List external files/databases in report

ihm/location.py

@@ -79,6 +79,10 @@ def __init__(self, db_code, version=None, details=None):
         self.access_code = db_code
         self.version = version
 
+    def __str__(self):
+        return "<%s.%s(%s)>" % (self.__module__, self.__class__.__name__,
+                                repr(self.access_code))
+
 
 class EMDBLocation(DatabaseLocation):
     """Something stored in the EMDB database.
@@ -207,6 +211,10 @@ def __init__(self, path, repo=None, details=None):
             # Store absolute path in case the working directory changes later
             self.path = os.path.abspath(path)
 
+    def __str__(self):
+        return "<%s.%s(%s)>" % (self.__module__, self.__class__.__name__,
+                                repr(self.path))
+
 
 class InputFileLocation(FileLocation):
     """An externally stored file used as input.
@@ -294,6 +302,9 @@ def __eq__(self, other):
     def __hash__(self):
         return hash((self.doi, self.url))
 
+    def __str__(self):
+        return "<ihm.location.Repository(%r)>" % self.doi
+
     def __init__(self, doi, root=None, url=None, top_directory=None,
                  details=None):
         # todo: DOI should be optional (could also use URL, local path)

ihm/report.py

@@ -11,6 +11,10 @@ class MissingDataWarning(UserWarning):
     pass
 
 
+class LocalFilesWarning(UserWarning):
+    pass
+
+
 class _SectionReporter(object):
     def __init__(self, title, fh):
         self.fh = fh
@@ -29,6 +33,8 @@ def report(self):
         print("Title: %s" % self.system.title, file=self.fh)
         self.report_entities()
         self.report_asyms()
+        self.report_databases()
+        self.report_files()
         self.report_citations()
         self.report_software()
 
@@ -69,3 +75,26 @@ def report_software(self):
             if not s.citation:
                 warnings.warn(
                     "No citation provided for %s" % s, MissingDataWarning)
+
+    def report_databases(self):
+        r = self._section("External databases referenced")
+        for loc in ihm._remove_identical(self.system._all_locations()):
+            if isinstance(loc, ihm.location.DatabaseLocation):
+                r.report(" - %s accession %s"
+                         % (loc.db_name, loc.access_code))
+
+    def report_files(self):
+        r = self._section("Additional files referenced")
+        locs_by_repo = collections.defaultdict(list)
+        for loc in ihm._remove_identical(self.system._all_locations()):
+            if not isinstance(loc, ihm.location.DatabaseLocation):
+                locs_by_repo[loc.repo].append(loc)
+        for repo, locs in locs_by_repo.items():
+            r.report("- %s" % ("DOI: " + repo.doi if repo else "Local files"))
+            for loc in locs:
+                r.report("  - %r, %s" % (loc.path, loc.details))
+        if None in locs_by_repo:
+            warnings.warn(
+                "The following local files are referenced (they will need to "
+                "be deposited in a database or with a DOI): %s"
+                % [loc.path for loc in locs_by_repo[None]], LocalFilesWarning)

test/test_report.py

@@ -12,6 +12,7 @@
 import ihm
 import ihm.report
 import ihm.reference
+import ihm.location
 
 
 class Tests(unittest.TestCase):
@@ -73,6 +74,41 @@ def test_software(self):
         soft.citation = c
         r.report_software()
 
+    def test_databases(self):
+        """Test report_databases"""
+        sio = StringIO()
+        s = ihm.System(title='test system')
+        s.locations.append(
+            ihm.location.BMRBLocation('27600', version='foo', details='bar'))
+        s.locations.append(
+            ihm.location.FileLocation(repo='mydoi', path='a'))
+        r = ihm.report.Reporter(s, sio)
+        r.report_databases()
+
+    def test_files(self):
+        """Test report_files"""
+        sio = StringIO()
+        s = ihm.System(title='test system')
+        repo = ihm.location.Repository(doi='1.2.3.4')
+        s.locations.append(
+            ihm.location.BMRBLocation('27600', version='foo', details='bar'))
+        s.locations.append(
+            ihm.location.FileLocation(repo=repo, path='a'))
+        r = ihm.report.Reporter(s, sio)
+        r.report_files()
+
+    def test_files_local(self):
+        """Test report_files with local files"""
+        sio = StringIO()
+        s = ihm.System(title='test system')
+        s.locations.append(
+            ihm.location.BMRBLocation('27600', version='foo', details='bar'))
+        s.locations.append(
+            ihm.location.FileLocation(repo=None, path='.'))
+        r = ihm.report.Reporter(s, sio)
+        # Should warn about local files
+        self.assertWarns(ihm.report.LocalFilesWarning, r.report_files)
+
 
 if __name__ == '__main__':
     unittest.main()