feat(tools): add neo4jsbml (#144)

* feat(tools): add `neo4jsbml` * docs(tools): update
brsynth · Oct 9, 2023 · 14f6dc2 · 14f6dc2
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diff --git a/tools/neo4jsbml/.shed.yml b/tools/neo4jsbml/.shed.yml
@@ -0,0 +1,8 @@
+categories:
+  - Systems Biology
+description: Import SBML file into Neo4j
+long_description: Import SBML file into Neo4j
+name: neo4jsbml
+owner: tduigou
+homepage_url: https://github.com/brsynth/neo4jsbml
+remote_repository_url: https://github.com/brsynth/neo4jsbml
diff --git a/tools/neo4jsbml/neo4jsbml.xml b/tools/neo4jsbml/neo4jsbml.xml
@@ -0,0 +1,76 @@
+<tool id="neo4jsbml" name="neo4jsbml" version="@TOOL_VERSION@" profile="21.09" license="MIT">
+    <description>Import SBML file into Neo4j</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.12.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m neo4jsbml
+            --input-auradb-file '$input_auradb_file'
+            --input-file-sbml '$input_file_sbml'
+            #if str($input_tag_str) != ""
+                --input-tag-str '$input_tag_str'
+            #end if
+            --input-modelisation-json '$input_modelisation_json' | tee '$output'
+    ]]></command>
+    <inputs>
+        <param name="input_auradb_file" type="data" format="txt" label="Config file provided by AuraDB"/>
+        <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
+        <param name="input_tag_str" type="text" label="Identifier of the model">
+            <validator type="regex" message="No special characters allowed">^(?:[\w-]*)$</validator>
+        </param>
+        <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} - log" />
+    </outputs>
+    <help><![CDATA[
+Neo4jSbml
+=========
+
+Step 1
+------
+
+Create a schema with `Arrows <https://arrows.app>`_
+
+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` or individual parameters
+- Password needs to be store in a file for safety security
+- If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
+
+Inputs
+------
+
+- **AuraDB config like**: a txt file with these variables NEO4J_URI, NEO4J_USERNAME, NEO4J_PASSWORD and AURA_INSTANCENAME. One per line like: NEO4J_USERNAME=neo4j
+- **SBML model**: SBML model
+- **Identifier of the model**: Associate an ID to the nodes (optional)
+- **Arrow's schema**: Schema created with Arrow
+
+Ouput
+-----
+
+- Traceback of the tool
+]]></help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{neo4jsbml
+                author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon},
+                title = {{Neo4jSbml}},
+                url = {https://github.com/brsynth/neo4jsbml/},
+            }
+        </citation>
+    </citations>
+</tool>
diff --git a/tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json b/tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json
@@ -0,0 +1,265 @@
+{
+  "style": {
+    "font-family": "sans-serif",
+    "background-color": "#ffffff",
+    "background-image": "",
+    "background-size": "100%",
+    "node-color": "#ffffff",
+    "border-width": 4,
+    "border-color": "#000000",
+    "radius": 50,
+    "node-padding": 5,
+    "node-margin": 2,
+    "outside-position": "auto",
+    "node-icon-image": "",
+    "node-background-image": "",
+    "icon-position": "inside",
+    "icon-size": 64,
+    "caption-position": "inside",
+    "caption-max-width": 200,
+    "caption-color": "#000000",
+    "caption-font-size": 50,
+    "caption-font-weight": "normal",
+    "label-position": "inside",
+    "label-display": "pill",
+    "label-color": "#000000",
+    "label-background-color": "#ffffff",
+    "label-border-color": "#000000",
+    "label-border-width": 4,
+    "label-font-size": 40,
+    "label-padding": 5,
+    "label-margin": 4,
+    "directionality": "directed",
+    "detail-position": "inline",
+    "detail-orientation": "parallel",
+    "arrow-width": 5,
+    "arrow-color": "#000000",
+    "margin-start": 5,
+    "margin-end": 5,
+    "margin-peer": 20,
+    "attachment-start": "normal",
+    "attachment-end": "normal",
