Added affiliations for zenodo framework

jose-luis-rs · Dec 7, 2024 · fc69756 · fc69756
1 parent 4a7126d
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diff --git a/.github/workflows/check_metadata.yaml b/.github/workflows/check_metadata.yaml
@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2024 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt, Germany
 #
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 name: Check AUTHORS and CONTRIBUTORS in metadata
 
@@ -9,13 +9,11 @@ on:
     paths:
     - AUTHORS
     - CONTRIBUTORS
-    - codemeta.json
     - .zenodo.json
   pull_request:
     paths:
     - AUTHORS
     - CONTRIBUTORS
-    - codemeta.json
     - .zenodo.json
 
 jobs:

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,65 +1,99 @@
 {
+    "description": "The SOFIA module within the R3BRoot framework encapsulates the configuration and functionality of the SOFIA detectors, specifically designed for fission experiments conducted with the GLAD spectrometer. R3BRoot, built on the FairRoot framework, serves as a software environment for performing detailed Monte Carlo simulations and processing experimental data from R3B (Reactions with Relativistic Radioactive Beams) experiments. These capabilities include precise modeling of detector geometry, particle tracking, event reconstruction, and physics analysis, supporting the investigation of fission dynamics and nuclear structure in high-energy heavy-ion collision scenarios at the GSI-FAIR facility.",
+    "related_identifiers": [
+        {
+            "identifier": "https://github.com/R3BRootGroup/sofia/",
+            "relation": "isSupplementTo",
+            "resource_type": "software",
+            "scheme": "url"
+        }
+    ],
+    "maintainers": [
+        {
+            "name": "Rodriguez-Sánchez, Jose Luis",
+            "orcid": "0000-0002-4702-5294",
+            "email": "[email protected]",
+            "affiliation": "CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain"
+        }
+    ],
+    "title": "SOFIA Software",
+    "upload_type": "software",
+    "softwareRequirements": [
+        "FairSoft, FairRoot, R3BRoot"
+    ],
+    "programmingLanguage": [
+        "C",
+        "C++"
+    ],
+    "runtimePlatform": [
+        "ROOT"
+    ],
+    "operatingSystem": [
+        "Linux",
+        "macOS"
+    ],
+    "keywords": [
+        "Geant4",
+        "c-plus-plus",
+        "cmake",
+        "vmc",
+        "modular",
+        "Track reconstruction",
+        "Simulation",
+        "Data analysis",
+        "Structure and dynamics of nuclei",
+        "Nuclear reactions",
+        "Nuclear fission",
+        "SOFIA/R3B experiments",
+        "GSI/FAIR facility"
+    ],
     "creators": [
         {
-            "name": "Alvarez Pol, Hector",
-            "orcid": "0000-0001-9643-6252"
+            "name": "Rodríguez-Sánchez, Jose Luis",
+            "orcid": "0000-0002-4702-5294",
+            "email": "[email protected]",
+            "affiliation": "CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain"
         },
         {
-            "name": "Chatillon, Audrey"
+            "name": "Alvarez Pol, Hector",
+            "orcid": "0000-0001-9643-6252",
+            "affiliation": "IGFAE, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain"
         },
         {
-            "name": "Garcia Jimenez, Gabriel"
+            "name": "Chatillon, Audrey",
+            "affiliation": "CEA, DAM, DIF, 91297 Arpajon, France"
         },
         {
-            "name": "Gra\u00f1a Gonzalez, Antia",
-            "orcid": "0000-0002-0842-4110"
+            "name": "García-Jiménez, Gabriel",
+            "affiliation": "IGFAE, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain"
         },
         {
-            "name": "Morfouace, Pierre",
-            "orcid": "0000-0002-2131-2199"
+            "name": "Graña-González, Antia",
+            "orcid": "0000-0002-0842-4110",
+            "affiliation": "CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain"
         },
         {
-            "name": "Rodriguez Sanchez, Jose Luis",
-            "orcid": "0000-0002-4702-5294"
+            "name": "Morfouace, Pierre",
+            "orcid": "0000-0002-2131-2199",
+            "affiliation": "CEA, DAM, DIF, 91297 Arpajon, France"
