Fixed publish bugs.

nomad/client/migration.py

@@ -116,12 +116,9 @@ def upload(paths: list, create_packages, local: bool, parallel: int):
             logger.info('migrated upload with result', upload_path=path, **report)
 
             task.put([
-                ('uploads: {:7d}', 1),
-                ('packages: {:7d}', report.packages),
-                ('total_source_calcs: {:7d}', report.total_source_calcs),
-                ('total_calcs: {:7d}', report.total_calcs),
-                ('failed_calcs: {:7d}', report.failed_calcs),
+                ('uploads: {:5d}', 1),
                 ('migrated_calcs: {:7d}', report.migrated_calcs),
+                ('failed_calcs: {:7d}', report.failed_calcs),
                 ('calcs_with_diffs: {:7d}', report.calcs_with_diffs),
                 ('new_calcs: {:7d}', report.new_calcs),
                 ('missing_calcs: {:7d}', report.missing_calcs)])

nomad/coe_repo/calc.py

@@ -262,12 +262,11 @@ class Calc(Base):
                 if dataset.doi is not None:
                     self._add_citation(coe_dataset_calc, dataset.doi['value'], 'INTERNAL', context)
 
-                # cause a flush to avoid future inconsistencies
-                # repo_db.flush()
+                # cause a flush to create the backdirection of the above established
+                # metadata-dataset_calc relation
+                repo_db.flush()
 
             self.parents.append(coe_dataset_calc)
-            # coe_dataset_rel = CalcSet(parent_calc_id=dataset_id, children_calc_id=self.coe_calc_id)
-            # repo_db.add(coe_dataset_rel)
 
             dataset.update(DataSet(coe_dataset_calc).to_popo())
 
@@ -377,8 +376,7 @@ class DataSet:
         return self._dataset_calc.calc_metadata.chemical_formula
 
     def to_popo(self):
-        popo = utils.POPO(id=self.id, name=self.name)
-        if self.doi is not None:
-            popo.update(doi=self.doi.to_popo())
-
-        return popo
+        return utils.POPO(
+           id=self.id, 
+           name=self.name,
+           doi=self.doi.to_popo() if self.doi is not None else None)

nomad/coe_repo/upload.py

@@ -147,7 +147,7 @@ class Upload(Base):  # type: ignore
                     checksum=calc.calc_id,
                     upload=coe_upload)
                 repo_db.add(coe_calc)
-                repo_db.flush()  # to avoid missing calc parent key constraint violation
+
                 coe_calc.apply_calc_with_metadata(calc, context=context)
                 logger.debug('added calculation, not yet committed', calc_id=coe_calc.calc_id)
 

ops/migration_env.sh

@@ -2,3 +2,12 @@ export NOMAD_URL=http://enc-staging-nomad.esc.rzg.mpg.de/fairdi/nomad/migration/
 export NOMAD_USER=admin
 export NOMAD_FILES_NOMAD_TMP_DIR=/nomad/mscheidg/migration_tmp
 export NOMAD_LOGSTASH_TCPPORT=15000
+
+export NOMAD_FILES_TMP_DIR=/scratch/nomad-fair/local/tmp
+export NOMAD_FILES_OBJECT_DIR=/scratch/nomad-fair/local/objects
+export NOMAD_FILES_NOMAD_TMP=/nomad/mscheidg/migration_tmp
+export NOMAD_ELASTIC_PORT=19200
+export NOMAD_ELASTIC_INDEX_NAME=fairdi_nomad_local
+export NOMAD_MONGO_PORT=37017
+export NOMAD_MONGO_DB_NAME=fairdi_nomad_local
+export NOMAD_COE_REPO_DB_NAME=fairdi_nomad_local