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Merge pull request #10 from NFDI4BIOIMAGE/fix_open_with
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Fix open-with
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@MicheleBortol
MicheleBortol authored Oct 15, 2024
2 parents f3345e1 + e08f218 commit bf67a3f
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192 changes: 192 additions & 0 deletions omero_vitessce/templates/omero_vitessce/vitessce_open_with.html
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<!DOCTYPE html>
{% extends "webgateway/base/base_header.html" %}
{% block content %}
<style>
.tooltip {
position: relative;
display: inline-block;
border-bottom: 1px dotted black;
text-align: left;
font-size: medium;
}

.tooltip .tooltiptext {
visibility: hidden;
width: 120px;
background-color: black;
color: #fff;
text-align: center;
border-radius: 6px;
padding: 5px 0;
position: absolute;
z-index: 1;
top: -5px;
left: 105%;

}
.tooltip:hover .tooltiptext {
visibility: visible;
}
</style>
<div style="text-align:center">
{% if json_configs %}
<p style="font-size:medium">Please select an attached config file from the list below:</p>
<ul>
{% for file, url in json_configs.items%}
<li><h1><a href={{url}} target="_blank"> {{file}}</a></h1></li>
{% endfor %}
</ul>
{% else %}
<p style="font-size:medium"> There are no config files attached! </p>
<p style="font-size:medium"> To use the viewer you can attach a .json config file and refresh the panel. </p>
{% endif %}
<br>
{% if form %}
<p style="font-size:medium"> Or use the form below to generate a new config file:</p>
<form action='/omero_vitessce/generate_config/{{obj_type}}/{{obj_id}}' method="post">
{% csrf_token %}
<table style="margin: 0px auto; width: 50%; height: 50%; font-size: medium">
<tr style="height:2vh">
<th colspan="2" style="text-align:center;vertical-align:middle;font-size:medium;font-weight:bold;">
Vitessce viewer configuration</th>
<tr style="height:4vh">
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.config_file_name.label_tag }}
<span class="tooltiptext">{{ form.config_file_name.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.config_file_name }}</th>
</tr>
<tr style="height:4vh">
<th colspan="2" style="text-align:center;vertical-align:middle;font-size:medium">
Images</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.images.label_tag }}
<span class="tooltiptext">{{ form.images.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.images }}</th>
<tr style="height:4vh">
<th colspan="2" style="text-align:center;vertical-align:middle;font-size:medium">
Cell Data</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.segmentation.label_tag }}
<span class="tooltiptext">{{ form.segmentation.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.segmentation }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.cell_identities.label_tag }}
<span class="tooltiptext">{{ form.cell_identities.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.cell_identities }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.cell_id_column.label_tag }}
<span class="tooltiptext">{{ form.cell_id_column.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.cell_id_column }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.cell_label_column.label_tag }}
<span class="tooltiptext">{{ form.cell_label_column.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.cell_label_column }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.expression.label_tag }}
<span class="tooltiptext">{{ form.expression.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.expression }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.embeddings.label_tag }}
<span class="tooltiptext">{{ form.embeddings.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.embeddings }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.embedding_x.label_tag }}
<span class="tooltiptext">{{ form.embedding_x.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.embedding_x }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.embedding_y.label_tag }}
<span class="tooltiptext">{{ form.embedding_y.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.embedding_y }}</th>
</tr>
<tr style="height:4vh">
<th colspan="2" style="text-align:center;vertical-align:middle;font-size:medium">
Molecule Data</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.molecule_id.label_tag }}
<span class="tooltiptext">{{form.molecule_id.help_text}}</span>
</div></th>
<th style="text-align:left;">{{ form.molecules }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.molecule_id.label_tag }}
<span class="tooltiptext">{{ form.molecule_id.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.molecule_id }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.molecule_label.label_tag }}
<span class="tooltiptext">{{ form.molecule_label.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.molecule_label }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.molecule_x.label_tag }}
<span class="tooltiptext">{{ form.molecule_x.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.molecule_x }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.molecule_y.label_tag }}
<span class="tooltiptext">{{ form.molecule_y.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.molecule_y }}</th>
</tr>
<tr style="height:4vh">
<th colspan="2" style="text-align:center;vertical-align:middle;font-size:medium">
Additional views</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.histograms.label_tag }}
<span class="tooltiptext">{{ form.histograms.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.histograms }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.heatmap.label_tag }}
<span class="tooltiptext">{{ form.heatmap.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.heatmap }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.status.label_tag }}
<span class="tooltiptext">{{ form.status.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.status }}</th>
</tr>
<tr style="height:2vh">
<th><div class="tooltip">{{ form.description.label_tag }}
<span class="tooltiptext">{{ form.description.help_text }}</span>
</div></th>
<th style="text-align:left;">{{ form.description }}</th>
</tr>
</table>
<input type = "submit" value = "Generate Config">
</form>
{% else %}
<p style="font-size:medium%"> Autogenerating config files requires the
<a href=https://github.com/ome/omero-web-zarr target="_blank">omero-web-zarr</a>
plugin which seems not to be available. </p>
{% endif %}
</div>
{% endblock %}
16 changes: 10 additions & 6 deletions omero_vitessce/views.py
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Expand Up @@ -73,13 +73,9 @@ def vitessce_open(request, conn=None, **kwargs):
if request.GET.get("dataset") is not None:
obj_type = "dataset"
obj_id = int(request.GET.get("dataset"))
elif request.GET.get("image") is not None:
if request.GET.get("image") is not None:
obj_type = "image"
obj_id = int(request.GET.get("image"))
else:
context = {"json_configs": dict(),
"obj_type": obj_type, "obj_id": obj_id}
return render(request, "omero_vitessce/vitessce_panel.html", context)

_, config_urls = get_attached_configs(obj_type, obj_id, conn)

Expand All @@ -88,4 +84,12 @@ def vitessce_open(request, conn=None, **kwargs):
else:
context = {"json_configs": dict(),
"obj_type": obj_type, "obj_id": obj_id}
return render(request, "omero_vitessce/vitessce_panel.html", context)
if OMERO_WEB_ZARR:
files, urls, img_files, img_urls = get_files_images(
obj_type, obj_id, conn)
form = ConfigForm(file_names=files, file_urls=urls,
img_names=img_files, img_urls=img_urls)
context["form"] = form
else:
context["form"] = None
return render(request, "omero_vitessce/vitessce_open_with.html", context)
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -2,7 +2,7 @@

setup(
name="omero-vitessce",
version="1.0.5",
version="1.0.6",
description="OMERO Vitessce multimodal data viewer plugin for OMERO.web",
long_description=open('README.md').read(),
long_description_content_type='text/markdown',
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