Bug fixes in Docker deployment + rel 1.3.2

CHANGELOG.md

@@ -1,6 +1,10 @@
 # Changelog
 
-## [CURRENT 1.3.2 SNAPSHOT] 2022-01-12
+## [CURRENT 1.3.2] 2023-08-23
+
+Add Docker deplyment.
+
+## [1.3.2 SNAPSHOT] 2022-01-12
 - fix bug in sha1() mixed path
 - document the sha1() mixed path
 - (partially) fix bug in pushDown: for any field that is an ObjectID with $oid field (such as "_id"), the value of the $oid is pushed instead of the serialization f the field itself

codemeta.json

@@ -4,14 +4,14 @@
     "license": "https://spdx.org/licenses/Apache-2.0",
     "codeRepository": "https://github.com/frmichel/morph-xr2rml",
     "datePublished": "2015-04-02",
-    "dateModified": "2021-07-30",
+    "dateModified": "2023-08-23",
     "downloadUrl": "https://www.dropbox.com/sh/djnztipsclvcskw/AABT1JagzD4K4aCALDNVj-yra?dl=0",
     "issueTracker": "https://github.com/frmichel/morph-xr2rml/issues",
-    "name": "Morph-xR2RML",
-    "version": "1.3.1",
+    "name": "Morph-xR2RML: MongoDB-to-RDF translation",
+    "version": "1.3.2",
     "identifier": "10.5281/zenodo.5148233",
-    "description": "Morph-xR2RML is an implementation of the xR2RML mapping language that enables the description of mappings from relational or non relational databases to RDF. It comes with connectors for relational databases (MySQL, PostgreSQL, MonetDB) and the MongoDB NoSQL database.",
-    "developmentStatus": "active",
+    "description": "Morph-xR2RML is an implementation of the xR2RML mapping language (https://www.i3s.unice.fr/~fmichel/xr2rml_specification_v5.1.html) that enables the description of mappings from relational or non relational databases to RDF. It comes with connectors for relational databases (MySQL, PostgreSQL, MonetDB) and the MongoDB NoSQL database.",
+    "developmentStatus": "inactive",
     "referencePublication": [
         "https://hal.science/hal-01207828",
         "https://hal.science/hal-01280951",

docker/README.md

@@ -30,32 +30,31 @@ docker-compose up -d
 
 Now, both containers are started and ready to process data.
 
-Script `run.sh` provides an example of how to (1) import data located in `mongo_import` into MongoDB, and (2) run Morph-xR2RML to translate the data to RDF and store the result in `xr2rml_output`.
+Script `run.sh` provides an example of how to run the different steps manually: (1) import data located in `mongo_import` into MongoDB, and (2) run Morph-xR2RML to translate the data to RDF and store the result in `xr2rml_output`.
 
 
 ### Description of each folder
 
-- `mongo_db`: will contain the actual Mongo database, so that you don't need to re-import files everytime you rerun it.
+- `mongo_db`: will contain the actual Mongo database, so that you don't need to re-import files everytime you rerun Morph-xR2RML.
 - `mongo_tools`: set of handy bash scripts to import json/csv/tsv data into MongoDB.
-- `mongo_import`: copy your files to import in this folder, it is mouned in the MongoDB container.
-- `xr2rml_config`: mapping files, morph.properties, log configuration file, and bash scripts to run Morph-xR2RML. This folder is mouned in the Morph-xR2RML container.
+- `mongo_import`: copy your files to import in this folder, it is moutned in the MongoDB container.
+- `xr2rml_config`: mapping files (morph.properties, log configuration file) and bash scripts to run Morph-xR2RML. This folder is mounted in the Morph-xR2RML container.
 - `xr2rml_config`: where the RDF files will be written.
-- `run.sh`: example script showing how to import data into MongoDB and run Morph-xR2RML to translate the data to RDF.
+- `run.sh`: example script showing how to use evrything from your machine, i.e. to import data into MongoDB and run Morph-xR2RML to translate the data to RDF.
 
 
 
 ### Accessing Logs
 
 The `docker-compose.yml` mounts the Morph-xR2RML log directory to the Docker host in directory `log`.
-
 Check it if an error occurs or if your mapping does not generate the expected triples.
 
 
 ### Changing Morph-xR2RML configuration and mappings
 
-Put your mapping files in folder `xr2rml_config`. Script `run_xr2rml.sh` will be used to run the transltation from within the container.
+Put your mapping files in folder `xr2rml_config`. Script `xr2rml_config/run_xr2rml.sh` will be used to run the transltation from within the container.
 
-Mapping files can also be templates, with 2 predefined placeholders: `{{collection}}` and  `{{dataset}}`. Script `run_xr2rml_template.sh` wil replace them before running the translation. Check the example mapping `xr2rml_config/mapping_movies.ttl` and how it is used by script `run.sh`.
+Mapping files can also be templates, with 2 predefined placeholders: `{{collection}}` and  `{{dataset}}`. Script `xr2rml_config/run_xr2rml_template.sh` will replace them before running the translation. Check the example mapping `xr2rml_config/mapping_movies.ttl` and how it is used by script `run.sh`.
 
 The main Morph-xR2RML configuration file is editable at ```xr2rml_config/morph.properties```. In particular that's where you would change the name of the MongoDB database.
 

docker/docker-compose.yml

@@ -2,7 +2,7 @@ version: '3.2'
 services:
 
   morph-xr2rml:
-    image: frmichel/morph-xr2rml
+    image: frmichel/morph-xr2rml:1.3.2
     container_name: morph-xr2rml
     networks:
       - xr2rml-net

docker/mongo_tools/import-file.sh

@@ -38,7 +38,7 @@ index_col=$5
 if [[ -z "$index_col" ]] ; then help; fi
 
 # Optional
-extra_script=$5
+extra_script=$6
 
 
 # Functions definitions

docker/mongo_tools/import-tools.sh

@@ -187,7 +187,7 @@ mongo_drop_import_file_index() {
     _collection_c=$4
     _index_col_c=$5
 
-    mongoimport --drop --type=_type --headerline --ignoreBlanks -d $_database_c -c $_collection_c $_file_c
+    mongoimport --drop --type=$_type --headerline --ignoreBlanks -d $_database_c -c $_collection_c $_file_c
     mongo --eval "db.${_collection_c}.createIndex({${_index_col_c}: 1})" localhost/$_database_c --quiet
     mongo --eval "db.${_collection_c}.count()" localhost/$_database_c --quiet
 }

docker/run.sh

@@ -16,9 +16,6 @@ docker exec -w /mongo_tools $MONGO_CONTAINER \
    /bin/bash import-json-files.sh $DB $COLLECTION id
 
 # --- Run the translation to RDF
-# Note that at start-up Morph-xR2RML shows these warning messages, just ignore them:
-#    SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-#    SLF4J: Defaulting to no-operation (NOP) logger implementation
-#    SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+# Note that at start-up Morph-xR2RML shows 3 SLF4J warning messages, just ignore them.
 docker exec -w /xr2rml_config $XR2RML_CONTAINER \
    /bin/bash run_xr2rml_template.sh mapping_movies.ttl movies.ttl dataset1.0 $COLLECTION

docker/xr2rml_config/run_xr2rml.sh

@@ -48,7 +48,7 @@ java -Xmx4g \
      -jar "$JAR" \
      --configDir $CONFIG_DIR \
      --configFile xr2rml.properties \
-     --mappingFile $CONFIG/$mappingFile \
+     --mappingFile $CONFIG_DIR/$mappingFile \
      --output $OUTPUT_DIR/$output \
      >> $log
 date >> $log