license is required to be
+          acknowledged prior to access.
+        </p>
+
+        {% include 'home/requests/access/snippets/agree-terms-modal.html' %}
+
+      </div>
+    </div>
+
+    <hr>
+
+    <div class="container mb-10">
+      {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
+    </div>
+
+    <div class="row mb-10">
+      <div class="col text-center">
+        <button class='ga-btn' type="submit"> Submit </button>
+      </div>
+    </div>
+  </form>
+
+</main>
+{% endblock %}
+
+
+{% block script %}
+<script src="{% static 'home/js/forms.js' %}"></script>
+<script>
+  function showAcceptLicense(acceptLicenseBtn) {
+    console.log("Button:")
+    console.log(acceptLicenseBtn);
+    $(acceptLicenseBtn).siblings('.form-check').show();
+  }
+</script>
+{% endblock %}
+
+
+{% block onload %}
+{% endblock %}
diff --git a/webapp/home/templates/home/requests/access/fgenesh.html b/webapp/home/templates/home/requests/access/fgenesh.html
@@ -179,15 +179,7 @@ <h3 class="mb-3">Select matrices</h3>
     <hr>
 
     <div class="container mb-10">
-      <b>Privacy Collection Notice:</b> By completing this form you agree that your
-      responses will be provided to the Australian BioCommons and Galaxy
-      Australia and will be used solely for the purposes of determining
-      suitability for access to the Australian FGENESH++ Service. Your
-      responses will be protected against unauthorised access and use; providing
-      your name is required to enable any follow ups. For more information,
-      please see the
-      <a href="https://www.biocommons.org.au/privacy/">
-        BioCommons Privacy Statement</a>.
+      {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
     </div>
 
     <div class="row mb-10">

diff --git a/webapp/home/templates/home/requests/access/snippets/agree-terms-modal.html b/webapp/home/templates/home/requests/access/snippets/agree-terms-modal.html
@@ -68,6 +68,14 @@ <h5 class="modal-title"></h5>
   </div>
 
   <script>
+
+    {% if form.terms.src|slice:"-4:" == ".txt" %}
+    const termsIframe = $('#termsModal iframe')
+    termsIframe.ready( () => termsIframe.contents()
+      .find('body')
+      .css('padding', '1rem'));
+    {% endif %}
+
     function agreeTermsAction(el) {
       enableTermsInput();
       $('#agreeTermsInput').attr('checked', true);
@@ -91,7 +99,7 @@ <h5 class="modal-title"></h5>
       }
       $('#termsModal iframe').contents().on('scroll', (event) => {
         const scrollFromEnd = $(termsContainer)[0].scrollHeight
-        - $(termsContainer).scrollTop()
+        - $('#termsModal iframe').contents().scrollTop()
         - $('#termsModal iframe').height();
         if (scrollFromEnd < 50) enableAgreeTermsButton();
       });

diff --git a/webapp/home/templates/home/requests/access/snippets/privacy-collection-notice.html b/webapp/home/templates/home/requests/access/snippets/privacy-collection-notice.html
@@ -0,0 +1,12 @@
+<h3>Data Privacy Notice</h3>
+<p>
+  By completing this form you agree that your
+  responses will be provided to the Australian BioCommons and Galaxy
+  Australia and will be used solely for the purposes of determining
+  suitability for access to the Australian {{ form.RESOURCE_NAME }} Service. Your
+  responses will be protected against unauthorised access and use; providing
+  your name is required to enable any follow ups. For more information,
+  please see the
+  <a href="https://www.biocommons.org.au/privacy/">
+    BioCommons Privacy Statement</a>.
+</p>
diff --git a/webapp/home/templates/home/requests/mail/access-request.html b/webapp/home/templates/home/requests/mail/access-request.html
@@ -13,12 +13,8 @@ <h3>Error actioning {{ resource_name }} access request - Galaxy Australia</h3>
   <em style="font-size: 16pt; color: firebrick;">
     &#128128; {{ failed_message }}
   </em>
-  <p>
-    Exception: <br>
-    <code style="background-color: #f0d5cc; color: #c43f1a; font-size: 12pt; padding: 8px; max-height: 600px; max-width: 80%; overflow: auto;">
-      {{ exception }}
-    </code>
-  </p>
+  <pre style="background-color: #f0d5cc; color: #c43f1a; font-size: 0.9rem; padding: .5rem; max-height: 300px; overflow: auto;">{{ exception }}</code>
+  </pre>
   {% else %}
   <h3>New {{ resource_name }} access request submitted - Galaxy Australia</h3>
   <em style="font-size: 16pt; color: forestgreen;">