Merge pull request #19 from Bayer-Group/issue14

Issue14

Author: a-hartens

docs/tutorials/CodelistPhenotype_Tutorial.ipynb

@@ -114,7 +114,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenex.phenotypes.codelist_phenotype import CodelistPhenotype\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
     "# Ex.1 \n",
     "# Which patients had an atrial fibrillation diagnosis at **any time** in the data source?\n",
     "af_phenotype = CodelistPhenotype(\n",
@@ -197,7 +197,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    GreaterThanOrEqualTo,\n",
     "    LessThan,\n",
     "    RelativeTimeRangeFilter, \n",
@@ -271,7 +271,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter\n",
     ")\n",
@@ -337,7 +337,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    CategoricalFilter\n",
     ")\n",
     "\n",
@@ -368,7 +368,8 @@
    "metadata": {},
    "source": [
     "<a id='example_7'></a>\n",
-    "#### Example 7"
+    "# CURRENTLY NOT IMPLEMENTED\n",
+    "#### ~Example 7~"
    ]
   },
   {
@@ -379,7 +380,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    CategoricalFilter\n",
     ")\n",
     "\n",
@@ -429,7 +430,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter, \n",
     "    CategoricalFilter\n",
@@ -499,8 +500,7 @@
    "outputs": [],
    "source": [
     "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.phenotypes import CodelistPhenotype\n",
-    "from phenex.operations.filters import (\n",
+    "from phenex.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter, \n",
     ")\n",

phenex/filters/__init__.py

@@ -1 +1,2 @@
 from .relative_time_range_filter import RelativeTimeRangeFilter
+from .value import GreaterThan, GreaterThanOrEqualTo, LessThan, LessThanOrEqualTo, EqualTo, Value

phenex/filters/categorical_filter.py

@@ -30,6 +30,13 @@ def __init__(
         self.domain = domain
         super(CategoricalFilter, self).__init__()
 
-    def _filter(self, table: Table):
-        table = table.filter(table[self.column_name].isin(self.allowed_values))
-        return table
+    def _filter(self, table: 'PhenexTable'):
+        return table.filter(table[self.column_name].isin(self.allowed_values))
+
+    def autojoin_filter(self, table: 'PhenexTable', tables:dict = None):
+        if self.column_name not in table.columns:
+            if self.domain not in tables.keys():
+                raise ValueError(f"Table required for categorical filter ({self.domain}) does not exist within domains dicitonary")
+            table = table.join(tables[self.domain], domains = tables)
+            # TODO downselect to original columns
+        return table.filter(table[self.column_name].isin(self.allowed_values))

phenex/filters/codelist_filter.py

@@ -58,4 +58,5 @@ def _filter(self, code_table: CodeTable) -> CodeTable:
             code_table.columns
         )
 
-        return filtered_table.select(input_columns)
+        # return table with downselected columns, of same type as input table
+        return type(code_table)(filtered_table.select(input_columns))