         },
         {
             "name": "Taniuchi, Ryo",
-            "orcid": "0000-0002-8057-7074"
+            "orcid": "0000-0002-8057-7074",
+            "affiliation": "School of Physics, Engineering and Technology, University of York, YO10 5DD York, UK"
         }
     ],
     "contributors": [
         {
             "type": "Other",
-            "name": "Mayer, Jan"
+            "name": "Mayer, Jan",
+            "affiliation": "Technical University of Berlin, 10587 Berlin, Germany"
         },
         {
             "type": "Other",
             "name": "Wang, Yanzhao",
-            "orcid": "0000-0002-7006-7986"
-        }
-    ],
-    "description": "The SOFIA module within the R3BRoot framework encapsulates the configuration and functionality of the SOFIA detectors, specifically designed for fission experiments conducted with the GLAD spectrometer. R3BRoot, built on the FairRoot framework, serves as a software environment for performing detailed Monte Carlo simulations and processing experimental data from R3B (Reactions with Relativistic Radioactive Beams) experiments. These capabilities include precise modeling of detector geometry, particle tracking, event reconstruction, and physics analysis, supporting the investigation of fission dynamics and nuclear structure in high-energy heavy-ion collision scenarios at the GSI-FAIR facility.",
-    "related_identifiers": [
-        {
-            "identifier": "https://github.com/R3BRootGroup/sofia/",
-            "relation": "isSupplementTo",
-            "resource_type": "software",
-            "scheme": "url"
+            "orcid": "0000-0002-7006-7986",
+            "affiliation": "Universität zu Köln, 50923 Köln, Germany"
         }
-    ],
-    "title": "SOFIA software",
-    "upload_type": "software",
-    "keywords": [
-        "Geant4",
-        "c-plus-plus",
-        "cmake",
-        "vmc",
-        "modular",
-        "Event reconstruction",
-        "Simulation",
-        "Data analysis",
-        "Structure and dynamics of nuclei",
-        "Nuclear reactions",
-        "Nuclear fission"
     ]
 }
diff --git a/AUTHORS b/AUTHORS
@@ -1,7 +1,7 @@
-Alvarez Pol, Hector [https://orcid.org/0000-0001-9643-6252]
-Chatillon, Audrey
-Garcia Jimenez, Gabriel
-Graña Gonzalez, Antia [https://orcid.org/0000-0002-0842-4110]
-Morfouace, Pierre [https://orcid.org/0000-0002-2131-2199]
-Rodriguez Sanchez, Jose Luis [https://orcid.org/0000-0002-4702-5294]
-Taniuchi, Ryo [https://orcid.org/0000-0002-8057-7074]
+Rodríguez-Sánchez, Jose Luis [[email protected]] [https://orcid.org/0000-0002-4702-5294] [CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain]
+Alvarez Pol, Hector [https://orcid.org/0000-0001-9643-6252] [IGFAE, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain]
+Chatillon, Audrey [CEA, DAM, DIF, 91297 Arpajon, France]
+García-Jiménez, Gabriel [IGFAE, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain]
+Graña-González, Antia [https://orcid.org/0000-0002-0842-4110] [CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain]
+Morfouace, Pierre [https://orcid.org/0000-0002-2131-2199] [CEA, DAM, DIF, 91297 Arpajon, France]
+Taniuchi, Ryo [https://orcid.org/0000-0002-8057-7074] [School of Physics, Engineering and Technology, University of York, YO10 5DD York, UK]
diff --git a/CONTRIBUTORS b/CONTRIBUTORS
@@ -1,2 +1,2 @@
-Mayer, Jan
-Wang, Yanzhao [https://orcid.org/0000-0002-7006-7986]
+Mayer, Jan [Technical University of Berlin, 10587 Berlin, Germany]
+Wang, Yanzhao [https://orcid.org/0000-0002-7006-7986] [Universität zu Köln, 50923 Köln, Germany]
diff --git a/COPYRIGHT b/COPYRIGHT
@@ -0,0 +1,9 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: sofia
+Upstream-Contact: Jose Luis Rodríguez-Sánchez <[email protected]>
+Source: https://github.com/R3BRootGroup/sofia
+
+Files: *
+Copyright: 2017-2024, GSI Helmholtzzentrum fuer Schwerionenforschung GmbH
+Copyright: 2017-2024, [see AUTHORS file]
+Copyright: 2017-2024, [see CONTRIBUTORS file]
diff --git a/meta_update.py b/meta_update.py
@@ -1,10 +1,13 @@
 #! /usr/bin/env python3
+# Copyright (C) 2019-2024 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
-from argparse import ArgumentParser
-import json
 import re
+import json
 from collections import OrderedDict
-
+from argparse import ArgumentParser
+import os
 
