adjust to MP changes + make diff optional

project.clj

@@ -16,12 +16,13 @@
                  ;; state management library
                  [mount "0.1.18"]
                  [org.clojure/tools.logging "1.3.0"]
-                 [ch.qos.logback/logback-classic "1.2.3"]
+                 [ch.qos.logback/logback-classic "1.5.7"
+                  :exclusions [org.slf4j/slf4j-api]]
                  [cheshire "5.13.0"]
                  [clj-http "3.13.0"]
                  [org.clojure/tools.cli "1.1.230"]
 
-                 [edu.ucsd.sbrg.ModelPolisher "2.1.8"]
+                 [edu.ucsd.sbrg.ModelPolisher "2.1.10"]
 
                  ;; dev time
                  [ring/ring-devel "1.12.2"]]

resources/default-request-config.json

@@ -1,5 +1,6 @@
 {
     "allow-model-to-be-saved-on-server": true,
+    "produce-diff": true,
     "sbo-terms": {
 	"add-generic-terms": true
     },

resources/logback.xml

@@ -1,4 +1,5 @@
 <configuration scan="true" scanPeriod="5 seconds">
+  <statusListener class="ch.qos.logback.core.status.NopStatusListener" />
   <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d [%thread] %X{run.id} %-5level %logger{36} - %msg%n</pattern>

src/edu/tue/csb/mpserver/http/handler.clj

@@ -12,24 +12,24 @@
   (let [{:keys [context sbml-doc]} params
         pre-validation-results     (validate/validate (:tempfile params))
         mp-parameters              (-> context :mp-parameters)]
-    (log/debug "Validation results:" pre-validation-results)
     (do
 
       (when (and (not (parameters/dont-fix? mp-parameters))
                  (not-empty (:validation pre-validation-results)))
-        (fixing/fix! sbml-doc))
+        (fixing/fix! sbml-doc context))
 
-      (when (or (empty? (:validation pre-validation-results))
-                (parameters/polish-even-if-model-invalid? mp-parameters))
-        (polishing/polish! sbml-doc context))
+      (let [polish? (or (empty? (:validation pre-validation-results))
+                            (parameters/polish-even-if-model-invalid? mp-parameters))]
+        (when polish?
+          (polishing/polish! sbml-doc context)
 
-      (when (parameters/annotate-with-bigg? mp-parameters)
-        (log/debug "Annotating with BiGG")
-        (annotation/annotate-with-bigg! sbml-doc context))
+          (when (parameters/annotate-with-bigg? mp-parameters)
+            (log/debug "Annotating with BiGG")
+            (annotation/annotate-with-bigg! sbml-doc context))
 
-      (when (parameters/annotate-with-adb? mp-parameters)
-        (log/debug "Annotating with ADB")
-        (annotation/annotate-with-adb! sbml-doc context))
+          (when (parameters/annotate-with-adb? mp-parameters)
+            (log/debug "Annotating with ADB")
+            (annotation/annotate-with-adb! sbml-doc context))))
 
       (let [base64-model (io/sbml-doc->base64 context sbml-doc)
             tmp          (java.io.File/createTempFile "postpolish-" ".xml")]

src/edu/tue/csb/mpserver/http/middleware.clj

@@ -106,17 +106,21 @@
   [handler]
   (fn wrapped-with-diff-handler
     [{:keys [params] :as req}]
-    (let [{:keys [sbml-doc]} params
+    (let [{:keys [config sbml-doc]} params
           old-doc            (.clone sbml-doc)
-          resp               (handler req)]
-      (log/debug "Calculating diff.")
-      (try
-        (let [diff  (diff/diff old-doc sbml-doc)]
-          (log/debug "Done calculating diff.")
-          (assoc-in resp [:body :diff] diff))
-        (catch Throwable t
-          (log/error t "Failed diff.")
-          (assoc-in resp [:body :diff] {:message "Sorry, calculating the diff failed for some reason."}))))))
+          resp               (handler req)
+          produce-diff?      (:produce-diff config)]
+      (if produce-diff?
+        (do
+          (log/debug "Calculating diff.")
+          (try
+            (let [diff (diff/diff old-doc sbml-doc)]
+              (log/debug "Done calculating diff.")
+              (assoc-in resp [:body :diff] diff))
+            (catch Throwable t
+              (log/error t "Failed diff.")
+              (assoc-in resp [:body :diff] {:message "Sorry, calculating the diff failed for some reason."}))))
+        resp))))
 
 
 (defn wrap-with-save-file!

src/edu/tue/csb/mpserver/wrapper/annotation.clj

@@ -9,7 +9,7 @@
 
 (defn annotate-with-bigg! [^SBMLDocument doc {:keys [mp-parameters registry observers]}]
   (let [bigg-params    (.. mp-parameters (annotation) (biggAnnotationParameters))
-        sbo-params     (.. mp-parameters (sboTerms))
+        sbo-params     (.. mp-parameters (sboParameters))
         bigg           (BiGGDB.)
         bigg-annotator (BiGGSBMLAnnotator. bigg bigg-params sbo-params registry observers)]
     (.annotate bigg-annotator doc)))

src/edu/tue/csb/mpserver/wrapper/fixing.clj

@@ -8,6 +8,6 @@
    (edu.ucsd.sbrg.fixing SBMLFixer)
    (java.io OutputStream)))
 
-(defn fix! [sbml-doc]
-  (let [fixer (SBMLFixer.)]
+(defn fix! [sbml-doc {:keys [mp-parameters]}]
+  (let [fixer (SBMLFixer. (.fixing mp-parameters))]
     (.fix fixer sbml-doc 0)))

src/edu/tue/csb/mpserver/wrapper/io.clj

@@ -14,7 +14,7 @@
   [input ^Parameters params]
   (try
     (let [registry (IdentifiersOrg.)]
-      (.read (ModelReader. (.sboTerms params) registry) input))
+      (.read (ModelReader. (.sboParameters params) registry) input))
     (catch Exception e
       (throw (ex-info "Reading file failed"
                       {:type   :parse/file

src/edu/tue/csb/mpserver/wrapper/parameters.clj

@@ -48,4 +48,4 @@
   (.. params (fixing) (dontFix)))
 
 (defn polish-even-if-model-invalid? [^Parameters params]
-  (.. params (fixing) (polishEvenIfModelInvalid)))
+  (.. params (polishing) (polishEvenIfModelInvalid)))

src/edu/tue/csb/mpserver/wrapper/polishing.clj

@@ -8,7 +8,7 @@
 
 (defn polish! [^SBMLDocument doc {:keys [mp-parameters registry observers]}]
   (let [polisher (SBMLPolisher. (.polishing mp-parameters)
-                                (.sboTerms mp-parameters)
+                                (.sboParameters mp-parameters)
                                 registry
                                 observers)]
     (.polish polisher doc)))