removed doctests

BIH-CEI · Oct 14, 2024 · 7f65e2f · 7f65e2f
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diff --git a/notebooks/hierarchical_data_model.ipynb b/notebooks/hierarchical_data_model.ipynb
@@ -6,22 +6,22 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2024-10-14T20:57:38.214684Z",
-     "start_time": "2024-10-14T20:57:38.210273Z"
+     "end_time": "2024-10-14T21:21:45.314262Z",
+     "start_time": "2024-10-14T21:21:45.309299Z"
     }
    },
    "source": [
     "from phenopacket_mapper.data_standards import DataField\n",
     "from phenopacket_mapper.data_standards import DataModel, ValueSet, DataSection, OrGroup"
    ],
    "outputs": [],
-   "execution_count": 6
+   "execution_count": 4
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-10-14T20:57:38.231064Z",
-     "start_time": "2024-10-14T20:57:38.224448Z"
+     "end_time": "2024-10-14T21:21:45.340239Z",
+     "start_time": "2024-10-14T21:21:45.334880Z"
     }
    },
    "cell_type": "code",
@@ -81,43 +81,95 @@
    ],
    "id": "2e979683ae450d9b",
    "outputs": [],
-   "execution_count": 7
+   "execution_count": 5
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-10-14T20:57:38.295528Z",
-     "start_time": "2024-10-14T20:57:38.291141Z"
+     "end_time": "2024-10-14T21:21:45.352293Z",
+     "start_time": "2024-10-14T21:21:45.347715Z"
     }
    },
    "cell_type": "code",
-   "source": "print(genomic_interpretation)",
+   "source": [
+    "s = str(genomic_interpretation)\n",
+    "\n",
+    "print(s)"
+   ],
    "id": "35a697d8b9b8236d",
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "DataModel(name=Phenopacket schema Genomic Interpretation\n",
+      "DataModel(\n",
+      "\tname: Phenopacket schema Genomic Interpretation\n",
       "\tDataField(\n",
       "\t\tid: subject_or_biosample_id,\n",
       "\t\tname: subject_or_biosample_id,\n",
-      "\t\tvalue_set: ValueSet(elements=[<class 'str'>], name='', description=''), required: True,\n",
+      "\t\trequired: True\n",
       "\t\tspecification: ValueSet(elements=[<class 'str'>], name='', description='')\n",
+      "\t\tcardinality: 1..n\n",
       "\t)\n",
       "\tDataField(\n",
       "\t\tid: interpretation_status,\n",
       "\t\tname: interpretation_status,\n",
-      "\t\tvalue_set: ValueSet(elements=['UNKNOWN_STATUS', 'REJECTED', 'CANDIDATE', 'CONTRIBUTORY', 'CAUSATIVE'], name='Interpretation Status Value Set', description=''), required: True,\n",
+      "\t\trequired: True\n",
       "\t\tspecification: ValueSet(elements=['UNKNOWN_STATUS', 'REJECTED', 'CANDIDATE', 'CONTRIBUTORY', 'CAUSATIVE'], name='Interpretation Status Value Set', description='')\n",
+      "\t\tcardinality: 1..n\n",
+      "\t)\n",
+      "\tOrGroup(\n",
+      "\t\tid: call,\n",
+      "\t\tname: call,\n",
+      "\t\trequired: False\n",
+      "\t\tcardinality: 0..n\n",
+      "\tDataSection(\n",
+      "\t\tid: genedescriptor,\n",
+      "\t\tname: GeneDescriptor,\n",
+      "\t\trequired: False\n",
+      "\t\tcardinality: 0..n\n",
+      "\tDataField(\n",
+      "\t\tid: value_id,\n",
+      "\t\tname: value_id,\n",
+      "\t\trequired: True\n",
+      "\t\tspecification: ValueSet(elements=[<class 'str'>], name='', description='')\n",
+      "\t\tcardinality: 1..n\n",
+      "\t)\n",
+      "\tDataField(\n",
+      "\t\tid: symbol,\n",
+      "\t\tname: symbol,\n",
+      "\t\trequired: True\n",
+      "\t\tspecification: ValueSet(elements=[<class 'str'>], name='', description='')\n",
+      "\t\tcardinality: 1..n\n",
+      "\t)\n",
+      "\tDataField(\n",
+      "\t\tid: description,\n",
+      "\t\tname: description,\n",
+      "\t\trequired: False\n",
+      "\t\tspecification: ValueSet(elements=[<class 'str'>], name='', description='')\n",
+      "\t\tcardinality: 0..n\n",
+      "\t)\n",
+      "\t)\n",
       "\t)\n",
-      "\tDataSection(name='call', id='call', fields=(OrGroup(fields=(DataSection(name='GeneDescriptor', id='genedescriptor', fields=(DataField(name='value_id', specification=ValueSet(elements=[<class 'str'>], name='', description=''), id='value_id', required=True, description='Official identifier of the gene. REQUIRED.', cardinality=Cardinality(min=0, max='n')), DataField(name='symbol', specification=ValueSet(elements=[<class 'str'>], name='', description=''), id='symbol', required=True, description='Official gene symbol. REQUIRED.', cardinality=Cardinality(min=0, max='n')), DataField(name='description', specification=ValueSet(elements=[<class 'str'>], name='', description=''), id='description', required=False, description='A free-text description of the gene', cardinality=Cardinality(min=0, max='n'))), required=False, cardinality=Cardinality(min=0, max='n')),), name='Or Group', id='or_group', description='', required=False, cardinality=Cardinality(min=0, max='n')),), required=False, cardinality=Cardinality(min=0, max='n'))\n",
       "---\n",
       ")\n"
      ]
     }
    ],
-   "execution_count": 8
+   "execution_count": 6
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-10-14T21:21:45.378046Z",
+     "start_time": "2024-10-14T21:21:45.375530Z"
+    }
+   },
+   "cell_type": "code",
+   "source": "",
+   "id": "4c78eb05ea58ff6c",
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {

diff --git a/src/phenopacket_mapper/data_standards/data_model.py b/src/phenopacket_mapper/data_standards/data_model.py
@@ -44,10 +44,6 @@ class DataField(DataNode):
 
     If the `value_set` is a single type, it can be passed directly as the `value_set` parameter.
 
-    e.g.:
-    >>> DataField(name="Field 1", specification=int)
-    DataField(name='Field 1', specification=ValueSet(elements=[<class 'int'>], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')
-
     :ivar name: Name of the field
     :ivar specification: Value set of the field, if the value set is only one type, can also pass that type directly
     :ivar id: The identifier of the field, adhering to the naming rules stated above
@@ -186,10 +182,6 @@ class DataModel:
     be accessed using the `id` as an attribute of the `DataModel` object. E.g.: `data_model.date_of_birth`. This is
     useful in the data reading and mapping processes.
 
-    >>> data_model = DataModel("Test data model", (DataField(name="Field 1", specification=ValueSet()),))
-    >>> data_model.field_1
-    DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')
-
     :ivar data_model_name: Name of the data model
     :ivar fields: List of `DataField` objects
     :ivar resources: List of `CodeSystem` objects