fixing prototype normalizer

normalizer/normalizer-prototypes/classify4me_prototypes.py

@@ -30,8 +30,7 @@ import fractions
 import setup_paths
 
 ### new updated location for the prototypes
-from nomadcore.structure_types import \
-    structure_types_by_spacegroup as str_types_by_spg
+from nomadcore.structure_types import structure_types_by_spacegroup as str_types_by_spg
 from nomadcore.parse_streamed_dicts import ParseStreamedDicts
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.parser_backend import JsonParseEventsWriterBackend
@@ -210,17 +209,24 @@ def classify_by_norm_wyckoff(sectionSystem):
         #as in the normalized version
         cell = None
         conf = sectionSystem
+        
         lab = conf.get("atom_labels", None)
+        if lab is None : return None
         ##periodicDirs = conf.get("configuration_periodic_dimensions", periodicDirs)
-        atomSpecies = [toAtomNr(l) for l in lab[0]['flatData']]
+        atomSpecies = [toAtomNr(l) for l in lab['flatData']]
         #print (atomSpecies)
         newCell = conf.get("simulation_cell")
+        
+        if newCell is None : return None
+        
         if newCell:
             cell = dictToNarray(newCell)
         symm = None
         #print("***full:",cell)
         #acell = cell.reshape(3,3)
-        atomPos = dictToNarray(conf.get("atom_positions")[0])
+        atomPos = dictToNarray(conf.get("atom_positions"))
+        
+        if atomPos is None : return None
         
         symm = systemToSpg(cell, atomSpecies, atomPos)
         wyckoffs = symm.get("wyckoffs")
@@ -262,9 +268,18 @@ def main():
                                       extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
                                       uri=None)
     backend = JsonParseEventsWriterBackend(metaInfoEnv)
+    #Start 
+    calcContext=sys.argv[1]
+    backend.startedParsingSession(
+      calcContext,
+      parserInfo = {'name':'PrototypesNormalizer', 'version': '1.0'})
+
+  
+
     dictReader = ParseStreamedDicts(sys.stdin)
     while True:
         sectSys = dictReader.readNextDict()
+        try:
             if sectSys is None:
                 break
                 label = classify_by_norm_wyckoff(sectSys)
@@ -272,6 +287,14 @@ def main():
                     backend.openContext(sectSys['uri'])
                     backend.addValue("prototype_label", label)
                     backend.closeContext(sectSys['uri'])
+                    sys.stdout.flush()
+        except:
+            logging.exception("exception trying to calculate prototype for %s",sectSys)
+
+    backend.finishedParsingSession("ParseSuccess", None)
+    sys.stdout.flush()
+ 
+
 
 if __name__ == '__main__':
     main()

normalizer/normalizer-prototypes/example3.inp

@@ -3,8 +3,8 @@
   "name": "section_system",
   "gIndex": 0,
   "uri": "nmd://NcC8TDWGWCtQLhWeB2a1N8y9Q7y4r/CCDeb8diABbP4BgHPwHeKgmdzadEM/section_run/0c/section_system/0c", 
-  "atom_labels": [{"flatData":["Sn","Sn"],"shape":[2]},{"flatData":["Sn","Sn"],"shape":[2]}], 
-  "atom_positions": [{"flatData":[0.0,0.0,0.0,1.6415278E-10,-9.477365356213973E-11,2.724677455E-10],"shape":[2,3]},{"flatData":[0.0,0.0,0.0,1.6415278E-10,-9.477365356213973E-11,2.724677455E-10],"shape":[2,3]}], 
-  "configuration_periodic_dimensions": [{"flatData":[true,true,true],"shape":[3]}], 
+  "atom_labels": {"flatData":["Sn","Sn"],"shape":[2]},
+  "atom_positions": {"flatData":[0.0,0.0,0.0,1.6415278E-10,-9.477365356213973E-11,2.724677455E-10],"shape":[2,3]}, 
+  "configuration_periodic_dimensions": {"flatData":[true,true,true],"shape":[3]}, 
   "simulation_cell": {"flatData":[1.6415278E-10,-2.84320955E-10,0.0,1.6415278E-10,2.84320955E-10,0.0,0.0,0.0,5.44935491E-10],"shape":[3,3]}
 }
\ No newline at end of file

