Move from panogram to open-pedigree

.gitignore

@@ -0,0 +1,4 @@
+.buildpath
+.idea
+.project
+.settings

PedigreeEditorExternalModule.php

@@ -38,8 +38,8 @@ function redcap_data_entry_form ($project_id, $record, $instrument, $event_id, $
 
         // At one stage these things were going to be in the settings for the editor
         // maybe in the future they will be exposed.
-        $hpoEditorPage = 'panogram/localEditor.html?mode=HPO';
-        $sctEditorPage = 'panogram/localEditor.html?mode=SCT';
+        $hpoEditorPage = 'open-pedigree/localEditor.html?mode=HPO';
+        $sctEditorPage = 'open-pedigree/localEditor.html?mode=SCT';
         $editorPageLocal = TRUE;
         $hpoTag = '@PEDIGREE_HPO';
         $sctTag = '@PEDIGREE_SCT';
@@ -134,8 +134,7 @@ function redcap_data_entry_form ($project_id, $record, $instrument, $event_id, $
         }
         else {
             $transportOptions = <<<EOD
-    pedigreeEditorEM.panogramDataKey = 'PANOGRAM_DIAGRAM_DATA';
-    pedigreeEditorEM.probandDataKey = 'PANOGRAM_PROBAND_DATA';
+    pedigreeEditorEM.openPedigreeDataKey = 'pedigreeData';
 EOD;
         }
 

README.md

@@ -44,4 +44,26 @@ In the data entry page, fields marked with the pedigree editor action tag will s
 
 ![Data Entry (with data)](documentation/data_entry_2.png)
 
-			
+# Limitations
+
+This module uses a FHIR based representation of the pedigree diagram. Unfortunately the specification is still being
+developed, so it is still not possible to map all of the data captured by the pedigree editor. This means that any 
+data with no mapping will be lost. Some other aspects of the mapping also do not translate directly, where possible
+naming conventions are used to try and account for these. For example the FHIR FamilyHistory resource has a single
+name field which is a string. The pedigree editor has a first name, last name and a last name at birth, this will
+be written into the FamilyHistory resource as <first name> <last name> (<last name at birth>). When importing the FHIR
+resource everything but the last word is the first name a trailing '(name)' will be taken as last name at birth.
+
+Heredity options - This can be 'Childless' or 'Infertile' in the editor, but is not currently stored on the fhir resource.
+Carrier Status - This can be 'Carrier' or 'Pre-symptomatic' in the editor, but is not currently stored on the fhir resource.
+Evaluated - This is a checkbox in the editor, but is not currently stored on the fhir resource.
+Lost Contact - This is a checkbox in the editor, but is not currently stored on the fhir resource. 
+Multiple Sibling Nodes - In the editor you can create a single node to represent multiple siblings, at the moment these
+will be saved as a single familiy history resource with no name and the number of siblings will be lost.
+
+Phenotype and Candidate Genes are both stored as Observation Resources associated with a family history resource. The
+system uses a naming convention to distinguish the two, otherwise it tries to match the code system to try and determine
+if the observation represents a Phenotype or Candidate gene.
+
+Life status - This can be 'unborn', 'stillborn' and 'aborted' with an associated gestation age. This will be written into
+the deceasedString field on the family history resource in a form like 'stillborn 34 weeks'.

