Merge pull request #20 from openkim/update-montydb

Update montydb

docker/config/excerpts/config.py

@@ -388,5 +388,3 @@ def __str__(self):
 # os.environ['ASAP_KIM_INC'] = conf.get('ASAP_KIM_INC')
 # os.environ['ASAP_KIM_LIB'] = conf.get('ASAP_KIM_LIB')
 
-# For montydb. Required because our `pipeline-database` tool uses pymongo
-os.environ["MONTY_ENABLE_BSON"] = "1"

docker/config/excerpts/mongodb.py

@@ -8,7 +8,7 @@
 import re
 import datetime
 
-from montydb import MontyClient
+from montydb import MontyClient,set_storage
 
 from . import config as cf
 from . import util
@@ -17,7 +17,8 @@
 
 PIPELINE_LOCAL_DB_PATH = cf.LOCAL_DATABASE_PATH
 
-client = MontyClient(PIPELINE_LOCAL_DB_PATH, cache_modified=0)
+set_storage(repository=PIPELINE_LOCAL_DB_PATH, use_bson=True, cache_modified="0")
+client = MontyClient(PIPELINE_LOCAL_DB_PATH)
 db = client.db
 
 PATH_RESULT = cf.LOCAL_REPOSITORY_PATH

docker/config/tools/pipeline-database

@@ -77,9 +77,11 @@ def action_delete(args):
 
 
 def action_import(args):
+    # To set up the directory and monty.storage.cfg if it does not exist
+    import excerpts.mongodb
     try:
         with open_repo(PIPELINE_LOCAL_DB_PATH):
-            montyimport("db", "data", args["database-file"])
+            montyimport("db", "data", args["database-file"], use_bson=True)
     except (UnicodeDecodeError, JSONDecodeError):
         print(
             "Database file {} is not valid JSON. Exiting...".format(
@@ -90,10 +92,12 @@ def action_import(args):
 
 def action_export(args):
     with open_repo(PIPELINE_LOCAL_DB_PATH):
-        montyexport("db", "data", args["database-file"])
+        montyexport("db", "data", args["database-file"], use_bson=True)
 
 
 def action_restore(args):
+    # To set up the directory and monty.storage.cfg if it does not exist
+    import excerpts.mongodb
     try:
         with open_repo(PIPELINE_LOCAL_DB_PATH):
             montyrestore("db", "data", args["database-file"])

docker/install/Dockerfile

@@ -46,7 +46,7 @@ RUN ${PIP} install numpy==1.19.5
 RUN ${PIP} install scipy==1.5.4
 RUN ${PIP} install matplotlib==3.7.1
 RUN ${PIP} install pymongo==3.11.3
-RUN ${PIP} install montydb==2.1.1
+RUN ${PIP} install montydb==2.5.3
 RUN ${PIP} install pybind11==2.6.2
 RUN ${PIP} install spglib==2.1.0
 RUN ${PIP} install numdifftools==0.9.41

test/run_all.sh

@@ -1,2 +1,2 @@
-DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && bash set_up_and_run_$2.sh && python compare_dbs.py $2 && bash compare_vcs.sh $2"
+DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && bash set_up_and_run_$2.sh && export PYTHONPATH=\$PYTHONPATH:/pipeline/ && python compare_dbs.py $2 && bash compare_vcs.sh $2"
 docker run --rm --mount type=bind,src=$PWD/test/test_scripts_and_data,target=/home/openkim/test_scripts_and_data --env LD_LIBRARY_PATH=:/usr/local/lib $1 /bin/bash -c "$DOCKER_COMMAND"