normalizer/normalizer-prototypes/example_new.inp

+[{
+  "type": "nomad_section_2_0",
+  "name": "section_system",
+  "gIndex": 0,
+  "uri": "nmd://NcC8TDWGWCtQLhWeB2a1N8y9Q7y4r/C-EE2qc_XLeNhj4VC1vjZGV-JXVtx/section_run/0c/section_system/0c",
+  "atom_labels": {"flatData":["Cr"],"shape":[1]},
+  "atom_positions": {"flatData":[0.0,0.0,0.0],"shape":[1,3]},
+  "configuration_periodic_dimensions": [{"flatData":[true,true,true],"shape":[3]}],
+  "simulation_cell": {"flatData":[-1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,-1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,-1.3940056000000002E-10],"shape":[3,3]}
+}
+,{
+  "type": "nomad_section_2_0",
+  "name": "section_system",
+  "gIndex": 2,
+  "uri": "nmd://NcC8TDWGWCtQLhWeB2a1N8y9Q7y4r/C-EE2qc_XLeNhj4VC1vjZGV-JXVtx/section_run/0c/section_system/2c",
+  "atom_labels": {"flatData":["Cr"],"shape":[1]},
+  "atom_positions": {"flatData":[0.0,0.0,0.0],"shape":[1,3]},
+  "configuration_periodic_dimensions": [{"flatData":[true,true,true],"shape":[3]}],
+  "simulation_cell": {"flatData":[-1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,-1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,1.3940056000000002E-10,-1.3940056000000002E-10],"shape":[3,3]}
+}
+]
\ No newline at end of file

normalizer/normalizer-prototypes/example_new2.inp

+ [{
+   "type": "nomad_section_2_0",
+   "name": "section_system",
+   "gIndex": 0,
+   "uri": "nmd://N0jqPXU7FP2SaaH8sMvXrW0DZsK0Z/CGivpJxhUx8d3FzFw7jHDjE51ZlOK/section_run/0c/section_system/0c",
+   "atom_labels": {"flatData":["Au","Au","Au","O","O","H"],"shape":[6]},
+   "atom_positions": {"flatData":[4.903707E-10,5.365501E-10,5.622263000000001E-10,7.491290000000001E-10,5.132975E-10,5.667301E-10,9.918509000000001E-10,5.750429E-10,5.194042E-10,1.1977479E-9,5.786581000000001E-10,5.245453000000001E-10,1.2591336E-9,5.101932E-10,4.114972E-10,1.2846226E-9,4.2635300000000006E-10,4.542142E-10],"shape":[6,3]}
+ }
+]

src/main/scala/eu/nomad_lab/normalizers/PrototypeNormalizer.scala

@@ -19,7 +19,7 @@ object PrototypesNormalizer extends ExternalNormalizerGenerator(
   name = "PrototypesNormalizer",
   info = jn.JObject(
     ("name" -> jn.JString("PrototypesNormalizer")) ::
-      ("normalizerId" -> jn.JString("PrototypesNormalizer" + lab.PrototypesVersionInfo.version)) ::
+      ("parserId" -> jn.JString("PrototypesNormalizer" + lab.PrototypesVersionInfo.version)) ::
       ("versionInfo" -> jn.JObject(
         ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
           case (k, v) => k -> jn.JString(v.toString)
@@ -49,14 +49,14 @@ object PrototypesNormalizer extends ExternalNormalizerGenerator(
   ) ++ DefaultPythonInterpreter.commonDirMapping(),
   metaInfoEnv = lab.meta.KnownMetaInfoEnvs.all
 ) {
-  val trace: Boolean = true
+  val trace: Boolean = false
 
   override def stdInHandler(context: ResolvedRef)(wrapper: ExternalParserWrapper)(pIn: java.io.OutputStream): Unit = {
-    val out: java.io.Writer = if (trace)
-      new java.io.BufferedWriter(new java.io.OutputStreamWriter(pIn));
+    val out: java.io.Writer = new java.io.BufferedWriter(new java.io.OutputStreamWriter(pIn));
+    val stringBuilder = if (trace)
+      new StringBuilder
     else
       null
-    val stringBuilder = new StringBuilder
     def writeOut(s: String): Unit = {
       out.write(s)
       if (trace) stringBuilder ++= s