Merge branch 'main' into stable

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/build.yml

@@ -57,7 +57,7 @@ jobs:
           echo "$USER $PROJECT"
           github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
       - name: 'Upload Artifact Changelog'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: changelog-artifact
           path: CHANGELOG.md
@@ -82,7 +82,7 @@ jobs:
           echo "version_path=$VERSION_PATH" >> "$GITHUB_OUTPUT"
           echo "version_dir=$VERSION_DIR" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Version'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: version-artifact
           path: ${{ steps.update_version.outputs.version_path }}
@@ -177,7 +177,7 @@ jobs:
           filename=$(find ${{ env.dirbuild }} | head -n 1)
           echo "asset=$filename" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Package'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: package-conda-artifact
           path: ${{ steps.identify_asset.outputs.asset }}

.gitignore

@@ -21,3 +21,6 @@ super-linter.log
 build
 debug
 .tox
+papier
+cmd.sh
+*.xml

CHANGELOG.md

@@ -1,12 +1,12 @@
 # Changelog
 
-## [0.8.0](https://github.com/brsynth/neo4jsbml/tree/0.8.0) (2023-01-16)
+## [0.8.2](https://github.com/brsynth/neo4jsbml/tree/0.8.2) (2023-01-16)
 
-[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.8.1...0.8.0)
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.8.0...0.8.2)
 
-## [0.8.1](https://github.com/brsynth/neo4jsbml/tree/0.8.1) (2023-01-16)
+## [0.8.0](https://github.com/brsynth/neo4jsbml/tree/0.8.0) (2023-01-16)
 
-[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/710ac296807b62182b8280c407d990537bacdce7...0.8.1)
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/710ac296807b62182b8280c407d990537bacdce7...0.8.0)
 
 **Implemented enhancements:**
 

README.md

@@ -16,17 +16,46 @@ pip install --no-deps .
 
 ## Usage
 
+### Step 1
+
+Create a schema with [arrows](https://arrows.app) like:  
+![schema](tests/dataset/PathwayModelisation-1.0.0.png "Schema SBML")
+Rules:
+* Nodes are labelled based on SBML object name as defined in the [SBML specification](https://sbml.org)
+* Properties are labelled based on SBML object properties as defined the [SBML specification](https://sbml.org)
+
+### Step 2
+
+Export your schema at the JSON format.
+
+### Step 3
+
+Import your data with `neo4jsbml` into Neo4j.  
+* Use either a configuration file `ini`, an example is provided in the `template` directory or individual parameters
+* Password needs to be store in a file for safety security
+* Pass a `tag` to identify the model loaded into the database
+
 ```sh
 python -m neo4jsbml \
     # Database parameters
     --input-protocol-str ["neo4j", "bolt"] \
-    --input-url-str "localhost:7687" \
+    --input-url-str "localhost" \
+    --input-port-int 7687 \
     --input-user-str "neo4j" \
     --input-password-file <file> \
-    --input-database-str <file> \
-    # Input file
+    --input-database-str <str> \
+    --input-batch-int <int> \
+    # Config file
+    --input-config-file <file> \
+
+    # Input
     --input-file-sbml <file> \
-    --input-id-str <id> \
-    # Parameters
-    --input-modelisation-str <modelisation>
+    --input-tag-str "" \
+    --input-modelisation-json <file>
+```
+
+## Test
+
+```sh
+python -m pytest
 ```

docker-compose.yml

@@ -0,0 +1,12 @@
+version: "2"
+
+services:
+  neo4j:
+    image: neo4j:5.3.0-community
+    container_name: neo4j
+    ports:
+      - "7474:7474"
+      - "7687:7687"
+    environment:
+      - NEO4J_PLUGINS=["apoc"]
+      - NEO4J_AUTH=none

src/neo4jsbml/__main__.py

@@ -75,62 +75,33 @@ def main():
         help="Modelisation created and downloaded from arrow",
     )
 
-    # Parameters
-    parser_parameters = parser.add_argument_group("Parameters")
-    parser_parameters.add_argument(
-        "--log-level",
-        choices=[
-            "debug",
-            "info",
-            "warning",
-            "error",
-            "critical",
-            "silent",
-        ],
-        default="info",
-        help="Adds a console logger for the specified level (default: info)",
-    )
     # Compute
     args = parser.parse_args()
 
     # Logging.
-    logger = logging.getLogger(name=_version.__app_name__)
-    formatter = logging.Formatter(
-        "%(asctime)s - %(levelname)s - %(message)s", datefmt="%d-%m-%Y %H:%M"
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s - %(levelname)s - %(message)s",
+        datefmt="%d-%m-%Y %H:%M",
     )
-    st_handler = logging.StreamHandler()
-    st_handler.setFormatter(formatter)
-    logger.addHandler(st_handler)
-    log_level = logging.NOTSET
-    if args.log_level == "debug":
-        log_level = logging.DEBUG
-    elif args.log_level == "info":
-        log_level = logging.INFO
-    elif args.log_level == "warning":
-        log_level = logging.WARNING
-    elif args.log_level == "error":
-        log_level = logging.ERROR
-    elif args.log_level == "critical":
-        log_level = logging.CRITICAL
-    logger.setLevel(log_level)
 
     # Check arguments.
-    logger.info("Start - %s" % (_version.__app_name__,))
+    logging.info("Start - %s" % (_version.__app_name__,))
     if not os.path.isfile(args.input_file_sbml):
-        logger.error("Model SBML file does not exist: %s" % (args.input_file_sbml,))
+        logging.error("Model SBML file does not exist: %s" % (args.input_file_sbml,))
         parser.exit(1)
     if not os.path.isfile(args.input_modelisation_json):
-        logger.error(
+        logging.error(
             "Modelisation JSON file does not exist: %s"
             % (args.input_modelisation_json,)
         )
         parser.exit(1)
 