js/pedigreeEditorEM.js

@@ -135,8 +135,8 @@ pedigreeEditorEM.save = function(field, value) {
 
 pedigreeEditorEM.sendDataToEditor = function(data){
 	if (pedigreeEditorEM.transportType == 'local'){
-		window.localStorage.setItem(pedigreeEditorEM.probandStorageKey, '');
-		window.localStorage.setItem(pedigreeEditorEM.panogramDataKey, JSON.stringify(data));
+		// window.localStorage.setItem(pedigreeEditorEM.probandStorageKey, '');
+		window.localStorage.setItem(pedigreeEditorEM.openPedigreeDataKey, JSON.stringify(data));
 	}
 	else {
 		// doesn't get sent until get the ready signal
@@ -148,13 +148,13 @@ pedigreeEditorEM.sendDataToEditor = function(data){
 pedigreeEditorEM.clearDataToEditor = function(){
 	pedigreeEditorEM.log("Clearing transport data");
 	if (pedigreeEditorEM.transportType == 'local'){
-		window.localStorage.setItem(pedigreeEditorEM.probandStorageKey, null);
-		window.localStorage.setItem(pedigreeEditorEM.panogramDataKey, null);
+		// window.localStorage.setItem(pedigreeEditorEM.probandStorageKey, null);
+		window.localStorage.setItem(pedigreeEditorEM.openPedigreeDataKey, null);
 	}
 	else {
 		if (pedigreeEditorEM.editorWindow) {
-			pedigreeEditorEM.editorWindow.postMessage({"messageType" : "panogram","panogramData" : null}, pedigreeEditorEM.editorPageOrigin);
-			pedigreeEditorEM.editorWindow.postMessage({"messageType" : "proband","probandData" : null}, pedigreeEditorEM.editorPageOrigin);
+			pedigreeEditorEM.editorWindow.postMessage({"messageType" : "openPedigree_data","openPedigreeData" : null}, pedigreeEditorEM.editorPageOrigin);
+			// pedigreeEditorEM.editorWindow.postMessage({"messageType" : "openPedigree_proband","probandData" : null}, pedigreeEditorEM.editorPageOrigin);
 		}
 	}
 };
@@ -164,21 +164,21 @@ pedigreeEditorEM.onMessageEvent = function(event) {
 	if (event.source == pedigreeEditorEM.editorWindow
 			&& event.origin == pedigreeEditorEM.editorPageOrigin) {
 		// the message is from editor window
-		if (event.data.messageType === "panogram_control") {
+		if (event.data.messageType === "openPedigree_control") {
 			if (event.data.message == "started"
 					&& pedigreeEditorEM.sendWhenReady) {
 
 				pedigreeEditorEM.log("Sending data to editor");
 
-				pedigreeEditorEM.editorWindow.postMessage({"messageType" : "proband","probandData" : null}, pedigreeEditorEM.editorPageOrigin);
-				pedigreeEditorEM.editorWindow.postMessage({"messageType" : "panogram","panogramData" : pedigreeEditorEM.messageData}, 
+				// pedigreeEditorEM.editorWindow.postMessage({"messageType" : "openPedigree_proband", "probandData" : null}, pedigreeEditorEM.editorPageOrigin);
+				pedigreeEditorEM.editorWindow.postMessage({"messageType" : "openPedigree_data", "openPedigreeData" : pedigreeEditorEM.messageData}, 
 						pedigreeEditorEM.editorPageOrigin);
 				pedigreeEditorEM.sendWhenReady = false;
 			}
-		} else if (event.data.messageType === "panogram") {
+		} else if (event.data.messageType === "openPedigree_data") {
 			pedigreeEditorEM.log("Got data from editor");
-			if (event.data.panogramData) {
-				pedigreeEditorEM.save(event.data.panogramData.context.field, event.data.panogramData.value);
+			if (event.data.openPedigreeData) {
+				pedigreeEditorEM.save(event.data.openPedigreeData.context.field, event.data.openPedigreeData.value);
 
 			}
 		}
@@ -187,7 +187,7 @@ pedigreeEditorEM.onMessageEvent = function(event) {
 
 pedigreeEditorEM.onStorageEvent = function(storageEvent) {
 
-	if (storageEvent.storageArea == window.localStorage && storageEvent.key == pedigreeEditorEM.panogramDataKey){
+	if (storageEvent.storageArea == window.localStorage && storageEvent.key == pedigreeEditorEM.openPedigreeDataKey){
 		// the data has been updated
 		var data = JSON.parse(storageEvent.newValue);
 

panogram/LICENSE → open-pedigree/LICENSE

@@ -1,14 +1,14 @@
-GNU LESSER GENERAL PUBLIC LICENSE
+                  GNU LESSER GENERAL PUBLIC LICENSE
                        Version 2.1, February 1999
 
  Copyright (C) 1991, 1999 Free Software Foundation, Inc.
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
-(This is the first released version of the Lesser GPL.  It also counts
+[This is the first released version of the Lesser GPL.  It also counts
  as the successor of the GNU Library Public License, version 2, hence
- the version number 2.1.)
+ the version number 2.1.]
 
                             Preamble
 
@@ -470,8 +470,8 @@ safest to attach them to the start of each source file to most effectively
 convey the exclusion of warranty; and each file should have at least the
 "copyright" line and a pointer to where the full notice is found.
 
-    {description}
-    Copyright (C) {year} {fullname}
+    <one line to give the library's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
 
     This library is free software; you can redistribute it and/or
     modify it under the terms of the GNU Lesser General Public
@@ -498,7 +498,7 @@ necessary.  Here is a sample; alter the names:
   library `Frob' (a library for tweaking knobs) written by James Random
   Hacker.
 
