diff toolfactory/galaxyxml/tool/__init__.py @ 92:6ce360759c28 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/galaxyxml/tool/__init__.py	Thu Nov 19 23:59:50 2020 +0000
@@ -0,0 +1,184 @@
+import copy
+import logging
+
+from galaxyxml import GalaxyXML, Util
+from galaxyxml.tool.parameters import XMLParam
+
+from lxml import etree
+
+VALID_TOOL_TYPES = ("data_source", "data_source_async")
+VALID_URL_METHODS = ("get", "post")
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class Tool(GalaxyXML):
+
+    def __init__(
+        self,
+        name,
+        id,
+        version,
+        description,
+        executable,
+        hidden=False,
+        tool_type=None,
+        URL_method=None,
+        workflow_compatible=True,
+        interpreter=None,
+        version_command="interpreter filename.exe --version",
+        command_override=None,
+    ):
+
+        self.executable = executable
+        self.interpreter = interpreter
+        self.command_override = command_override
+        kwargs = {
+            "name": name,
+            "id": id,
+            "version": version,
+            "hidden": hidden,
+            "workflow_compatible": workflow_compatible,
+        }
+        self.version_command = version_command
+
+        # Remove some of the default values to make tools look a bit nicer
+        if not hidden:
+            del kwargs["hidden"]
+        if workflow_compatible:
+            del kwargs["workflow_compatible"]
+
+        kwargs = Util.coerce(kwargs)
+        self.root = etree.Element("tool", **kwargs)
+
+        if tool_type is not None:
+            if tool_type not in VALID_TOOL_TYPES:
+                raise Exception("Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES))
+            else:
+                kwargs["tool_type"] = tool_type
+
+                if URL_method is not None:
+                    if URL_method in VALID_URL_METHODS:
+                        kwargs["URL_method"] = URL_method
+                    else:
+                        raise Exception("URL_method must be one of %s" % ",".join(VALID_URL_METHODS))
+
+        description_node = etree.SubElement(self.root, "description")
+        description_node.text = description
+
+    def add_comment(self, comment_txt):
+        comment = etree.Comment(comment_txt)
+        self.root.insert(0, comment)
+
+    def append_version_command(self):
+        version_command = etree.SubElement(self.root, "version_command")
+        try:
+            version_command.text = etree.CDATA(self.version_command)
+        except Exception:
+            pass
+
+    def append(self, sub_node):
+        if issubclass(type(sub_node), XMLParam):
+            self.root.append(sub_node.node)
+        else:
+            self.root.append(sub_node)
+
+    def clean_command_string(self, command_line):
+        clean = []
+        for x in command_line:
+            if x is not [] and x is not [""]:
+                clean.append(x)
+
+        return "\n".join(clean)
+
+    def export(self, keep_old_command=False):  # noqa
+
+        export_xml = copy.deepcopy(self)
+
+        try:
+            export_xml.append(export_xml.edam_operations)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.edam_topics)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.requirements)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.configfiles)
+        except Exception:
+            pass
+
+        if self.command_override:
+            command_line = self.command_override
+        else:
+            command_line = []
+            try:
+                command_line.append(export_xml.inputs.cli())
+            except Exception as e:
+                logger.warning(str(e))
+
+            try:
+                command_line.append(export_xml.outputs.cli())
+            except Exception:
+                pass
+
+        # Add stdio section
+        stdio = etree.SubElement(export_xml.root, "stdio")
+        etree.SubElement(stdio, "exit_code", range="1:", level="fatal")
+
+        # Append version command
+        export_xml.append_version_command()
+
+        # Steal interpreter from kwargs
+        command_kwargs = {}
+        if export_xml.interpreter is not None:
+            command_kwargs["interpreter"] = export_xml.interpreter
+
+        # Add command section
+        command_node = etree.SubElement(export_xml.root, "command", **command_kwargs)
+
+        if keep_old_command:
+            if getattr(self, "command", None):
+                command_node.text = etree.CDATA(export_xml.command)
+            else:
+                logger.warning("The tool does not have any old command stored. " + "Only the command line is written.")
+                command_node.text = export_xml.executable
+        else:
+            if self.command_override:
+                actual_cli = export_xml.clean_command_string(command_line)
+            else:
+                actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line))
+            command_node.text = etree.CDATA(actual_cli.strip())
+
+        try:
+            export_xml.append(export_xml.inputs)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.outputs)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.tests)
+        except Exception:
+            pass
+
+        help_element = etree.SubElement(export_xml.root, "help")
+        help_element.text = etree.CDATA(export_xml.help)
+
+        try:
+            export_xml.append(export_xml.citations)
+        except Exception:
+            pass
+
+        return super(Tool, export_xml).export()