Merge pull request #18 from joerivandervelde/main

Inclusion criteria lookup and better Markdown documentation

fair-genomes.yml

@@ -73,10 +73,10 @@ modules:
             description: The age at which death occurred.
             ontology: NCIT:C135383 [http://purl.obolibrary.org/obo/NCIT_C135383]
             values: Integer
-          - name: Inclusion criterion
+          - name: Inclusion criteria
             description: An inclusion criterion defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process.
             ontology: OBI:0500027 [http://purl.obolibrary.org/obo/OBI_0500027]
-            values: Text
+            values: LookupMany [lookups/InclusionCriteria.txt]
           - name: Primary affiliated institute
             description: The most significant institute for medical consultation and/or study inclusion in context of the genetic disease of a person.
             ontology: SIO:000688 [https://semanticscience.org/resource/SIO_000688.rdf]

lookups/InclusionCriteria.txt

@@ -0,0 +1,12 @@
+value	description	codesystem	code	iri
+Health status	Health status	MIABIS-2.0-22	inclusion-criteria#Health status	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Health status
+Hospital patient	Hospital patient	MIABIS-2.0-22	inclusion-criteria#Hospital patient	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Hospital patient
+Use of medication	Use of medication	MIABIS-2.0-22	inclusion-criteria#Use of medication	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Use of medication
+Gravidity	Gravidity	MIABIS-2.0-22	inclusion-criteria#Gravidity	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Gravidity
+Age group	Age group	MIABIS-2.0-22	inclusion-criteria#Age group	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Age group
+Familial status	Familial status	MIABIS-2.0-22	inclusion-criteria#Familial status	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Familial status
+Sex	Sex	MIABIS-2.0-22	inclusion-criteria#Sex	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Sex
+Country of residence	Country of residence	MIABIS-2.0-22	inclusion-criteria#Country of residence	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Country of residence
+Ethnic origin	Ethnic origin	MIABIS-2.0-22	inclusion-criteria#Ethnic origin	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Ethnic origin
+Population representative sampling	Population representative sampling	MIABIS-2.0-22	inclusion-criteria#Population representative sampling	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Population representative sampling
+Lifestyle/Exposure	Lifestyle/Exposure	MIABIS-2.0-22	inclusion-criteria#Lifestyle/Exposure	https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#inclusion-criteria#Lifestyle/Exposure

src/main/java/org/fairgenomes/transformer/datastructures/Element.java

@@ -71,7 +71,7 @@ public String valueTypeToMarkDown()
             return "[" + lookup.srcFile.getName().replace(".txt", "") + "](../../lookups/"+lookup.srcFile.getName()+") lookup (" + lookup.lookups.size() + " choices)";
         }else if(isReference())
         {
-            return "Reference to "+ referenceTo +" module";
+            return "Reference to instances of "+ referenceTo;
         }
         else
         {

src/main/java/org/fairgenomes/transformer/datastructures/Module.java

@@ -28,4 +28,13 @@ public String toString() {
                 ", elements=" + elements +
                 '}';
     }
+
+    /**
+     * Helper function to convert name into a Markdown anchor
+     * @return
+     */
+    public String toMarkdownAnchor()
+    {
+        return "#module-" + name.replace(" ", "-").toLowerCase();
+    }
 }

src/main/java/org/fairgenomes/transformer/implementations/markdown/ToMD.java

@@ -2,6 +2,7 @@
 
 import org.fairgenomes.transformer.datastructures.Element;
 import org.fairgenomes.transformer.datastructures.FAIRGenomes;
+import org.fairgenomes.transformer.datastructures.Lookup;
 import org.fairgenomes.transformer.datastructures.Module;
 
 import java.io.BufferedWriter;
@@ -30,9 +31,23 @@ public ToMD(FAIRGenomes fg, File outputFolder) throws Exception {
     }
 
     public void go() throws IOException {
+        int totalNrOfElements = 0;
+        for (Module m : fg.modules) {
+            totalNrOfElements += m.elements.size();
+        }
+
         FileWriter fw = new FileWriter(new File(outputFolder, "fairgenomes-semantic-model.md"));
         BufferedWriter bw = new BufferedWriter(fw);
         bw.write("# FAIR Genomes semantic metadata model" + RN + RN);
+        bw.write(fg.description + " Version "+fg.version + ", "+fg.date+". This model consists of __" + fg.modules.size() + " modules__ that contain __" + totalNrOfElements + " metadata elements__ in total." + RN + RN);
+
+        bw.write("## Module overview" + RN + RN);
+        bw.write("| Name | Description | Ontology | Nr. of elements |" + RN);
+        bw.write("|---|---|---|---|" + RN);
+        for (Module m : fg.modules) {
+            bw.write("| ["+m.name+"](" + m.toMarkdownAnchor() + ") | " + m.description + " | [" + m.codeSystem + ":" + m.code + "](" + m.iri + ") | " + m.elements.size() + " |" + RN);
+        }
+        bw.write(RN);
 
         for (Module m : fg.modules) {
             bw.write("## Module: " + m.name + RN);
@@ -48,12 +63,13 @@ public void go() throws IOException {
         }
 
         bw.write("## Null flavors" + RN);
-        bw.write("Each lookup in FAIR Genomes is supplemented with so-called 'null flavors' from HL7. These can be used to indicate precisely why a particular value could not be entered into the system, providing substantially more insight than simply leaving a field empty. The null flavors are:" + RN + RN);
-        bw.write("| Value | Description |" + RN);
-        bw.write("|---|---|" + RN);
+        bw.write("Each lookup in FAIR Genomes is supplemented with so-called 'null flavors' from HL7. These can be used to indicate precisely why a particular value could not be entered into the system, providing substantially more insight than simply leaving a field empty." + RN + RN);
+        bw.write("| Value | Description | Ontology |" + RN);
+        bw.write("|---|---|---|" + RN);
         for(String key: fg.lookupGlobalOptionsInstance.lookups.keySet())
         {
-            bw.write("| " + key.substring(0,key.indexOf("(")-1) + " | " + fg.lookupGlobalOptionsInstance.lookups.get(key).description + " |" + RN);
+            Lookup nf = fg.lookupGlobalOptionsInstance.lookups.get(key);
+            bw.write("| " + key.substring(0,key.indexOf("(")-1) + " | " + nf.description + " | " + "[" + nf.codesystem + ":" + nf.code + "](" + nf.iri + ") |" + RN);
         }
         bw.write(RN);