     # Connection to database
-    logger.info("Connection to database")
+    logging.info("Connection to database")
     con = None
     if args.input_config_file:
-        logger.warning("Configuration file is provided, ignore indiviual arguments")
+        logging.warning("Configuration file is provided, ignore indiviual arguments")
         con = connect.Connect.from_config(path=args.input_config_file)
     else:
         con = connect.Connect(
@@ -147,31 +118,31 @@ def main():
         parser.exit(1)
 
     # Load model
-    logger.info("Load SBML file")
+    logging.info("Load SBML file")
     sbm = sbml.Sbml.from_sbml(path=args.input_file_sbml, tag=args.input_tag_str)
 
     # Load modelisation
-    logger.info("Load modelisation file")
+    logging.info("Load modelisation file")
     arr = arrows.Arrows.from_json(path=args.input_modelisation_json)
 
     # Mapping
-    logger.info("Map schema to data - nodes")
+    logging.info("Map schema to data - nodes")
     nod = sbm.format_nodes(nodes=arr.nodes)
 
-    logger.info("Map schema to data - relationships")
+    logging.info("Map schema to data - relationships")
     rel = sbm.format_relationships(relationships=arr.relationships)
 
     # Import into neo4j
-    logger.info("Import into neo4j - nodes")
+    logging.info("Import into neo4j - nodes")
     con.create_nodes(nodes=nod)
 
     if arr.relationships is not None and len(arr.relationships) > 0:
-        logger.info("Import into neo4j - relationships")
+        logging.info("Import into neo4j - relationships")
         con.create_relationships(relationships=rel)
     else:
-        logger.info("None relationship created")
+        logging.info("None relationship created")
 
-    logger.info("End - %s" % (_version.__app_name__,))
+    logging.info("End - %s" % (_version.__app_name__,))
 
     return 0
 

src/neo4jsbml/_version.py

@@ -1,2 +1,2 @@
 __app_name__ = "neo4jsbml"
-__version__ = "0.8.2"
+__version__ = "0.8.3"

src/neo4jsbml/arrows.py

@@ -49,7 +49,6 @@ def from_json(cls, path: str) -> "Arrows":
         ------
         Arrows
         """
-        logger = logging.getLogger(name=_version.__app_name__)
         data = {}
         with open(path) as hd:
             data = json.load(hd)
@@ -68,13 +67,14 @@ def from_json(cls, path: str) -> "Arrows":
                 arrow_node["properties"][snode.SNode.LABEL_ID] = arrow_node[
                     "properties"
                 ].pop(id_label)
-                logger.warning(
+                logging.warning(
                     'Entity: %s has an "%s" in properties, but it will be renamed into: %s'
-                    % (" ".join(arrow_node["labels"]), id_label, snode.SNode.LABEL_ID)
+                    % (":".join(arrow_node["labels"]), id_label, snode.SNode.LABEL_ID)
                 )
             if not is_id_found:
-                logger.warning(
+                logging.warning(
                     'Entity: %s has not "id" in properties, it will be added'
+                    % (":".join(arrow_node["labels"]),)
                 )
                 arrow_node["properties"][snode.SNode.LABEL_ID] = "str"
             # Append node
@@ -83,7 +83,7 @@ def from_json(cls, path: str) -> "Arrows":
         relationships = []
         for arrow_rel in data["relationships"]:
             if arrow_rel["type"] == "str":
-                logger.warning(
+                logging.warning(
                     "A relationship must be have a type filled, %s will be skipped"
                     % (arrow_rel["id"],)
                 )

src/neo4jsbml/cmd.py

@@ -0,0 +1,26 @@
+import logging
+import subprocess
+from typing import List
+
+
+def run(args: List[str], show_output: bool = True) -> subprocess.CompletedProcess:
+    """Run a command line.
+
+    Parameters
+    ----------
+    args: List[str]
+        A list of argument
+    show_output: bool (default: True)
+        Output command line
+
+    Return
+    ------
+    subprocess.CompletedProcess
+        Return result obtained with subprocess
+    """
+    ret = subprocess.run(args, capture_output=True, encoding="utf8")
+    if show_output and ret.stdout is not None:
+        logging.info(ret.stdout)
+    if show_output and ret.stderr is not None:
+        logging.warning(ret.stderr)
+    return ret

src/neo4jsbml/entity.py

@@ -18,6 +18,20 @@ class Entity(metaclass=ABCMeta):
         The properties as defined by arrows.
         Key are the name of the property to search in the SBML.
         Values are unused.
+
+    Methods
+    -------
+    add_property(self, label: str, value: str, overwrite: bool = True) -> None
+        Add a property to the properties attribute
+
+    has_property(self, label: str) -> bool
+        Check if a node has a property
+
+    clean_properties(self)
+        Remove empty values
+
+    properties_to_neo4j() -> str
+        Format properties to insert in query
     """
 
     def __init__(self, id: str, properties: Dict[str, str], *args, **kwargs) -> None:
@@ -76,6 +90,12 @@ def add_property(self, label: str, value: str, overwrite: bool = True) -> None:
             self.properties[label] = value
 
     def properties_to_neo4j(self) -> str:
+        """Format properties to insert in query
+
+        Return
+        ------
+        str
+        """
         data = "{"
         for k, v in self.properties.items():
             data += k