notebook for reporting classes that can't be aggregated in a Database instance

notebooks/in-repo-anaggregateds-report.ipynb

@@ -0,0 +1,248 @@
+{
+ "cells": [
+  {
+   "cell_type": "raw",
+   "source": [
+    "## This notebook just reports the nmdc-schema classes for which there's not slot to aggregate the class instances in a Database"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "c5ab1e5a4842b2c7"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "outputs": [],
+   "source": [
+    "from linkml_runtime import SchemaView"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:48.257190841Z",
+     "start_time": "2023-10-26T17:35:48.213037258Z"
+    }
+   },
+   "id": "9f4bdf7c057f2b62"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "outputs": [],
+   "source": [
+    "local_schema_file = \"../src/schema/nmdc.yaml\""
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:48.727871066Z",
+     "start_time": "2023-10-26T17:35:48.713324998Z"
+    }
+   },
+   "id": "15b8c7c5a5cbe272"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "outputs": [],
+   "source": [
+    "target_class = \"Database\""
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:49.158342115Z",
+     "start_time": "2023-10-26T17:35:49.154137528Z"
+    }
+   },
+   "id": "6e8eacd9ea93f492"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "outputs": [],
+   "source": [
+    "schema_view = SchemaView(local_schema_file)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:50.067096805Z",
+     "start_time": "2023-10-26T17:35:49.550408252Z"
+    }
+   },
+   "id": "58bc42c5d64a43"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "'NMDC'"
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "schema_view.schema.name"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:50.078747622Z",
+     "start_time": "2023-10-26T17:35:50.072438952Z"
+    }
+   },
+   "id": "f0ec13d56a627848"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "outputs": [],
+   "source": [
+    "nmdc_classes = schema_view.all_classes()\n",
+    "\n",
+    "nmdc_class_names = []"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.534377790Z",
+     "start_time": "2023-10-26T17:35:50.623681692Z"
+    }
+   },
+   "id": "2edc737a2ecca55"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "outputs": [],
+   "source": [
+    "for ck, cv in nmdc_classes.items():\n",
+    "    nmdc_class_names.append(cv.name)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.585166952Z",
+     "start_time": "2023-10-26T17:35:53.537178124Z"
+    }
+   },
+   "id": "7f51633981a8ed3c"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "outputs": [],
+   "source": [
+    "database_slots = schema_view.class_induced_slots(target_class)\n",
+    "\n",
+    "database_slots_to_ranges = {}\n",
+    "database_slot_ranges = []"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.629344497Z",
+     "start_time": "2023-10-26T17:35:53.585007303Z"
+    }
+   },
+   "id": "4f0dad8c4e071cd9"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "outputs": [],
+   "source": [
+    "for i in database_slots:\n",
+    "    database_slots_to_ranges[i.name] = i.range\n",
+    "    database_slot_ranges.append(i.range)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.629584895Z",
+     "start_time": "2023-10-26T17:35:53.629062467Z"
+    }
+   },
+   "id": "9dc38dc6f6ed34a4"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "outputs": [],
+   "source": [
+    "non_database_classes = list(set(nmdc_class_names) - set(database_slot_ranges))\n",
+    "non_database_classes.sort()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.629714870Z",
+     "start_time": "2023-10-26T17:35:53.629308789Z"
+    }
+   },
+   "id": "f1c81b6f02d0c47c"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "['Activity',\n 'AnalyticalSample',\n 'AttributeValue',\n 'BiosampleProcessing',\n 'BooleanValue',\n 'ChemicalEntity',\n 'ControlledIdentifiedTermValue',\n 'ControlledTermValue',\n 'CreditAssociation',\n 'Database',\n 'EnvironmentalMaterialTerm',\n 'FunctionalAnnotationTerm',\n 'GeneProduct',\n 'GeolocationValue',\n 'ImageValue',\n 'Instrument',\n 'InstrumentValue',\n 'IntegerValue',\n 'LabDevice',\n 'MagBin',\n 'MaterialContainer',\n 'MaterialEntity',\n 'MetaboliteQuantification',\n 'MetatranscriptomeAnnotationActivity',\n 'MetatranscriptomeAssembly',\n 'NamedThing',\n 'OntologyClass',\n 'OrthologyGroup',\n 'Pathway',\n 'PeptideQuantification',\n 'PersonValue',\n 'PlannedProcess',\n 'ProteinQuantification',\n 'Protocol',\n 'QualityControlReport',\n 'QuantityValue',\n 'Reaction',\n 'ReactionParticipant',\n 'Site',\n 'TextValue',\n 'TimestampValue',\n 'UrlValue']"
+     },
+     "execution_count": 23,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "non_database_classes"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-10-26T17:35:53.630475480Z",
+     "start_time": "2023-10-26T17:35:53.629442737Z"
+    }
+   },
+   "id": "bf7d109513dd46db"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "3971d41bfafd02bf"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}