Merge branch 'main' into stable

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [0.11.1](https://github.com/brsynth/neo4jsbml/tree/0.11.1) (2023-09-22)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.11.0...0.11.1)
+
+**Merged pull requests:**
+
+- Add `dry-run` argument [\#10](https://github.com/brsynth/neo4jsbml/pull/10) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- chore\(deps\): bump actions/checkout from 3 to 4 [\#9](https://github.com/brsynth/neo4jsbml/pull/9) ([dependabot[bot]](https://github.com/apps/dependabot))
+- chore\(deps\): bump github/super-linter from 4 to 5 [\#8](https://github.com/brsynth/neo4jsbml/pull/8) ([dependabot[bot]](https://github.com/apps/dependabot))
+
 ## [0.11.0](https://github.com/brsynth/neo4jsbml/tree/0.11.0) (2023-03-28)
 
 [Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.10.1...0.11.0)

docs/CHANGELOG.data.rst

@@ -1,6 +1,26 @@
 Changelog
 =========
 
+`0.11.1 <https://github.com/brsynth/neo4jsbml/tree/0.11.1>`__ (2023-09-22)
+--------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/0.11.0...0.11.1>`__
+
+**Merged pull requests:**
+
+-  Add ``dry-run`` argument
+   `#10 <https://github.com/brsynth/neo4jsbml/pull/10>`__
+   (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
+-  chore(deps): bump actions/checkout from 3 to 4
+   `#9 <https://github.com/brsynth/neo4jsbml/pull/9>`__
+   (`dependabot[bot] <https://github.com/apps/dependabot>`__)
+-  chore(deps): bump github/super-linter from 4 to 5
+   `#8 <https://github.com/brsynth/neo4jsbml/pull/8>`__
+   (`dependabot[bot] <https://github.com/apps/dependabot>`__)
+
+.. _section-1:
+
 `0.11.0 <https://github.com/brsynth/neo4jsbml/tree/0.11.0>`__ (2023-03-28)
 --------------------------------------------------------------------------
 
@@ -13,15 +33,15 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.10.1...0.11.0>`__
    `#7 <https://github.com/brsynth/neo4jsbml/pull/7>`__
    (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
 
-.. _section-1:
+.. _section-2:
 
 `0.10.1 <https://github.com/brsynth/neo4jsbml/tree/0.10.1>`__ (2023-03-17)
 --------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.10.0...0.10.1>`__
 
-.. _section-2:
+.. _section-3:
 
 `0.10.0 <https://github.com/brsynth/neo4jsbml/tree/0.10.0>`__ (2023-03-17)
 --------------------------------------------------------------------------
@@ -37,23 +57,23 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.2...0.10.0>`__
 -  Read the docs `#5 <https://github.com/brsynth/neo4jsbml/pull/5>`__
    (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
 
-.. _section-3:
+.. _section-4:
 
 `0.9.2 <https://github.com/brsynth/neo4jsbml/tree/0.9.2>`__ (2023-02-23)
 ------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.1...0.9.2>`__
 
-.. _section-4:
+.. _section-5:
 
 `0.9.1 <https://github.com/brsynth/neo4jsbml/tree/0.9.1>`__ (2023-02-21)
 ------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.0...0.9.1>`__
 
-.. _section-5:
+.. _section-6:
 
 `0.9.0 <https://github.com/brsynth/neo4jsbml/tree/0.9.0>`__ (2023-01-27)
 ------------------------------------------------------------------------
@@ -67,15 +87,15 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.8.3...0.9.0>`__
    `#4 <https://github.com/brsynth/neo4jsbml/pull/4>`__
    (`dependabot[bot] <https://github.com/apps/dependabot>`__)
 
-.. _section-6:
+.. _section-7:
 
 `0.8.3 <https://github.com/brsynth/neo4jsbml/tree/0.8.3>`__ (2023-01-16)
 ------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.8.0...0.8.3>`__
 
-.. _section-7:
+.. _section-8:
 
 `0.8.0 <https://github.com/brsynth/neo4jsbml/tree/0.8.0>`__ (2023-01-16)
 ------------------------------------------------------------------------

src/neo4jsbml/__main__.py

@@ -110,9 +110,19 @@ def main():
     logging.info("Connection to database")
     con = None
     if args.input_config_file:
+        if not os.path.isfile(args.input_config_file):
+            logging.error(
+                "File provided does not exist: %s" % (args.input_config_file,)
+            )
+            parser.exit(1)
         logging.warning("Configuration file is provided, ignore indiviual arguments")
         con = connect.Connect.from_config(path=args.input_config_file)
     elif args.input_auradb_file:
+        if not os.path.isfile(args.input_auradb_file):
+            logging.error(
+                "File provided does not exist: %s" % (args.input_auradb_file,)
+            )
+            parser.exit(1)
         logging.warning(
             "Configuration file AuraDB is provided, ignore indiviual arguments"
         )

