Merge pull request #264 from IFCA-Advanced-Computing/feature/module_structure

Move current code to a Python package structure

Author: orviz

.gitignore

@@ -1,8 +1,3 @@
-#
-## FAIR-eva
-#
-config.ini
-
 #
 ## Python
 #

README.rst

@@ -6,6 +6,6 @@ Running:
 
 .. code-block:: bash
 
-    $ ./fair.py
+    $ fair-eva
 
 Now open your browser and go to http://localhost:9090/v1.0/ui/ to see the Swagger UI.

api/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+
+import connexion
+from connexion.resolver import RestyResolver
+
+
+def main():
+    app = connexion.FlaskApp(__name__)
+    app.add_api(
+        "fair-api.yaml",
+        arguments={"title": "FAIR evaluator"},
+        resolver=RestyResolver("fair_eva.api"),
+    )
+    app.run(port=9090)

fair.py

@@ -0,0 +1,4 @@
+from . import main
+
+if __name__ == "__main__":
+    main()

fair_eva/__init__.py

@@ -0,0 +1 @@
+import fair_eva.api.rda  # noqa

fair_eva/__main__.py

@@ -1,4 +1,5 @@
 import ast
+import configparser
 import csv
 import gettext
 import logging
@@ -8,12 +9,13 @@
 import xml.etree.ElementTree as ET
 from abc import ABC, abstractmethod
 from functools import wraps
+from importlib.resources import read_text
 
 import idutils
 import pandas as pd
 import requests
 
-import api.utils as ut
+import fair_eva.api.utils as ut
 
 logger = logging.getLogger("api.plugin.evaluation_steps")
 
@@ -92,13 +94,25 @@ def __init__(
         self, item_id, api_endpoint=None, lang="en", config=None, name=None, **kwargs
     ):
         self.item_id = item_id
-        self.api_endpoint = api_endpoint
         self.lang = lang
         self.config = config
         self.name = name
         self.metadata = None
         self.cvs = []
 
+        # API endpoint
+        self.api_endpoint = api_endpoint
+        if not self.api_endpoint:
+            try:
+                self.api_endpoint = self.config.get("Generic", "endpoint")
+            except configparser.NoOptionError as e:
+                raise (e)
+            else:
+                logger.debug(
+                    "API endpoint not passed as input argument, getting it from configuration: %s"
+                    % self.api_endpoint
+                )
+
         # Config attributes
         self.identifier_term = ast.literal_eval(
             self.config[self.name]["identifier_term"]
@@ -119,41 +133,15 @@ def __init__(
         self.terms_relations = ast.literal_eval(
             self.config[self.name]["terms_relations"]
         )
-        self.metadata_access_manual = ast.literal_eval(
-            self.config[self.name]["metadata_access_manual"]
-        )
-        self.data_access_manual = ast.literal_eval(
-            self.config[self.name]["data_access_manual"]
-        )
         self.terms_access_protocols = ast.literal_eval(
             self.config[self.name]["terms_access_protocols"]
         )
-
-        # self.vocabularies = ast.literal_eval(self.config[self.name]["vocabularies"])
-
-        self.dict_vocabularies = ast.literal_eval(
-            self.config[self.name]["dict_vocabularies"]
-        )
-
-        self.vocabularies = list(self.dict_vocabularies.keys())
         self.metadata_standard = ast.literal_eval(
             self.config[self.name]["metadata_standard"]
         )
-
-        self.metadata_authentication = ast.literal_eval(
-            self.config[self.name]["metadata_authentication"]
-        )
-        self.metadata_persistence = ast.literal_eval(
-            self.config[self.name]["metadata_persistence"]
-        )
-        self.terms_vocabularies = ast.literal_eval(
-            self.config[self.name]["terms_vocabularies"]
-        )
-
         self.fairsharing_username = ast.literal_eval(
             self.config["fairsharing"]["username"]
         )
-
         self.fairsharing_password = ast.literal_eval(
             self.config["fairsharing"]["password"]
         )
@@ -169,6 +157,29 @@ def __init__(
         global _
         _ = self.translation()
 
+    @staticmethod
+    def load_config(plugin_path, fail_if_no_config=True):
+        """Find the path to a data file."""
+        config = configparser.ConfigParser()
+        try:
+            config.read_string(read_text("fair_eva", "config.ini"))
+            config.read_string(read_text(plugin_path, "config.ini"))
+        except FileNotFoundError as e:
+            logging.error("Could not load config file: %s" % str(e))
+            if fail_if_no_config:
+                raise (e)
+        except configparser.MissingSectionHeaderError as e:
+            message = "Bad INI format in main and/or plugin's configuration files"
+            logging.error(message)
+            logging.debug(e)
+            error = {"code": 500, "message": "%s" % message}
+            logging.debug("Returning API response: %s" % error)
+            return json.dumps(error), 500
+        else:
+            logging.debug("Successfully loaded main & plugin's configuration files")
+
+        return config
+
     def translation(self):
         # Translations
         t = gettext.translation(
@@ -1598,7 +1609,7 @@ def rda_r1_1_02m(self, license_list=[], machine_readable=False, **kwargs):
         terms_license_list = terms_license["list"]
         terms_license_metadata = terms_license["metadata"]
 
-        if not license_list:
+        if license_list is None or len(license_list) == 0:
             license_list = terms_license_metadata.text_value.values
 
         license_num = len(license_list)