Mint Plazi resource IRIs with https:// as the canonical scheme

README.md

@@ -21,6 +21,35 @@ This webserver also exposes the follwing paths:
 - `/full_update`: send a `POST` here to run the full_update script. Note that
   this will not delete any files (yet).
 
+## Resource IRIs
+
+Every IRI gg2rdf mints for a Plazi resource uses the `https://` scheme:
+
+| Resource                  | IRI                                                     |
+| ------------------------- | ------------------------------------------------------- |
+| treatment                 | `https://treatment.plazi.org/id/<treatment-id>`         |
+| material citation         | `https://tb.plazi.org/GgServer/dwcaRecords/<id>.mc.<n>` |
+| taxon name                | `https://taxon-name.plazi.org/id/<kingdom>/<name>`      |
+| taxon concept             | `https://taxon-concept.plazi.org/id/<kingdom>/<name>`   |
+| publication without a DOI | `https://publication.plazi.org/id/<masterDocId>`        |
+
+`https://` is canonical: it is the scheme that resolves on every Plazi host, and
+it is the scheme the loaders (`turtle-hook`, `turtle-hook-nq`) name their graphs
+with, so a treatment and the graph it lands in share one IRI. A `httpUri`
+attribute TreatmentBank supplies with `http://` is rewritten to `https://` when
+it points at a Plazi host; identifiers of other publishers (DOIs, GBIF) are
+taken as they are.
+
+Vocabulary namespaces are a different matter and stay as they are — `trt:` is
+`http://plazi.org/vocab/treatment#`, alongside `dwc:`, `cito:` and `fabio:`,
+which are `http://` by convention. Changing a vocabulary namespace breaks every
+consumer's prefix declarations and belongs to a redesign of the ontologies, not
+to this pipeline.
+
+Output produced before this change (plazi/gg2rdf#33) carries `http://` subjects.
+Rewriting a store that holds such data in place, without replaying every file,
+is described in turtle-hook's README.
+
 ## Usage
 
 Build as a docker container.

src/gg2rdf.ts

@@ -233,7 +233,7 @@ export function gg2rdf(
    *
    * replaces <xsl:template match="document"> and <xsl:template match="treatment"> */
   function makeTreatment() {
-    const t = new Subject(URI(`http://treatment.plazi.org/id/${id}`));
+    const t = new Subject(URI(`https://treatment.plazi.org/id/${id}`));
 
     if (treatmentTaxon) {
       const taxon = treatmentTaxon.el;
@@ -772,16 +772,21 @@ export function gg2rdf(
   /** replaces <xsl:template match="materialsCitation[@specimenCode]" mode="subject"> */
   function makeCitedMaterial(c: Element): string {
     const mcId = c.getAttribute("id");
-    const httpUri = c.getAttribute("httpUri");
+    // TreatmentBank still hands out http:// for its own resources; https:// is
+    // the canonical scheme for everything under plazi.org (see issue #33)
+    const httpUri = c.getAttribute("httpUri")?.replace(
+      /^http:\/\/(?=[a-z0-9-]+\.plazi\.org\/)/,
+      "https://",
+    );
     const gbifOccurrenceId = c.getAttribute("ID-GBIF-Occurrence");
     const specimenCode = c.getAttribute("specimenCode");
 
     const uri = mcId
-      ? URI(`http://tb.plazi.org/GgServer/dwcaRecords/${id}.mc.${mcId}`)
+      ? URI(`https://tb.plazi.org/GgServer/dwcaRecords/${id}.mc.${mcId}`)
       : (gbifOccurrenceId
         ? URI(`https://www.gbif.org/occurrence/${gbifOccurrenceId}`)
         : (httpUri ? URI(httpUri) : URI(
-          `http://treatment.plazi.org/id/${id}/${partialURI(specimenCode)}`,
+          `https://treatment.plazi.org/id/${id}/${partialURI(specimenCode)}`,
           "_",
         )));
 
@@ -1247,7 +1252,7 @@ export function gg2rdf(
 
   /** replaces <xsl:call-template name="taxonNameBaseURI"> */
   function taxonNameBaseURI({ kingdom }: { kingdom: string }) {
-    return `http://taxon-name.plazi.org/id/${
+    return `https://taxon-name.plazi.org/id/${
       kingdom ? partialURI(kingdom) : "INVALID"
     }`;
   }
@@ -1374,7 +1379,7 @@ export function gg2rdf(
    *
    * replaces <xsl:call-template name="taxonConceptBaseURI"> */
   function taxonConceptBaseURI({ kingdom }: { kingdom: string }) {
-    return `http://taxon-concept.plazi.org/id/${kingdom}`;
+    return `https://taxon-concept.plazi.org/id/${kingdom}`;
   }
 
   /** returns valid turtle uri
@@ -1423,7 +1428,7 @@ export function gg2rdf(
     const doiID: string | undefined = doc.getAttribute("ID-DOI");
     if (!doiID) {
       return URI(
-        `http://publication.plazi.org/id/${
+        `https://publication.plazi.org/id/${
           partialURI(doc.getAttribute("masterDocId"))
         }`,
       );