From 3da8f9645ae817e2c3dc5e228281376fb6d75241 Mon Sep 17 00:00:00 2001 From: Cameron Hyde Date: Fri, 23 Aug 2024 05:58:03 +1000 Subject: [PATCH 1/3] Clean up diann form --- webapp/home/forms.py | 30 ++++- .../home/requests/access/alphafold.html | 10 +- .../home/requests/access/cellranger.html | 10 +- .../templates/home/requests/access/diann.html | 116 ++++++++++++++++++ .../home/requests/access/fgenesh.html | 10 +- .../snippets/privacy-collection-notice.html | 12 ++ 6 files changed, 156 insertions(+), 32 deletions(-) create mode 100644 webapp/home/templates/home/requests/access/diann.html create mode 100644 webapp/home/templates/home/requests/access/snippets/privacy-collection-notice.html diff --git a/webapp/home/forms.py b/webapp/home/forms.py index 02267294..2e142886 100644 --- a/webapp/home/forms.py +++ b/webapp/home/forms.py @@ -410,7 +410,7 @@ 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 +426,7 @@ 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 +437,34 @@ 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-end-user-license.html'), + '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/templates/home/requests/access/alphafold.html b/webapp/home/templates/home/requests/access/alphafold.html index d31bfa01..94c94087 100644 --- a/webapp/home/templates/home/requests/access/alphafold.html +++ b/webapp/home/templates/home/requests/access/alphafold.html @@ -130,15 +130,7 @@

Galaxy Australia AlphaFold 2 Access Request

- 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 - - BioCommons Privacy Statement. + {% include 'home/request/access/snippets/privacy-collection-notice.html' %}
diff --git a/webapp/home/templates/home/requests/access/cellranger.html b/webapp/home/templates/home/requests/access/cellranger.html index 835d661e..fc70c8a3 100644 --- a/webapp/home/templates/home/requests/access/cellranger.html +++ b/webapp/home/templates/home/requests/access/cellranger.html @@ -93,15 +93,7 @@

Galaxy Australia Cell Ranger Access Request

- 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 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 - - BioCommons Privacy Statement. + {% include 'home/request/access/snippets/privacy-collection-notice.html' %}
diff --git a/webapp/home/templates/home/requests/access/diann.html b/webapp/home/templates/home/requests/access/diann.html new file mode 100644 index 00000000..542fd492 --- /dev/null +++ b/webapp/home/templates/home/requests/access/diann.html @@ -0,0 +1,116 @@ +{% extends 'home/header.html' %} + +{% load static %} + + +{% block head %} + + +{% endblock %} + + +{% block content %} +
+ +
+

Galaxy Australia DIA-NN Access Request

+ + + arrow_back + Back to tool access menu + + +
+ +

+ DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing by the Demichev, Ralser and Lilley labs. +

+ +

+ 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). +

+ +

+ 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. +

+ +
+ + {% csrf_token %} + + {{ form.non_field_errors }} + + {% include 'home/requests/access/snippets/personal-details-fields.html' %} + +
+ +
+

Your research (optional)

+
+ + +
+
+ + +
+
+ +
+ +
+
+

License acknowledgement statement

+

+ The {{ form.RESOURCE_NAME }} DIA-NN license is required to be + acknowledged prior to access. +

+ + {% include 'home/requests/access/snippets/agree-terms-modal.html' %} + +
+
+ +
+ +
+ {% include 'home/requests/access/snippets/privacy-collection-notice.html' %} +
+ +
+
+ +
+
+
+ +
+{% endblock %} + + +{% block 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 index 3d07fffd..6900be74 100644 --- a/webapp/home/templates/home/requests/access/fgenesh.html +++ b/webapp/home/templates/home/requests/access/fgenesh.html @@ -179,15 +179,7 @@

Select matrices

- 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 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 - - BioCommons Privacy Statement. + {% include 'home/request/access/snippets/privacy-collection-notice.html' %}
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 new file mode 100644 index 00000000..9f16ad5a --- /dev/null +++ b/webapp/home/templates/home/requests/access/snippets/privacy-collection-notice.html @@ -0,0 +1,12 @@ +

Data Privacy 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 {{ 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 + + BioCommons Privacy Statement. +

\ No newline at end of file From 09b8f4cd9e892f996d97fabeffa6269c01dca0cc Mon Sep 17 00:00:00 2001 From: Cameron Hyde Date: Mon, 26 Aug 2024 19:40:07 +1000 Subject: [PATCH 2/3] Fix up diann form --- webapp/home/forms.py | 2 +- .../home/documents/diann-1.8-license.txt | 46 +++++++++++++++++++ .../home/requests/access/alphafold.html | 2 +- .../home/requests/access/cellranger.html | 2 +- .../home/requests/access/fgenesh.html | 2 +- .../access/snippets/agree-terms-modal.html | 10 +++- 6 files changed, 59 insertions(+), 5 deletions(-) create mode 100644 webapp/home/static/home/documents/diann-1.8-license.txt diff --git a/webapp/home/forms.py b/webapp/home/forms.py index 2e142886..775c2d58 100644 --- a/webapp/home/forms.py +++ b/webapp/home/forms.py @@ -457,7 +457,7 @@ class DiannRequestForm(BaseAccessRequestForm): terms = { 'button_text': 'View license', - 'src': static('home/documents/diann-end-user-license.html'), + 'src': static('home/documents/diann-1.8-license.txt'), 'agreement_name': f'{RESOURCE_NAME} End User Licence Agreement', } diff --git a/webapp/home/static/home/documents/diann-1.8-license.txt b/webapp/home/static/home/documents/diann-1.8-license.txt new file mode 100644 index 00000000..fd05d499 --- /dev/null +++ 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 index 94c94087..bce61b95 100644 --- a/webapp/home/templates/home/requests/access/alphafold.html +++ b/webapp/home/templates/home/requests/access/alphafold.html @@ -130,7 +130,7 @@

Galaxy Australia AlphaFold 2 Access Request

- {% include 'home/request/access/snippets/privacy-collection-notice.html' %} + {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
diff --git a/webapp/home/templates/home/requests/access/cellranger.html b/webapp/home/templates/home/requests/access/cellranger.html index fc70c8a3..a7642261 100644 --- a/webapp/home/templates/home/requests/access/cellranger.html +++ b/webapp/home/templates/home/requests/access/cellranger.html @@ -93,7 +93,7 @@

Galaxy Australia Cell Ranger Access Request

- {% include 'home/request/access/snippets/privacy-collection-notice.html' %} + {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
diff --git a/webapp/home/templates/home/requests/access/fgenesh.html b/webapp/home/templates/home/requests/access/fgenesh.html index 6900be74..c8e1304c 100644 --- a/webapp/home/templates/home/requests/access/fgenesh.html +++ b/webapp/home/templates/home/requests/access/fgenesh.html @@ -179,7 +179,7 @@

Select matrices

- {% include 'home/request/access/snippets/privacy-collection-notice.html' %} + {% include 'home/requests/access/snippets/privacy-collection-notice.html' %}
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 index 39c9b716..9439aad1 100644 --- 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 @@