ADD extra storage formats

After working with Julie from dada2.org, support was added to use some alternative formats for storing the pedigree. This was so we could using piping to build a simple pedigree based on fields earlier in the form.

Add ability to set terminologies to use with a new action tag.

Added a new action tag @PEDIGREE which allows configuration of terminology to use.

The existing two actions tags @PEDIGREE_SCT and @PEDIGREE_HPO tags hard code the terminologies used to either SNOMEDCT or HPO. The new tag will use the terminologies defined in the module settings. This could be either the same as SCT or HPO versions, or a custom set can be used.

Minor Bug Fix in open-pedigree

Upgrade open-pedigree to new version

• fixed bug in failing to load pedigrees with gene or phenotype with no terminology
• fixed display bug for gene colours in nodes.
• Added extra error handling to fail more gracefully

Pedigree editor external module for redcap V0.3

Upgrade the version of open-pedigree to a version which includes the new GA4GH FHIR format, which is the new recommended storage format.
Change open-pedigree terminology bindings to use a redcap web-service to fetch terminology data from a FHIR terminology server.

Warning this version may have issues loading existing stored pedigree data due to changes in terminology code system changes.

Minor Bug Fix

Fix issues reported by Warren Welch in redcap forums.

• Don't try to validate the fhir server url if curl is not available in the php install. Missing curl meant the validatation failed even when it could be valid. This way its possible to enter a url if curl is missing.
• Don't use the REDCap api endpoint for referencing the open pedigree files as this did not work.

Display pedigree diagram inside redcap

Upgrade open-pedigree version to allow use of the svg image encoded in the pedigree data to show real representation of the diagram, add compression for large diagrams.

The fhir format returned from the open_pedigree editor will now have a new section called 'Pedigree Diagram' which will contain a DocumentReference which will have an SVG representation of the pedigree diagram. This diagram will be used by the redcap plugin to show the pedigree diagram. Because there are size limitations for the text in the redcap database associated with the pedigree field the
addition of the 'Pedigree Diagram' section can quite easilly exceed the limit. A new option 'Compress Data' has been added to tell the
system how to deal with the returned text exceeding 64K. The options are:

• Never Compress - (this is the default) Compression is not used. If the data exceeds 65K characters the diagram will
  be stripped from the result and any future views of the diagram inside redcap will instead show a placeholder image.
• Compress Large Diagrams >65K - The data is compressed if its over 65K. If its still too large after being
  compressed, the diagram is stripped and the if its greater than 65K its compressed.
• Always Compress - The data is always compressed. If the compressed data is greater than 65K the diagram is stripped.

Allow use in Survey

Originally the external module would only activate in a standard redcap form and not in a survey. This was done because of possible browser issues in a survey. This release allows the control to also show in a survey.

Initial Release

Initial release of pedigree editor external module for redcap.

The pedigree editor external module allows a notes field to be marked with an anotation to indicate the field will represent a pedigree diagram.

The module will then hide or disable the notes field and instead spawn a new window to allow the entry of the pedigree diagram. The diagram will then be serialised as a FHIR Composition JSON string and written into the notes field. The pedigree editor used is https://github.com/aehrc/open-pedigree which is an open version of the phenotips pedigree editor.