src/neo4jsbml/_version.py

@@ -1,2 +1,2 @@
 __app_name__ = "neo4jsbml"
-__version__ = "0.11.1"
+__version__ = "0.11.2"

src/neo4jsbml/connect.py

@@ -261,3 +261,27 @@ def from_auradb(cls, path: str) -> "Connect":
                     elif var == "AURA_INSTANCENAME":
                         data["database"] = value
         return Connect(**data)
+
+    def __repr__(self):
+        msg = []
+        msg.append("Url: %s" % (self.url,))
+        msg.append("Protocol: %s" % (self.protocol,))
+        msg.append("Database: %s" % (self.database,))
+        user = "<empty>"
+        if self.user:
+            user = self.user
+        msg.append("User: %s" % (user,))
+        port = "<empty>"
+        if self.port:
+            port = self.port
+        msg.append("Port: %s" % (port,))
+        password = "<empty>"
+        if self.password:
+            password = "initialized"
+        msg.append("Password: " + password)
+        msg.append("Uri: " + self.uri)
+        is_connected = "false"
+        if self.is_connected():
+            is_connected = "true"
+        msg.append("Connected: " + is_connected)
+        return "\n".join(msg)

src/neo4jsbml/entity.py

@@ -43,17 +43,24 @@ def __init__(self, id: str, properties: Dict[str, str], *args, **kwargs) -> None
 
     def clean_properties(self):
         """Remove empty values.
+        Sanitize string:
+            - remove return line
+            - append a backslash in front of double quotes
 
         Return
         ------
         None
         """
         keys = []
-        for k, v in self.properties.items():
-            if v is None or v == "":
-                keys.append(k)
-        for k in keys:
-            del self.properties[k]
+        for key, value in self.properties.items():
+            if value is None or value == "":
+                keys.append(key)
+            elif isinstance(value, str):
+                value = value.replace('"', '\\"')
+                value = value.replace("\n", "")
+                self.properties[key] = value
+        for key in keys:
+            del self.properties[key]
 
     def has_property(self, label: str) -> bool:
         """Check if a node has a property.

tests/conftest.py

@@ -1,7 +1,7 @@
 import os
 
 import pytest
-from neo4jsbml import connect, sbml
+from neo4jsbml import connect, sbml, singleton
 
 cur_dir = os.path.abspath(os.path.dirname(__file__))
 data_dir = os.path.join(cur_dir, "dataset")
@@ -148,6 +148,7 @@ def rel_two_arrow():
 
 @pytest.fixture(scope="function")
 def init_driver():
+    singleton.Singleton.clean()
     return connect.Connect(
         protocol="neo4j",
         url="localhost",

tests/dataset/database/localhost.ini

@@ -1,3 +1,4 @@
 [connection]
 protocol = neo4j
 url = localhost
+port = 7687

tests/test_neo4jsbml.py

@@ -46,7 +46,6 @@ def load_iAF1260(init_driver, config_path, pathway_two_path, iaf1260_path):
 class TestiML1515:
     def test_nodes(self, init_driver, load_iML1515):
         query = "CALL db.labels() YIELD label CALL apoc.cypher.run('MATCH (:`'+label+'`) RETURN count(*) as count',{}) YIELD value RETURN label, value.count"
-        singleton.Singleton.clean()
         data = init_driver.query(value=query, expect_data=True)
 
         assert data == [
@@ -61,7 +60,6 @@ def test_nodes(self, init_driver, load_iML1515):
 
     def test_relationships(self, init_driver, load_iML1515):
         query = "CALL db.relationshipTypes() YIELD relationshipType as type CALL apoc.cypher.run('MATCH ()-[:`'+type+'`]->() RETURN count(*) as count',{}) YIELD value RETURN type, value.count"
-        singleton.Singleton.clean()
         data = init_driver.query(value=query, expect_data=True)
 
         assert data == [
@@ -80,7 +78,6 @@ def test_relationships(self, init_driver, load_iML1515):
 class TestiAF1260:
     def test_nodes(self, init_driver, load_iAF1260):
         query = "CALL db.labels() YIELD label CALL apoc.cypher.run('MATCH (:`'+label+'`) RETURN count(*) as count',{}) YIELD value RETURN label, value.count"
-        singleton.Singleton.clean()
         data = init_driver.query(value=query, expect_data=True)
 
         assert data == [
@@ -95,7 +92,6 @@ def test_nodes(self, init_driver, load_iAF1260):
 
     def test_relationships(self, init_driver, load_iAF1260):
         query = "CALL db.relationshipTypes() YIELD relationshipType as type CALL apoc.cypher.run('MATCH ()-[:`'+type+'`]->() RETURN count(*) as count',{}) YIELD value RETURN type, value.count"
-        singleton.Singleton.clean()
         data = init_driver.query(value=query, expect_data=True)
 
         assert data == [