updating springer normalizer

normalizer/normalizer-springer/classify4me_SM_normalizer.py

@@ -12,6 +12,7 @@ __date__ = "05/04/17"
 
 import setup_paths
 from nomadcore.parser_backend import JsonParseEventsWriterBackend
+from nomadcore.parse_streamed_dicts import ParseStreamedDicts
 import json
 import sqlite3
 import sys, time, os.path
@@ -19,7 +20,6 @@ from io import open
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 import logging
 
-INPUT_FORMULA = sys.argv[1]
 DB_FILE = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "SM_all08.db"))
 #OUTPUT_FILE = sys.argv[2]    
 
@@ -32,12 +32,7 @@ DB = os.path.exists(DB_FILE)
 conn = sqlite3.connect(DB_FILE)
 cur = conn.cursor()
 
-fOut = sys.stdout
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../../nomad-meta-info/meta_info/nomad_meta_info/public.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
-backend = JsonParseEventsWriterBackend(metaInfoEnv, fOut)
-
-def classify4me():
+def classify4me(INPUT_FORMULA, backend):
     logging.info('(%r) classified according to Springer Materials as follow: \n  \n', INPUT_FORMULA )
     
     ##print('***',INPUT_FORMULA,  ' classified in Springer Materials as:','\n{')
@@ -224,11 +219,48 @@ def classify4me():
             
             
         backend.closeSection("section_springer_material",matS)
-    
-classify4me()
-fOut.flush()
-           
-  #  con.create_function("", 1, )
-cur.close()    
-conn.close()
+
+def main():
+    metapath = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
+          'common.nomadmetainfo.json'
+    metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), metapath))
+  
+    metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
+                                      dependencyLoader=None,
+                                      extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
+                                      uri=None)
+    fOut = sys.stdout
+    backend = JsonParseEventsWriterBackend(metaInfoEnv, fOut)
+
+    #Start 
+    calcContext=sys.argv[1]
+    backend.startedParsingSession(
+      calcContext,
+      parserInfo = {'name':'SpringerNormalizer', 'version': '1.0'})
+  
+    dictReader = ParseStreamedDicts(sys.stdin)
+    while True:
+        sectSys = dictReader.readNextDict()
+        if sectSys is None:
+            break
+        try:
+            formula = sectSys.get("system_composition")
+            if formula:
+                backend.openContext(calcContext)
+                for f in formula:
+                    classify4me(f, backend)
+                fOut.flush()
+                backend.closeContext(calcContext)
+        except:
+            logging.exception("exception trying to calculate springer data for %s", sectSys)
+    backend.finishedParsingSession("ParseSuccess", None)
+    fOut.flush()
+    ### 
+    #  con.create_function("", 1, )
+    cur.close()
+    conn.close()
+
+if __name__ == '__main__':
+    main()
 

normalizer/normalizer-springer/input.txt

+{
+"system_composition": ["MgNd"],
+"calculation_uri": "nmd://R.../C..."
+}

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

@@ -22,6 +22,13 @@ import scala.collection.breakOut
 import eu.nomad_lab.normalize.ExternalNormalizerGenerator
 import eu.nomad_lab.meta
 import eu.nomad_lab.query
+import eu.nomad_lab.resolve._
+import eu.nomad_lab.h5.EmitJsonVisitor
+import eu.nomad_lab.h5.H5EagerScanner
+import eu.nomad_lab.h5.SectionH5
+import eu.nomad_lab.parsers.ExternalParserWrapper
+import eu.nomad_lab.JsonUtils
+import scala.collection.mutable.StringBuilder
 
 object SpringerNormalizer extends ExternalNormalizerGenerator(
   name = "SpringerNormalizer",
@@ -44,6 +51,7 @@ object SpringerNormalizer extends ExternalNormalizerGenerator(
     "${contextUri}", "${archivePath}"),
   resList = Seq(
     "normalizer-springer/classify4me_SM_normalizer.py",
+    "normalizer-springer/setup_paths.py",
     "normalizer-springer/SM_all08.db",
     "nomad_meta_info/public.nomadmetainfo.json",
     "nomad_meta_info/common.nomadmetainfo.json",
@@ -56,4 +64,65 @@ object SpringerNormalizer extends ExternalNormalizerGenerator(
     "python" -> "python-common/common/python/nomadcore"
   ) ++ DefaultPythonInterpreter.commonDirMapping(),
   metaInfoEnv = lab.meta.KnownMetaInfoEnvs.common
-)
+) {
+  val trace: Boolean = false
+
+  override def stdInHandler(context: ResolvedRef)(wrapper: ExternalParserWrapper)(pIn: java.io.OutputStream): Unit = {
+    val out: java.io.Writer = new java.io.BufferedWriter(new java.io.OutputStreamWriter(pIn));
+    val stringBuilder = if (trace)
+      new StringBuilder
+    else
+      null
+    def writeOut(s: String): Unit = {
+      out.write(s)
+      if (trace) stringBuilder ++= s
+    }
+    def flush(): Unit = {
+      out.flush()
+      if (trace) {
+        logger.info(stringBuilder.result())
+        stringBuilder.clear()
+      }
+    }
+    writeOut("[")
+    var isFirst = true
+    try {
+      context match {
+        case Calculation(archiveSet, c) =>
+          val sysTable = c.sectionTable(Seq("section_run", "section_system"))
+
+          def outputSysSection(sysSection: SectionH5): Unit = {
+            if (!isFirst)
+              writeOut(",")
+            else
+              isFirst = false
+            //writeOut(s"""{
+            //              |  "context": ${JsonUtils.escapeString(m.toRef.toUriStr(archiveSet.objectKind))},
+            //              |  "section_system": """.stripMargin)
+            val visitor = new EmitJsonVisitor(
+              writeOut = writeOut
+            )
+            val scanner = new H5EagerScanner
+            scanner.scanResolvedRef(Section(archiveSet, sysSection), visitor)
+            //writeOut("}")
+            flush()
+          }
+
+          val nSys = sysTable.lengthL
+          if (nSys > 0)
+            //  outputSysSection(sysTable(0))
+            //if (nSys > 1)
+            outputSysSection(sysTable(nSys - 1))
+
+          writeOut("]")
+          flush()
+        case r =>
+          throw new Exception(s"FhiAimsBasisNormalizer expected a calculation as context, but got $r")
+      }
+    } finally {
+      out.close()
+      pIn.close()
+      wrapper.sendStatus = ExternalParserWrapper.SendStatus.Finished
+    }
+  }
+}