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let people view open access series

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Ross
2024-09-27 08:14:06 +01:00
parent 24590ee2b1
commit 9c61068026
5 changed files with 82 additions and 67 deletions
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atlas/decorators.py
+2 -1
View File
@@ -2,11 +2,12 @@ from django.core.exceptions import PermissionDenied
from .models import Case, CaseCollection, Series from .models import Case, CaseCollection, Series
def user_is_author_or_atlas_series_checker_or_atlas_marker(function): def user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access(function):
def wrap(request, *args, **kwargs): def wrap(request, *args, **kwargs):
series = Series.objects.get(pk=kwargs["pk"]) series = Series.objects.get(pk=kwargs["pk"])
if ( if (
request.user in series.get_author_objects() request.user in series.get_author_objects()
or series.open_access
or request.user.groups.filter(name="atlas_editor").exists() or request.user.groups.filter(name="atlas_editor").exists()
or request.user.groups.filter(name="atlas_marker").exists() or request.user.groups.filter(name="atlas_marker").exists()
or request.user.is_superuser or request.user.is_superuser
atlas/templates/atlas/series.html
+3 -1
View File
@@ -4,7 +4,9 @@
{% block navigation%} {% block navigation%}
{{ block.super }} {{ block.super }}
{% include 'atlas/series_headers.html' %} {% if can_edit %}
{% include 'atlas/series_headers.html' %}
{% endif %}
{% endblock %} {% endblock %}
{% block content %} {% block content %}
atlas/templates/atlas/series_viewer.html
+70 -62
View File
@@ -16,20 +16,24 @@
<div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''> <div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
</div> </div>
{% if editing_finding < 1 %} {% if can_edit %}
<button id="add-finding-button">Add finding</button> {% if editing_finding < 1 %}
{% endif %} <button id="add-finding-button">Add finding</button>
<button id="reset-viewport-button">Reset viewport</button> {% endif %}
<div id="finding-form"> <button id="reset-viewport-button">Reset viewport</button>
<div class="hide" id="hidden-form"> <div id="finding-form">
<form method="post" id="series_finding_form"> <div class="hide" id="hidden-form">
{% csrf_token %} <form method="post" id="series_finding_form">
{{series_finding_form|crispy}} {% csrf_token %}
<input type="submit" value="Submit"> {{series_finding_form|crispy}}
<button id="cancel-add-finding-button">Cancel</button> <input type="submit" value="Submit">
</form> <button id="cancel-add-finding-button">Cancel</button>
</form>
</div>
</div> </div>
</div> {% else %}
<button id="reset-viewport-button">Reset viewport</button>
{% endif %}
<details open> <details open>
<summary>Findings</summary> <summary>Findings</summary>
@@ -47,43 +51,46 @@
Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br /> Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
Condition(s): {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br /> Condition(s): {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
Description: {{finding.description}}<br /> Description: {{finding.description}}<br />
{% if request.user.is_superuser %} {% if request.user.is_superuser %}
<span _="on click toggle .hidden on next .extra-details">+</span> <span _="on click toggle .hidden on next .extra-details">+</span>
<div class="hidden extra-details"> <div class="hidden extra-details">
<h4>Annotation JSON</h4> <h4>Annotation JSON</h4>
<pre>{{finding.annotation_json}}</pre> <pre>{{finding.annotation_json}}</pre>
<h4>Viewport JSON</h4> <h4>Viewport JSON</h4>
<pre>{{finding.viewport_json}}</pre> <pre>{{finding.viewport_json}}</pre>
<h4>Image ID</h4> <h4>Image ID</h4>
<pre>{{finding.current_image_id_index}}</pre> <pre>{{finding.current_image_id_index}}</pre>
</div> </div>
{% endif %} {% endif %}
</span> </span>
<a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a> {% if can_edit %}
<a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a>
<a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a>
<a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a> {% endif %}
</div> </div>
{% endfor %} {% endfor %}
</details> </details>
<details> {% if can_edit %}
<summary>Truncate series</summary> <details>
<p> <summary>Truncate series</summary>
This will limit the series to the selected bounds (the rest of the images will be deleted). This is useful when you have a large volume of which only a small area is relevant to the case. NOTE: once deleted the images cannot be recovered on the site (they would have to be reuploaded if required). Make sure your images are shown in the correct order above and use test the test truncate button first. <p>
</p> This will limit the series to the selected bounds (the rest of the images will be deleted). This is useful when you have a large volume of which only a small area is relevant to the case. NOTE: once deleted the images cannot be recovered on the site (they would have to be reuploaded if required). Make sure your images are shown in the correct order above and use test the test truncate button first.
