Merge pull request #309 from madgik/dev/518/formula

Dev/518/formula
madgik · Dec 21, 2021 · c0d92f7 · c0d92f7
2 parents bf2fc7a + b42b006
commit c0d92f7
Show file tree

Hide file tree

Showing 42 changed files with 8,853 additions and 7,077 deletions.
diff --git a/...me-master/src/main/java/madgik/exareme/master/queryProcessor/HBP/AlgorithmProperties.java b/...me-master/src/main/java/madgik/exareme/master/queryProcessor/HBP/AlgorithmProperties.java
@@ -264,6 +264,8 @@ private static void validateAlgorithmParameterValueType(
             ParameterProperties parameterProperties
     ) throws AlgorithmException, BadUserInputException {
         if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.json)) {
+            if (value.equals(""))
+                return;
             try {
                 new JSONObject(value);
             } catch (JSONException ex) {

diff --git a/...me-master/src/main/java/madgik/exareme/master/queryProcessor/HBP/ParameterProperties.java b/...me-master/src/main/java/madgik/exareme/master/queryProcessor/HBP/ParameterProperties.java
@@ -21,6 +21,7 @@ public class ParameterProperties {
     public enum ParameterType {
         column,                // used for selecting specific columns from the database
         formula,               // used for parsing the input as a formula of R, '+ - * : 0' are allowed.
+        formula_description,    // used for providing a formula description to the algorithm in json format
         filter,                // used for filtering on the database input
         dataset,               // used for choosing database input
         pathology,             // used for specifying what database to use
@@ -33,7 +34,6 @@ public enum ParameterValueType {
         real,
         json
     }
-
     public ParameterProperties() {
     }
 
@@ -50,13 +50,15 @@ public void validateParameterPropertiesInitialization(String algorithmName) thro
         if (type == null) {
             throw new AlgorithmException(algorithmName, "The parameter field 'type' was not initialized in the properties.json file.");
         } else if (type.equals(ParameterType.column) || type.equals(ParameterType.formula)) {
-            if (columnValuesSQLType == null) {
-            }
-
             if (columnValuesIsCategorical == null) {
                 throw new AlgorithmException(algorithmName, "The parameter field 'columnValuesIsCategorical' was not initialized in the properties.json file.");
             }
-        } else if (valueType.equals(ParameterValueType.json)){
+        }else if (type.equals(ParameterType.formula_description)) {
+            if (!valueType.equals(ParameterValueType.json)) {
+                throw new AlgorithmException(algorithmName, "The parameter field 'valueType' must be json since the 'type' is formula_description.");
+            }
+        }
+        if (valueType.equals(ParameterValueType.json)){
             if(valueMultiple) {
                 throw new AlgorithmException(algorithmName, "The parameter field 'valueMultiple' cannot be true because the 'valueType' is json.");
             }

diff --git a/Exareme-Docker/src/mip-algorithms/.gitignore b/Exareme-Docker/src/mip-algorithms/.gitignore
@@ -8,7 +8,7 @@
 
 # db files
 *.db
-# !mipframework/runner/dbs/datasets.db
+!mipframework/runner/dbs/datasets.db
 # !mipframework/runner/dbs/1LocalDBs/local_dataset0.db
 # !mipframework/runner/dbs/10LocalDBs/local_dataset0.db
 # !mipframework/runner/dbs/10LocalDBs/local_dataset1.db

diff --git a/Exareme-Docker/src/mip-algorithms/DESCRIPTIVE_STATS/__init__.py b/Exareme-Docker/src/mip-algorithms/DESCRIPTIVE_STATS/__init__.py
@@ -1,3 +1,3 @@
-from descriptive_stats import DescriptiveStats
+from .descriptive_stats import DescriptiveStats
 
 __all__ = ["DescriptiveStats"]