-  {signature of Ty Coon}, 1 April 1990
+  <signature of Ty Coon>, 1 April 1990
   Ty Coon, President of Vice
 
 That's all there is to it!

open-pedigree/README.md

@@ -0,0 +1,96 @@
+<p align="center">
+  <img src="https://repository-images.githubusercontent.com/212736090/2759df80-fe9e-11e9-8fa0-8237e35cbaf7" width="400px" alt="Open Pedigree logo"/>
+</p>
+
+<p align="center">
+  <a href="https://opensource.org/licenses/LGPL-2.1" target="_blank">
+    <img src="https://img.shields.io/badge/license-LGPL--2.1-blue.svg" alt="LGPL-2.1">
+  </a>
+  <img src="https://img.shields.io/badge/made%20in-canada-red.svg" alt="Made with love">
+</p>
+
+
+## A free and open-source pedigree tool powered by PhenoTips
+
+Open Pedigree is a robust browser-based genomic pedigree drawing solution using [Prototype](prototypejs.org), [Raphaël](https://dmitrybaranovskiy.github.io/raphael/), and [PhenoTips](https://phenotips.org).
+
+<img width="983" alt="image" src="https://user-images.githubusercontent.com/4251264/68103796-e1048080-fe9d-11e9-9353-6b491aae588d.png">
+
+
+## Features
+
+✔ Robust support for complext families, intergenerational linkages, and consanguinity
+
+✔ Shade nodes with disorders and/or candidate genes
+
+✔ Quickly start with family templates
+
+✔ Automatic consanguinity detection
+
+✔ Import from PED, LINKAGE, GEDCOM (Cyrillic), or BOADICEA
+
+
+## Getting started
+
+Quickly get started with open pedigree on your computer:
+```
+git clone git@github.com:phenotips/open-pedigree.git
+cd open-pedigree
+npm install
+npm start
+```
+Open a browser to http://localhost:9000/
+
+
+
+## Contributing
+
+Contributions welcome! Fork the repository and create a pull request to share your improvements with the community.
+
+In order to ensure that the licensing is clear and stays open, you'll be asked to sign a CLA with your first pull request.
+
+
+## Support
+
+This is free software! Create an issue in GitHub to ask others for help, or try fixing the issue yourself and then make a pull request to contribute it back to the core.
+
+For commercial support or for information about the paid Enterprise version, please contact [Gene42](https://gene42.com/).
+
+
+## License
+
+Copyright (c) 2019 Gene42 Inc.
+
+Open Pedigree is distributed under the [LGPL-2.1](https://opensource.org/licenses/LGPL-2.1) (GNU Lesser General Public License).
+
+You can easily comply with this license by:
+* including prominent notice of the use of Open Pedigree in your software that uses it
+* retaining all copyright notices in the software
+* ensuring that any and all changes you make to the software are disclosed and open-sourced under the LGPL
+
+
+# FHIR export/import
+
+The FHIR import/export does not have an actual specification to follow. There is a specification in development, though
+we have deviated from it, choosing to use a Composition so that the family history resources and observations can be
+bundled together, rather then the List of family history resources in the current specification. Not all data gathered
+by the editor has a mapping in the FHIR representation. This means that any  data with no mapping will be lost. 
+Some other aspects of the mapping also do not translate directly, where possible
+naming conventions are used to try and account for these. For example the FHIR FamilyHistory resource has a single
+name field which is a string. The pedigree editor has a first name, last name and a last name at birth, this will
+be written into the FamilyHistory resource as <first name> <last name> (<last name at birth>). When importing the FHIR
+resource everything but the last word is the first name and a trailing name in brackets will be taken as last name at birth.
+
+Heredity options - This can be 'Childless' or 'Infertile' in the editor, but is not currently stored on the fhir resource.
+Carrier Status - This can be 'Carrier' or 'Pre-symptomatic' in the editor, but is not currently stored on the fhir resource.
+Evaluated - This is a checkbox in the editor, but is not currently stored on the fhir resource.
+Lost Contact - This is a checkbox in the editor, but is not currently stored on the fhir resource. 
+Multiple Sibling Nodes - In the editor you can create a single node to represent multiple siblings, at the moment these
+will be saved as a single familiy history resource with no name and the number of siblings will be lost.
+
+Phenotype and Candidate Genes are both stored as Observation Resources associated with a family history resource. The
+system uses a naming convention to distinguish the two, otherwise it tries to match the code system to try and determine
+if the observation represents a Phenotype or Candidate gene.
+
+Life status - This can be 'unborn', 'stillborn' and 'aborted' with an associated gestation age. This will be written into
+the deceasedString field on the family history resource in a form like 'stillborn 34 weeks'.