Merge pull request #212 from EOSC-synergy/release/3.0.0

New release 3.0.0: FAIR report in DT-GEO's D4.1v2

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
   - id: trailing-whitespace
   - id: end-of-file-fixer
   - id: check-yaml
-  - id: check-added-large-files
+  # - id: check-added-large-files
 - repo: https://github.com/psf/black-pre-commit-mirror
   rev: 24.3.0
   hooks:

api/rda.py

@@ -17,8 +17,6 @@
 )
 logger = logging.getLogger("api")
 
-config = load_config()
-
 
 def load_evaluator(wrapped_func):
     @wraps(wrapped_func)
@@ -35,9 +33,9 @@ def wrapper(body, **kwargs):
             msg = "Neither the identifier nor the pattern to query was provided. Exiting.."
             logger.error(msg)
             return msg, 400
-
         # Get the identifiers through a search query
         ids = [item_id]
+
         # FIXME oai-pmh should be no different
         downstream_logger = evaluator.logger
         if repo not in ["oai-pmh"]:
@@ -61,15 +59,18 @@ def wrapper(body, **kwargs):
         evaluator_handler = ut.EvaluatorLogHandler()
         downstream_logger.addHandler(evaluator_handler)
 
+        # Load configuration
+        config_data = load_config(plugin=repo)
+
         # Collect FAIR checks per metadata identifier
         result = {}
         exit_code = 200
         for item_id in ids:
             # FIXME oai-pmh should be no different
             if repo in ["oai-pmh"]:
-                eva = evaluator.Evaluator(item_id, oai_base, lang)
+                eva = evaluator.Evaluator(item_id, oai_base, lang, config=config_data)
             else:
-                eva = plugin.Plugin(item_id, oai_base, lang)
+                eva = plugin.Plugin(item_id, oai_base, lang, config=config_data)
             _result, _exit_code = wrapped_func(body, eva=eva)
             logger.debug(
                 "Raw result returned for indicator ID '%s': %s" % (item_id, _result)
@@ -99,8 +100,8 @@ def endpoints(plugin=None, plugins_path="plugins"):
 
     # Obtain endpoint from each plugin's config
     for plug in plugins_list:
-        config = load_config(plugin=plug, fail_if_no_config=False)
-        endpoint = config.get("Generic", "endpoint", fallback="")
+        _config = load_config(plugin=plug, fail_if_no_config=False)
+        endpoint = _config.get("Generic", "endpoint", fallback="")
         if not endpoint:
             logger.debug(
                 "Plugin's config does not contain 'Generic:endpoint' section: %s" % plug
@@ -1339,14 +1340,14 @@ def rda_all(body, eva):
     result_points = 10
     num_of_tests = 10
 
-    generic_config = config["Generic"]
+    generic_config = eva.config["Generic"]
     api_config = os.path.join(
         app_dirname, generic_config.get("api_config", "fair-api.yaml")
     )
     try:
         with open(api_config, "r") as f:
             documents = yaml.full_load(f)
-        logging.debug("API configuration successfully loaded: %s" % api_config)
+        logger.debug("API configuration successfully loaded: %s" % api_config)
     except Exception as e:
         message = "Could not find API config file: %s" % api_config
         logger.error(message)
@@ -1360,7 +1361,7 @@ def rda_all(body, eva):
             if documents["paths"][e]["x-indicator"]:
                 indi_code = e.split("/")
                 indi_code = indi_code[len(indi_code) - 1]
-                logger.debug("Running - %s" % indi_code)
+                logger.info("Running - %s" % indi_code)
                 points, msg = getattr(eva, indi_code)()
                 x_principle = documents["paths"][e]["x-principle"]
                 if "Findable" in x_principle:

api/utils.py

@@ -1,5 +1,6 @@
 import json
 import logging
+import os
 import re
 import sys
 import urllib
@@ -704,12 +705,15 @@ def orcid_basic_info(orcid):
         "Authorization": "Bearer a354d82e-37fa-47de-b4a2-740dbe90f355",
     }
     try:
+        if not idutils.is_orcid(orcid):
+            raise Exception("Malformed ORCID value: %s" % orcid)
         url = "https://pub.orcid.org/v3.0/" + orcid
         r = requests.get(url, verify=False, headers=headers)  # GET with headers
         xmlTree = ET.fromstring(r.text)
-        item = xmlTree.findall(
-            ".//{http://www.orcid.org/ns/common}assertion-origin-name"
-        )
+        for prop in ["assertion-origin-name", "source-name"]:
+            item = xmlTree.findall(".//{http://www.orcid.org/ns/common}%s" % prop)
+            if item:
+                break
     except Exception as e:
         logging.error(e)
         return basic_info
@@ -883,9 +887,11 @@ def resolve_handle(handle_id):
     return resolves, msg, values
 
 
-def check_link(address):
+def check_link(address, return_http_code=False):
     req = urllib.request.Request(url=address)
     resp = urllib.request.urlopen(req)
+    if return_http_code:
+        return resp.status
     if resp.status in [400, 404, 403, 408, 409, 501, 502, 503]:
         return False
     else:
@@ -918,76 +924,6 @@ def make_http_request(url, request_type="GET", verify=False):
     return payload
 
 
-def get_fairsharing_metadata(offline=True, username="", password="", path=""):
-    if offline == True:
-        f = open(path)
-        fairlist = json.load(f)
-        f.close()
-
-    else:
-        url = "https://api.fairsharing.org/users/sign_in"
-        payload = {"user": {"login": username, "password": password}}
-        headers = {"Accept": "application/json", "Content-Type": "application/json"}
-
-        response = requests.request(
-            "POST", url, headers=headers, data=json.dumps(payload)
-        )
-
-        # Get the JWT from the response.text to use in the next part.
-        data = response.json()
-        jwt = data["jwt"]
-
-        url = "https://api.fairsharing.org/search/fairsharing_records?page[size]=2500&fairsharing_registry=standard&user_defined_tags=metadata standardization"
-
-        headers = {
-            "Accept": "application/json",
-            "Content-Type": "application/json",
-            "Authorization": "Bearer {0}".format(jwt),
-        }
-
-        response = requests.request("POST", url, headers=headers)
-        fairlist = response.json()
-        user = open(path, "w")
-        json.dump(fairlist, user)
-        user.close()
-    return fairlist
-
-
-def get_fairsharing_formats(offline=True, username="", password="", path=""):
-    if offline == True:
-        f = open(path)
-        fairlist = json.load(f)
-        f.close()
-
-    else:
-        url = "https://api.fairsharing.org/users/sign_in"
-        payload = {"user": {"login": username, "password": password}}
-        headers = {"Accept": "application/json", "Content-Type": "application/json"}
-
-        response = requests.request(
-            "POST", url, headers=headers, data=json.dumps(payload)
-        )
-
-        # Get the JWT from the response.text to use in the next part.
-        data = response.json()
-        jwt = data["jwt"]
-
-        url = "https://api.fairsharing.org/search/fairsharing_records?page[size]=2500&user_defined_tags=Geospatial data"
-
-        headers = {
-            "Accept": "application/json",
-            "Content-Type": "application/json",
-            "Authorization": "Bearer {0}".format(jwt),
-        }
-
-        response = requests.request("POST", url, headers=headers)
-        fairlist = response.json()
-        user = open(path, "w")
-        json.dump(fairlist, user)
-        user.close()
-    return fairlist
-
-
 def check_fairsharing_abbreviation(fairlist, abreviation):
     for standard in fairlist["data"]:
         if abreviation == standard["attributes"]["abbreviation"]: