From acbb2e5b5d924e6d87984c71e967f6839553fdc5 Mon Sep 17 00:00:00 2001
From: Luca Venturini <lucventurini@gmail.com>
Date: Wed, 3 Oct 2018 11:36:36 +0100
Subject: [PATCH] Initial modifications to address #130. Now the metric should
 be considered correctly and the configuration file should be parsed and
 checked appropriately

---
 Mikado/configuration/configurator.py        | 4 ++++
 Mikado/configuration/scoring_blueprint.json | 9 +++++++--
 Mikado/loci/abstractlocus.py                | 9 ++++++++-
 3 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/Mikado/configuration/configurator.py b/Mikado/configuration/configurator.py
index 2bed91d74..bcb3abb3a 100644
--- a/Mikado/configuration/configurator.py
+++ b/Mikado/configuration/configurator.py
@@ -177,6 +177,10 @@ def check_scoring(json_conf):
             elif json_conf["scoring"][parameter]["use_raw"] is True:
                 invalid_raw.add(parameter)
 
+        if "filter" in json_conf["scoring"][parameter] and "metric" in json_conf["scoring"][parameter]["filter"]:
+            if json_conf["scoring"][parameter]["filter"]["metric"] not in available_metrics:
+                parameters_not_found.append(json_conf["scoring"][parameter]["filter"]["metric"])
+
     if len(parameters_not_found) > 0 or len(double_parameters) > 0 or len(invalid_filter) > 0 or len(invalid_raw) > 0:
         err_message = ''
         if len(parameters_not_found) > 0:
diff --git a/Mikado/configuration/scoring_blueprint.json b/Mikado/configuration/scoring_blueprint.json
index 5f5ab7832..9537b4ea6 100644
--- a/Mikado/configuration/scoring_blueprint.json
+++ b/Mikado/configuration/scoring_blueprint.json
@@ -12,10 +12,12 @@
         "oneOf": [
           {
             "operator": { "oneOf": ["gt", "ge", "lt", "le"], "optional": false},
-            "value": {"type": "number", "optional": false}
+            "value": {"type": "number", "optional": false},
+            "metric": {"type": "string", "optional": true}
           },
           {
             "operator": { "oneOf": ["ne", "eq"], "optional": false},
+            "metric": {"type": "string", "optional": true},
             "value": {
               "oneOf": [{"type": "number"}, {"type": "boolean"}],
               "optional": false}
@@ -28,7 +30,8 @@
               ],
               "optional": false
             },
-            "value": {"type": "array"}
+            "metric": {"type": "string", "optional": true},
+            "value": {"type": "array", "optional": false}
           },
           {
             "operator": {
@@ -38,7 +41,9 @@
               ],
               "optional": false
             },
+            "metric": {"type": "string", "optional": true},
             "value": {
+              "optional": false,
               "type": "array",
               "items": {
                 "type": "number"
diff --git a/Mikado/loci/abstractlocus.py b/Mikado/loci/abstractlocus.py
index 2b81a61a5..47013f422 100644
--- a/Mikado/loci/abstractlocus.py
+++ b/Mikado/loci/abstractlocus.py
@@ -1102,7 +1102,14 @@ def _calculate_score(self, param):
             check = True
             if ("filter" in self.json_conf["scoring"][param] and
                     self.json_conf["scoring"][param]["filter"] != {}):
-                check = self.evaluate(tid_metric, self.json_conf["scoring"][param]["filter"])
+                if "metric" not in self.json_conf["scoring"][param]["filter"]:
+                    metric_to_evaluate = tid_metric
+                else:
+                    metric_key = self.json_conf["scoring"][param]["filter"]["metric"]
+                    if not hasattr(self.transcripts[tid], metric_key):
+                        raise KeyError("Asked for an invalid metric in filter: {}".format(metric_key))
+                    metric_to_evaluate = getattr(self.transcripts[tid], metric_key)
+                check = self.evaluate(metric_to_evaluate, self.json_conf["scoring"][param]["filter"])
 
             if check is True:
                 if use_raw is True: