Skip to content

Target new API endpoint /extra_files/raw #104

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Target new API endpoint /extra_files/raw #104

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions tools/vitessce/main_macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">3.5.1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@VERSION_SUFFIX@">3</token>
<token name="@PROFILE@">22.01</token>

<xml name="vitessce_requirements">
Expand Down Expand Up @@ -78,7 +78,6 @@
#end if
&&
cp '$__tool_directory__/index.html' '$output' &&
sed -i 's|display?filename=/|display?filename=|g' ${output.files_path}/config.json &&
echo "export var config = \$(cat ${output.files_path}/config.json)" >> '${output.files_path}/config.js' &&
cat '${output.files_path}/config.json' >> '$vitessce_config';
]]>
Expand Down
2 changes: 1 addition & 1 deletion tools/vitessce/vitessce_spatial.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ def main(inputs, output, image, offsets=None, anndata=None, masks=None, config_p
h=lc_dims[1])

# Build the prefix that Vitessce should use
display_prefix = (f"{galaxy_url}/api/datasets/{dataset_id}/display?filename=")
display_prefix = f"{galaxy_url}/api/datasets/{dataset_id}/extra_files/raw"

# if no anndata file, export the config with these minimal components
if not anndata:
Expand Down