 class Manipulator(object):
     def __str__(self):
@@ -13,95 +16,72 @@ def __str__(self):
     def load(self, filename=None):
         if filename is None:
             filename = self.default_filename
-        with open(filename, 'rb') as fp:
-            self.data = json.load(fp, object_pairs_hook=OrderedDict)
+        try:
+            with open(filename, 'r', encoding='utf8') as fp:
+                self.data = json.load(fp, object_pairs_hook=OrderedDict)
+        except FileNotFoundError as e:
+            print(f'Error: The file {filename} was not found. {e}')
+        except json.JSONDecodeError as e:
+            print(f'Error in JSON file: {e}')
+            raise  # Raise the error and stop execution
 
     def save(self, filename=None, indent=2):
         if filename is None:
             filename = self.default_filename
-        with open(filename, 'w', encoding='utf8') as fp:
-            json.dump(self.data, fp, indent=indent)
-            fp.write('\n')
+        try:
+            with open(filename, 'w', encoding='utf8') as fp:
+                json.dump(self.data, fp, indent=indent, ensure_ascii=False)
+                fp.write('\n')
+        except IOError as e:
+            print(f'Error saving the file {filename}: {e}')
 
     @staticmethod
     def _dict_entry_cmp(dict1, dict2, field1, field2=None):
         if field2 is None:
             field2 = field1
         if (field1 in dict1) and (field2 in dict2):
             return dict1[field1] == dict2[field2]
-        else:
-            return False
+        return False
 
     def _handle_person_list_file(self, filename, field_name, **kwargs):
-        fp = open(filename, 'r', encoding='utf8')
-        person_list = self.data.setdefault(field_name, [])
-        for i, line in enumerate(fp, start=0):
-            line = line.strip()
-            m = self.findregex.match(line)
-            if m is None:
-                raise RuntimeError("Could not analyze line %r" % line)
-            found_entry = self._find_person_entry(person_list, m.groupdict())
-            entry = self.update_person_entry(found_entry, m.groupdict(),
-                                             **kwargs)
-            if found_entry is None:
-                person_list.insert(i, entry)
-
-
-class CodeMetaManipulator(Manipulator):
-    default_filename = 'codemeta.json'
-    findregex = re.compile(r'^(?P<familyName>[-\w\s]*[-\w]),\s*'
-                           r'(?P<givenName>[-\w\s]*[-\w])\s*'
-                           r'(?:<(?P<email>\S+@\S+)>)?\s*'
-                           r'(\[(?P<orcid>\S+)\])?$')
-
-    @classmethod
-    def _find_person_entry(cls, person_list, matchdict):
-        # orcid is unique
-        for entry in person_list:
-            if cls._dict_entry_cmp(entry, matchdict, '@id', 'orcid'):
-                return entry
-        for entry in person_list:
-            if cls._dict_entry_cmp(entry, matchdict, 'email'):
-                return entry
-            if cls._dict_entry_cmp(entry, matchdict, 'familyName') \
-                    and cls._dict_entry_cmp(entry, matchdict, 'givenName'):
-                return entry
-        return None
-
-    @staticmethod
-    def update_person_entry(entry, matchdict):
-        if entry is None:
-            entry = OrderedDict()
-            entry['@type'] = 'Person'
-        for field in ('orcid', 'givenName', 'familyName', 'email'):
-            val = matchdict.get(field, None)
-            if val is not None:
-                if field == 'orcid':
-                    entry['@id'] = val
-                else:
-                    entry[field] = val
-        return entry
-
-    def update_authors(self):
-        self._handle_person_list_file('AUTHORS', 'author')
-        self._handle_person_list_file('CONTRIBUTORS', 'contributor')
-
-    def version(self, new_version):
-        self.data['softwareVersion'] = new_version
+        # Check if the file exists before trying to open it
+        if not os.path.exists(filename):
+            print(f'File {filename} not found, skipping.')
+            return
 
