From e98abeb61d98bf2a3535d176b472a4753f7a1582 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 26 Aug 2023 00:25:12 +0200
Subject: [PATCH] Create links only for inputs of type data

---
 server/galaxyls/services/links.py          | 22 ++++++++++++++++------
 server/galaxyls/services/tools/document.py | 11 +++++++++++
 2 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/server/galaxyls/services/links.py b/server/galaxyls/services/links.py
index 44b90f7..98afdec 100644
--- a/server/galaxyls/services/links.py
+++ b/server/galaxyls/services/links.py
@@ -4,6 +4,7 @@
 
 from galaxyls.services.tools.document import GalaxyToolXmlDocument
 from galaxyls.services.xml.document import XmlDocument
+from galaxyls.services.xml.nodes import XmlElement
 from galaxyls.services.xml.utils import convert_document_offsets_to_range
 
 
@@ -20,18 +21,17 @@ def _get_test_data_file_links(self, tool: GalaxyToolXmlDocument) -> List[Documen
         for test in tool.get_tests():
             params = filter(lambda e: e.name == "param", test.elements)
             for param in params:
-                value_attr = param.attributes.get("value")
-                if value_attr is None or value_attr.value is None:
+                value_attribute = param.attributes.get("value")
+                filename = param.get_attribute_value("value")
+                if not value_attribute or not value_attribute.value or not filename:
                     # Must have a value
                     continue
 
-                filename = value_attr.get_value()
-                if filename is None or "." not in filename:
-                    # Must be a filename with extension
+                if not self._is_data_input_param(param, tool):
                     continue
 
                 test_data_file_path = tool.get_test_data_path() / filename
-                start_offset, end_offset = value_attr.value.get_unquoted_content_offsets()
+                start_offset, end_offset = value_attribute.value.get_unquoted_content_offsets()
                 link_range = convert_document_offsets_to_range(tool.xml_document.document, start_offset, end_offset)
                 result.append(
                     DocumentLink(
@@ -40,3 +40,13 @@ def _get_test_data_file_links(self, tool: GalaxyToolXmlDocument) -> List[Documen
                     )
                 )
         return result
+
+    def _is_data_input_param(self, param: XmlElement, tool: GalaxyToolXmlDocument) -> bool:
+        param_name = param.get_attribute_value("name")
+        inputs = tool.get_inputs()
+        for input in inputs:
+            input_name = input.get_attribute_value("name")
+            if input_name == param_name:
+                input_type = input.get_attribute_value("type")
+                return input_type == "data"
+        return False
diff --git a/server/galaxyls/services/tools/document.py b/server/galaxyls/services/tools/document.py
index 96050cf..198416c 100644
--- a/server/galaxyls/services/tools/document.py
+++ b/server/galaxyls/services/tools/document.py
@@ -147,6 +147,17 @@ def analyze_inputs(self) -> GalaxyToolInputTree:
         inputs = self.find_element(INPUTS)
         return GalaxyToolInputTree(inputs)
 
+    def get_inputs(self) -> List[XmlElement]:
+        """Gets the inputs of this document as a list of elements.
+
+        Returns:
+            List[XmlElement]: The outputs defined in the document.
+        """
+        outputs = self.find_element(INPUTS)
+        if outputs:
+            return outputs.elements
+        return []
+
     def get_outputs(self) -> List[XmlElement]:
         """Gets the outputs of this document as a list of elements.