Add ER write capability to IO backend (#910)

Author: mavaylon1

CHANGELOG.md

@@ -1,6 +1,9 @@
 # HDMF Changelog
 
-## HDMF 3.7.1 (Upcoming)
+## HDMF 3.8.0 (Upcoming)
+
+### New features and minor improvements
+- Added the ability to write ExternalResources if the path is provided and the container has a linked instance of ExternalResources. @mavaylon1 [#910](https://github.com/hdmf-dev/hdmf/pull/910)
 
 ### Bug fixes
 - Fixed bug on `add_ref_term_set` in which attributes that were not subscribtable returned an error. @mavaylon1 [#909](https://github.com/hdmf-dev/hdmf/pull/909)

src/hdmf/backends/io.py

@@ -82,6 +82,14 @@ def write(self, **kwargs):
         f_builder = self.__manager.build(container, source=self.__source, root=True)
         self.write_builder(f_builder, **kwargs)
 
+        if self.external_resources_path is not None:
+            external_resources = container.get_linked_resources()
+            if external_resources is not None:
+                external_resources.to_norm_tsv(path=self.external_resources_path)
+            else:
+                msg = "Could not find linked ExternalResources. Container was still written to IO source."
+                warn(msg)
+
     @docval({'name': 'src_io', 'type': 'HDMFIO', 'doc': 'the HDMFIO object for reading the data to export'},
             {'name': 'container', 'type': Container,
              'doc': ('the Container object to export. If None, then the entire contents of the HDMFIO object will be '

tests/unit/test_io_hdf5_h5tools.py

@@ -1020,6 +1020,41 @@ def test_io_read_external_resources_value_warn(self):
 
         self.remove_er_files()
 
+    def test_io_write_er(self):
+        er = ExternalResources()
+        self.foofile.link_resources(er)
+
+        data = Data(name="species", data=['Homo sapiens', 'Mus musculus'])
+        er.add_ref(file=self.foofile,
+                   container=data,
+                   key='key1',
+                   entity_id='entity_id1',
+                   entity_uri='entity1')
+
+        with HDF5IO(self.path, manager=self.manager, mode='w', external_resources_path='./') as io:
+            io.write(self.foofile)
+
+        with HDF5IO(self.path, manager=self.manager, mode='r', external_resources_path='./') as io:
+            container = io.read()
+            self.assertIsInstance(io.external_resources, ExternalResources)
+            self.assertIsInstance(container.get_linked_resources(), ExternalResources)
+
+        self.remove_er_files()
+
+    def test_io_warn(self):
+        er = ExternalResources()
+
+        data = Data(name="species", data=['Homo sapiens', 'Mus musculus'])
+        er.add_ref(file=self.foofile,
+                   container=data,
+                   key='key1',
+                   entity_id='entity_id1',
+                   entity_uri='entity1')
+        with HDF5IO(self.path, manager=self.manager, mode='w', external_resources_path='./') as io:
+            with self.assertWarns(Warning):
+                io.write(self.foofile)
+
+
 class TestMultiWrite(TestCase):
 
     def setUp(self):