Start <input id="lower-truncation-bound-input" type="number" value="1"> <button id="set-lower-truncation-bound-button">Set</button><br/> </p>
End <input id="upper-truncation-bound-input"type="number" value="{{image_url_array_and_count.1}}"> <button id="set-upper-truncation-bound-button">Set</button><br/> Start <input id="lower-truncation-bound-input" type="number" value="1"> <button id="set-lower-truncation-bound-button">Set</button><br/>
<button id="truncate-test-button">Test truncate</button> End <input id="upper-truncation-bound-input"type="number" value="{{image_url_array_and_count.1}}"> <button id="set-upper-truncation-bound-button">Set</button><br/>
<button id="truncate-button">Trucate series</button> <button id="truncate-test-button">Test truncate</button>
<div id="truncate-output"></div> <button id="truncate-button">Trucate series</button>
<div id="truncate-output"></div>
</details> </details>
{% endif %}
{% endwith %} {% endwith %}
<div>Author: {{ series.get_author_display }}</div> <div>Author: {{ series.get_author_display }}</div>
{% if can_edit %}
<details> <details>
<summary>Series info</summary> <summary>Series info</summary>
<div> <div>
@@ -105,25 +112,25 @@
Image details Image details
</summary> </summary>
<form hx-post="{% url 'atlas:image_diff' %}" <form hx-post="{% url 'atlas:image_diff' %}"
hx-target="#temp" hx-target="#temp"
> >
{% for image in series.get_images %} {% for image in series.get_images %}
[{{ image.id }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}} [{{ image.id }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}}
{% if image.image %} {% if image.image %}
[{{image.get_file_size|filesizeformat}}] [{{image.get_file_size|filesizeformat}}]
{% endif %} {% endif %}
{{image.image_md5_hash}} ({{image.is_dicom}}) {{image.image_blake3_hash}} {{image.image_md5_hash}} ({{image.is_dicom}}) {{image.image_blake3_hash}}
<input type="checkbox" name="image-id" value="{{image.id}}"> <input type="checkbox" name="image-id" value="{{image.id}}">
<br /> <br />
{% comment %} {{image.get_dicom_info|safe}}<br /> {% endcomment %} {% comment %} {{image.get_dicom_info|safe}}<br /> {% endcomment %}
{% endfor %} {% endfor %}
<button>Diff files</button> <button>Diff files</button>
</form> </form>
<span id="temp"></span> <span id="temp"></span>
</details> </details>
@@ -131,21 +138,22 @@
<p>Total image size: {{series.get_total_image_size|filesizeformat}}</p> <p>Total image size: {{series.get_total_image_size|filesizeformat}}</p>
<p><a href="{% url 'atlas:series_download' pk=series.pk %}">Download images</a></p> <p><a href="{% url 'atlas:series_download' pk=series.pk %}">Download images</a></p>
</details> </details>
<span id="diff-controls">show <span id="diff-show-all" _="on click <span id="diff-controls">show <span id="diff-show-all" _="on click
log '1' log '1'
for row in .diff.rows for row in .diff.rows
show row show row
end">all</span> <span id="diff-show-diff" _=" end">all</span> <span id="diff-show-diff" _="
on click on click
log 'go' log 'go'
for row in <.diff tr/> for row in <.diff tr/>
log row.children[0].innerHTML log row.children[0].innerHTML
if row.children[0].innerHTML is empty if row.children[0].innerHTML is empty
hide row hide row
end end
end end
">diff</span></span> ">diff</span></span>
{% endif %}
<script> <script>
$(document).ready(function () { $(document).ready(function () {
atlas/urls.py
+1
View File
@@ -297,6 +297,7 @@ urlpatterns = [
), ),
path("structure/create", views.StructureCreate.as_view(), name="structure_create"), path("structure/create", views.StructureCreate.as_view(), name="structure_create"),
path("series/<int:pk>/thumbnail", views.series_thumbnail, name="series_thumbnail"), path("series/<int:pk>/thumbnail", views.series_thumbnail, name="series_thumbnail"),
# TODO: case context series viewing (so that we can view series in the context of a case)
path("series/<int:pk>", views.series_detail, name="series_detail"), path("series/<int:pk>", views.series_detail, name="series_detail"),
path("series/<int:pk>/authors", views.SeriesAuthorUpdate.as_view(), name="series_authors"), path("series/<int:pk>/authors", views.SeriesAuthorUpdate.as_view(), name="series_authors"),
path("series/", views.SeriesView.as_view(), name="series_view"), path("series/", views.SeriesView.as_view(), name="series_view"),
atlas/views.py
+6 -3
View File
@@ -121,7 +121,7 @@ from autocomplete import HTMXAutoComplete
from .decorators import ( from .decorators import (
user_is_author_or_atlas_editor, user_is_author_or_atlas_editor,
user_has_case_view_access, user_has_case_view_access,
user_is_author_or_atlas_series_checker_or_atlas_marker, user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access,
user_is_atlas_editor, user_is_atlas_editor,
user_is_author_or_atlas_series_checker, user_is_author_or_atlas_series_checker,
user_is_atlas_marker, user_is_atlas_marker,
@@ -198,7 +198,7 @@ def case_detail(request, pk):
@login_required @login_required
@user_is_author_or_atlas_series_checker_or_atlas_marker @user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
def series_thumbnail(request, pk, finding_pk=None): def series_thumbnail(request, pk, finding_pk=None):
series = get_object_or_404(Series, pk=pk) series = get_object_or_404(Series, pk=pk)
@@ -208,10 +208,12 @@ def series_thumbnail(request, pk, finding_pk=None):
@login_required @login_required
@user_is_author_or_atlas_series_checker_or_atlas_marker @user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
def series_detail(request, pk, finding_pk=None): def series_detail(request, pk, finding_pk=None):
series = get_object_or_404(Series, pk=pk) series = get_object_or_404(Series, pk=pk)
can_edit = series.check_user_can_edit(request.user)
editing_finding = -1 editing_finding = -1
if finding_pk is not None: if finding_pk is not None:
finding = get_object_or_404(SeriesFinding, pk=finding_pk) finding = get_object_or_404(SeriesFinding, pk=finding_pk)
@@ -228,6 +230,7 @@ def series_detail(request, pk, finding_pk=None):
"series": series, "series": series,
"series_finding_form": series_finding_form, "series_finding_form": series_finding_form,
"editing_finding": editing_finding, "editing_finding": editing_finding,
"can_edit": can_edit,
}, },
) )