h5Tool rename fixes

archive/h5-tool/src/main/docker/meta-values-replacements.txt

+# section_run/program_basis_set_type
+ MM -> none
+ Gaussians -> GTOs
+ gaussians -> GTOs
+ "Real-space grid" -> "real-space grid"
+# section_calculation_info/calculation_uploader_name
+ "danilo brambila" -> "Danilo Brambila"
+ "-" -> none
+ "–" -> none
+# section_run/section_method/section_XC_functionals/XC_functional_name
+ x_qe_VDW_DF1    -> vDW_DF
+ x_qe_VDW_DF2    -> vDW_DF2
+ x_qe_GGA_X_GAUP    ->     HYB_GGA_XC_GAU_PBE

archive/h5-tool/src/main/docker/renameWorker.sh

+#!/bin/bash
+
+cmd="java -Djava.library.path=/lib -jar /app/h5Tool.jar"
+baseName=${baseName:-toRename-}
+targetDir=${targetDir:---target-dir=/normalized/productionH5-patched}
+globPattern=${globPattern:-??}
+renames=${renames:---renames=/app/meta-values-replacements.txt}
+cmdArgs=${cmdArgs:-rename  $renames $targetDir --source-paths-file=\$f}
+
+if [ -e /config.sh ] ; then
+   source /config.sh
+fi
+cd /work
+for f in /work/$baseName$globPattern ; do
+  (
+  if [[ -e "$f" ]] ; then
+      echo $cmd $cmdArgs  "out-$(basename $f).txt"
+      eval $cmd $cmdArgs >& "out-$(basename $f).txt"
+  fi
+) &
+done
+wait

core/src/main/scala/eu/nomad_lab/h5/H5Renamer.scala

@@ -22,18 +22,18 @@ object H5Rename {
   /**
    * Renames the values of the value table at repl.metaPath of all calculations in the archive according to the repl.replacements mapping
    */
-  def renameStr(file: FileH5, repl: Replacements): Unit = {
+  def renameStr(file: FileH5, repls: Seq[Replacements]): Unit = {
     for (arch <- file.archives()) {
-      renameStr(arch, repl)
+      renameStr(arch, repls)
     }
   }
 
   /**
    * Renames the values of the value table at repl.metaPath of all calculations in the archive according to the repl.replacements mapping
    */
-  def renameStr(archive: ArchiveH5, repl: Replacements): Unit = {
+  def renameStr(archive: ArchiveH5, repls: Seq[Replacements]): Unit = {
     for (calculation <- archive.calculations()) {
-      renameStr(calculation, repl)
+      renameStr(calculation, repls)
     }
   }
 
@@ -41,10 +41,12 @@ object H5Rename {
    * Renames the values of the value table at repl.metaPath of the given calculation
    * according to the repl.replacements mapping
    */
-  def renameStr(calculation: CalculationH5, repl: Replacements): Unit = {
-    val valueTablePath = repl.metaPath
-    val valueTable = calculation.sectionTable(valueTablePath.dropRight(1)).subValueTable(valueTablePath.last)
-    renameStr(valueTable, repl.replacements)
+  def renameStr(calculation: CalculationH5, repls: Seq[Replacements]): Unit = {
+    for (repl <- repls) {
+      val valueTablePath = repl.metaPath
+      val valueTable = calculation.sectionTable(valueTablePath.dropRight(1)).subValueTable(valueTablePath.last)
+      renameStr(valueTable, repl.replacements)
+    }
   }
 
   /**
@@ -79,8 +81,10 @@ object H5Rename {
             }
           }
         }
-        if (hasRenames)
+        if (hasRenames) {
+          //logger.debug(s"$valueTable has replacements")
           H5Lib.datasetWrite(valueDatasetId, value = vals, dtypeStr = "C")
+        }
       } finally {
         H5Lib.datasetClose(valueDatasetId)
       }