Documentation justifying each XSL file

Must contain an entry for each XSL file justifying the need for this. The more detail the better.

Documentation should include recommendations for how each XSL file could ultimately be removed by one of:

• improved biorXiv XML
• better handling of XML in Encoda
• better support for Encoda output in EPP client

Please provide links to github issues which express these requirements.

In the entry for each XSL file please link to the file in github.

Global xslt

/src/change-label-and-title-elements.xsl

This stylesheet is transforming an XML document by adding a "label" element to any "title" element that has a preceding "label" element, and removing any "label" element that has a following "title" element.

TODO: We need an expression of whether we believe this is work for biorXiv, encoda or EPP team.

Modify bioRxiv XML in preparation for Encoda

Prerequisites:

• docker
• libxml2-utils (if running on host)

XSL files

To apply an xslt transform to all biorXiv XML place it in the ./src folder.

To apply an xslt transform to a specific manuscript place it in the ./src/[DOI-SUFFIX] folder.

To apply an xslt transform to a specific version of a manuscript place it in the ./src/[DOI-SUFFIX] and express in the xslt the query to only apply the changes to that version number.

Tests for XSL files

Each xsl file must have at least one accompanying test. It is recommended that the ./test/fixtures/kitchen-sink.xml express at least one example which could be successfully targetted by the global xsl files in ./src/*.xsl.

You must drop an XML file in test folder for each XSL file in a folder name that corresponds to the filename of the xsl.

For example, an expected result of the ./src/change-label-and-title-elements.xsl transform can be found in ./test/change-label-and-title-elements. The filenames of the expected XML are the same as in the ./test/fixtures folder.

Some examples:

• ./test/change-label-and-title-elements/kitchen-sink.xml contains the expected XML of ./test/fixtures/kitchen-sink.xml that has gone through the ./src/change-label-and-title-elements.xsl transform.

• ./test/all/kitchen-sink.xml contains the expected XML of ./test/fixtures/kitchen-sink.xml that has gone through all of the transforms directly in the ./src folder.

• ./test/2022.05.30.22275761/remove-supplementary-materials/2022.05.30.22275761.xml contains the expected XML of ./test/fixtures/2022.05.30.22275761/2022.05.30.22275761.xml that has gone through the ./src/2022.05.30.22275761/remove-supplementary-materials.xsl transform.

Build docker image

docker buildx build -t epp-biorxiv-xslt .

Apply transform to XML

cat test/fixtures/2022.05.30.22275761/2022.05.30.22275761.xml | docker run --rm -i epp-biorxiv-xslt /app/scripts/transform.sh --doi 2022.05.30.22275761

Output to a file:

cat test/fixtures/2022.05.30.22275761/2022.05.30.22275761.xml | docker run --rm -i epp-biorxiv-xslt /app/scripts/transform.sh --doi 2022.05.30.22275761 > output.xml

Introduce logging:

touch session.log
cat test/fixtures/2022.05.30.22275761/2022.05.30.22275761.xml | docker run --rm -i -v "./session.log:/session.log" epp-biorxiv-xslt /app/scripts/transform.sh --doi 2022.05.30.22275761 --log /session.log

Apply only a single xslt:

cat test/fixtures/kitchen-sink.xml | docker run --rm -i epp-biorxiv-xslt /app/scripts/transform.sh /app/src/change-label-and-title-elements.xsl

Process a folder of biorXiv XML

The structure of the xml within the source folder will be preserved in the destination folder.

./scripts/process-folder.sh /path/to/SOURCE_DIR /path/to/DEST_DIR

Run with logs:

./scripts/process-folder.sh /path/to/SOURCE_DIR /path/to/DEST_DIR --log ./process-folder.log

Run tests

./project_tests.sh

Run with logs:

./project_tests.sh --log ./project-tests.log

Run projects tests entirely within docker container

docker buildx build -t epp-biorxiv-xslt .
docker buildx build -t epp-biorxiv-xslt-test -f Dockerfile.test .
docker run --rm epp-biorxiv-xslt-test /app/project_tests.sh