Phil's IRI fix

deps.edn

@@ -21,8 +21,7 @@
                      io.github.nextjournal/clerk {:mvn/version "0.15.957"}
                      generateme/fastmath {:mvn/version "2.4.0"
                                           :exclusions [com.github.haifengl/smile-mkl]}}
-        :jvm-opts ["-agentpath:/Applications/YourKit-Java-Profiler-2024.3.app/Contents/Resources/bin/mac/libyjpagent.dylib=disablestacktelemetry,exceptions=disable,delay=10000"
-                   "-XX:+UseZGC" "-XX:+ZGenerational" "-XX:MaxRAMPercentage=50"]}}
+        :jvm-opts ["-XX:+UseZGC" "-XX:+ZGenerational" "-XX:MaxRAMPercentage=50"]}}
 
  :jvm-opts ["-XX:+UseZGC" "-XX:+ZGenerational" "-XX:MaxRAMPercentage=75"]
 

resources/base.edn

@@ -108,7 +108,7 @@
   :target "mondo.owl",
   :format :genegraph.framework.storage.rdf/rdf-xml}
  {:name "https://www.genenames.org/"
-  :source "https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json"
+  :source "https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json"
   :target "hgnc.json",
   :format :genegraph.gene-validity.base/hgnc}
  {:name "http://dataexchange.clinicalgenome.org/terms"

src/genegraph/gene_validity/graphql/schema/resource.clj

@@ -132,4 +132,7 @@
    :type :Resource
    :resolve (fn [context args _]
               (let [r (rdf/resource (:iri args) (:db context))]
-                (or (rdf/ld1-> r [[:cg/website-legacy-id :<]]) r)))})
+                (or (rdf/ld1-> r [[:cg/website-legacy-id :<]])
+                    ;; Phil sends requests from the website that match neither the direct IRI,
+                    ;; nor the assertion_ syntax. This should address that issue.
+                    (s/replace r #"assertion_" ""))))}) 

src/genegraph/gv_setup.clj

@@ -108,7 +108,7 @@
                           ::event/key (:name %)})))
 
   (->> (-> "base.edn" io/resource slurp edn/read-string)
-       (filter #(= "http://dataexchange.clinicalgenome.org/missing-dosage-curations" (:name %)))
+       (filter #(= "https://www.genenames.org/" (:name %)))
        (run! #(p/publish (get-in gv-seed-base-event
                                  [:topics :fetch-base-events])
                          {::event/data %

src/genegraph/user.clj

@@ -1919,3 +1919,74 @@ select ?sop where {
                           ::event/key (:name %)})))
 
   )
+
+;; Erin report -- quarterly update of reports published per
+;; GCEP
+(comment
+  (storage/restore-snapshot
+   (get-in gv-test-app [:storage :gv-tdb]))
+  (tap> (get-in gv-test-app [:storage :gv-tdb]))
+
+  (let [q (rdf/create-query "
+select ?x where { ?x a :sepio/GeneValidityProposition } limit 1")
+        tdb @(get-in gv-test-app [:storage :gv-tdb :instance])]
+    (rdf/tx tdb
+      (->> (q tdb)
+           (mapv #(storage/read tdb (str %)))
+           (run! rdf/pp-model))))
+  )
+
+
+
+;; testing partial updates
+(comment
+  (def last-50-gv
+    (event-store/with-event-reader [r "/Users/tristan/data/genegraph-neo/gene_validity_complete-2024-10-16.edn.gz"]
+      (->> (event-store/event-seq r)
+           (take-last 10)
+           (into []))))
+
+  (defn process-gv-event [e]
+    (p/process (get-in gv-test-app [:processors :gene-validity-transform])
+               (assoc e
+                      ::event/completion-promise (promise)
+                      ::event/skip-local-effects true
+                      ::event/skip-publish-effects true)))
+
+  (->> last-50-gv
+       #_(map #(-> % ::event/timestamp Instant/ofEpochMilli))
+       (take-last 1)
+       (map #(:gene-validity/model (process-gv-event %)))
+       (run! rdf/pp-model))
+
+  (defn process-gv-event [e]
+    (p/process (get-in gv-test-app [:processors :gene-validity-transform])
+               (assoc e 
+                      ::event/completion-promise (promise)
+                      ::event/skip-local-effects true
+                      ::event/skip-publish-effects true)))
+
+  (def sop-query
+    (rdf/create-query "
+select ?sop where {
+  ?curation a :sepio/GeneValidityEvidenceLevelAssertion ;
+  :sepio/is-specified-by ?sop .
+} "))
+
+  (->> last-10-gv
+       (map process-gv-event)
+       (map :gene-validity/model)
+       (map sop-query)
+       (map first)
+       tap>) 
+
+  (->> (-> "base.edn" io/resource slurp edn/read-string)
+       (filter #(= "http://purl.obolibrary.org/obo/sepio-clingen-gene-validity"
+                   (:name %)))
+       (run! #(p/publish (get-in gv-test-app
+                                 [:topics :fetch-base-events])
+                         {::event/data %
+                          ::event/key (:name %)})))
+
+  )
+