+    "relationship-icon-image": "",
+    "type-color": "#000000",
+    "type-background-color": "#ffffff",
+    "type-border-color": "#000000",
+    "type-border-width": 0,
+    "type-font-size": 16,
+    "type-padding": 5,
+    "property-position": "outside",
+    "property-alignment": "colon",
+    "property-color": "#000000",
+    "property-font-size": 16,
+    "property-font-weight": "normal"
+  },
+  "nodes": [
+    {
+      "id": "n0",
+      "position": {
+        "x": 0,
+        "y": 0
+      },
+      "caption": "",
+      "style": {},
+      "labels": [],
+      "properties": {}
+    },
+    {
+      "id": "n1",
+      "position": {
+        "x": 884.6635137872785,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "Compartment"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "spatialDimensions": "int (optional)",
+        "size": "int (optional)",
+        "constant": "bool (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n2",
+      "position": {
+        "x": 560.2494455950304,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "Species"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "initialAmount": "float (optional)",
+        "hasOnlySubstanceUnits": "bool (optional)",
+        "boundaryCondition": "bool (optional)",
+        "constant": "bool (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n3",
+      "position": {
+        "x": 432.24944559503035,
+        "y": 204.94864525928773
+      },
+      "caption": "",
+      "labels": [
+        "Parameter"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "value": "float (optional)",
+        "constant": "bool"
+      },
+      "style": {}
+    },
+    {
+      "id": "n4",
+      "position": {
+        "x": 833.1523435518487,
+        "y": 204.94864525928796
+      },
+      "caption": "",
+      "labels": [
+        "Reaction"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "reversible": "bool"
+      },
+      "style": {}
+    },
+    {
+      "id": "n5",
+      "position": {
+        "x": 129,
+        "y": 204.94864525928773
+      },
+      "caption": "",
+      "labels": [
+        "model"
+      ],
+      "properties": {
+        "id": "str",
+        "name": "str",
+        "metaid": "str",
+        "sboTerm": "str"
+      },
+      "style": {}
+    },
+    {
+      "id": "n6",
+      "position": {
+        "x": 129,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "UnitDefinition"
+      ],
+      "properties": {
+        "id": "str (optional)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n7",
+      "position": {
+        "x": 560.2494455950304,
+        "y": -4
+      },
+      "caption": "",
+      "labels": [
+        "GeneProduct"
+      ],
+      "properties": {
+        "id": "str",
+        "name": "str"
+      },
+      "style": {}
+    }
+  ],
+  "relationships": [
+    {
+      "id": "n0",
+      "fromId": "n2",
+      "toId": "n1",
+      "type": "IN_COMPARTMENT",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n1",
+      "fromId": "n4",
+      "toId": "n2",
+      "type": "HAS_PRODUCT",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n2",
+      "fromId": "n4",
+      "toId": "n3",
+      "type": "HAS_LOWERFLUXBOUND",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n3",
+      "fromId": "n5",
+      "toId": "n3",
+      "type": "HAS_PARAMETER",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n4",
+      "type": "HAS_UNITS",
+      "style": {},
+      "properties": {},
+      "fromId": "n3",
+      "toId": "n6"
+    },
+    {
+      "id": "n5",
+      "fromId": "n4",
+      "toId": "n3",
+      "type": "HAS_UPPERFLUXBOUND",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n6",
+      "fromId": "n4",
+      "toId": "n7",
+      "type": "IS_IMPLIED",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n7",
+      "fromId": "n2",
+      "toId": "n4",
+      "type": "IS_REACTANT",
+      "properties": {},
+      "style": {}
+    }
+  ]
+}
diff --git a/tools/neo4jsbml/test-data/e_coli_core.xml.gz b/tools/neo4jsbml/test-data/e_coli_core.xml.gz