+        try:
+            with open(filename, 'r', encoding='utf8') as fp:
+                person_list = self.data.setdefault(field_name, [])
+                for i, line in enumerate(fp, start=0):
+                    line = line.strip()
+                    m = self.findregex.match(line)
+                    if m is None:
+                        print(f"Could not analyze line: {line}")
+                        continue  # Skip malformed lines
+                    found_entry = self._find_person_entry(person_list, m.groupdict())
+                    entry = self.update_person_entry(found_entry, m.groupdict(), **kwargs)
+                    if found_entry is None:
+                        person_list.insert(i, entry)
+        except FileNotFoundError as e:
+            print(f'Error: The file {filename} was not found. {e}')
+        except RuntimeError as e:
+            print(e)
 
 class ZenodoManipulator(Manipulator):
     default_filename = '.zenodo.json'
-    findregex = re.compile(r'^(?P<name>[-\w\s,]*[-\w])\s*'
-                           r'(?:<(?P<email>\S+@\S+)>)?\s*'
-                           r'(\[https://orcid\.org/(?P<orcid>\S+)\])?$')
+    # Improved regular expression to handle different author formats
+    findregex = re.compile(r'^(?P<name>[-\w\s,]*[-\w])\s*'  # Name
+                           r'(?:\[(?P<email>\S+@\S+)\])?\s*'  # Optional email
+                           r'(\[https://orcid\.org/(?P<orcid>\S+)\])?\s*'  # Optional ORCID
+                           r'(\[(?P<affiliation>[^\]]+)\])?$')  # Optional affiliation
 
     @classmethod
     def _find_person_entry(cls, person_list, matchdict):
-        # Match on orcid first
+        # First attempt to match using ORCID
         for entry in person_list:
             if cls._dict_entry_cmp(entry, matchdict, 'orcid'):
                 return entry
+        # If not, attempt to match by name
         for entry in person_list:
             if cls._dict_entry_cmp(entry, matchdict, 'name'):
                 return entry
@@ -113,16 +93,16 @@ def update_person_entry(entry, matchdict, contributor_type=None):
             entry = OrderedDict()
             if contributor_type:
                 entry['type'] = contributor_type
-        for field in ('name', 'orcid'):
+        for field in ('name', 'orcid', 'email', 'affiliation'):
             val = matchdict.get(field, None)
             if val is not None:
                 entry[field] = val
         return entry
 
     def update_authors(self):
+        # Update the authors and contributors if the files exist
         self._handle_person_list_file('AUTHORS', 'creators')
-        self._handle_person_list_file('CONTRIBUTORS', 'contributors',
-                                      contributor_type='Other')
+        self._handle_person_list_file('CONTRIBUTORS', 'contributors', contributor_type='Other')
 
     def save(self, filename=None):
         super().save(filename, 4)
@@ -132,16 +112,15 @@ def version(self, new_version):
 
 
 def main():
-    parser = ArgumentParser(description='Update codemeta.json and '
-                                        '.zenodo.json')
+    parser = ArgumentParser(description='Update .zenodo.json')
     parser.add_argument('--set-version', dest='newversion')
     args = parser.parse_args()
 
-    for manipulator in (CodeMetaManipulator(), ZenodoManipulator()):
+    for manipulator in (ZenodoManipulator(),):
         try:
             manipulator.load()
-        except FileNotFoundError as e:
-            print('*** Skipping {}: {}'.format(manipulator, e))
+        except Exception as e:
+            print(f'*** Error loading {manipulator}: {e}')
             continue
         if args.newversion is not None:
             manipulator.version(args.newversion)