Merge branch 'master' into master

Author: guzman-raphael

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ### 0.13.4 -- TBA
 * Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995
+* Bugfix - Fix external store key name doesn't allow '-' (#1005) PR #1006
 
 ### 0.13.3 -- Feb 9, 2022
 * Bugfix - Fix error in listing ancestors, descendants with part tables.

datajoint/autopopulate.py

@@ -193,7 +193,7 @@ def handler(signum, frame):
             # spawn multiple processes
             self.connection.close()  # disconnect parent process from MySQL server
             del self.connection._conn.ctx  # SSLContext is not pickleable
-            with mp.Pool(processes, _initialize_populate, (self, populate_kwargs)) as pool:
+            with mp.Pool(processes, _initialize_populate, (self, jobs, populate_kwargs)) as pool:
                 if display_progress:
                     with tqdm(desc="Processes: ", total=nkeys) as pbar:
                         for error in pool.imap(_call_populate1, keys, chunksize=1):

datajoint/declare.py

@@ -23,10 +23,10 @@
     BOOL=r'bool(ean)?$',   # aliased to tinyint(1)
     TEMPORAL=r'(date|datetime|time|timestamp|year)(\s*\(.+\))?$',
     INTERNAL_BLOB=r'(tiny|small|medium|long|)blob$',
-    EXTERNAL_BLOB=r'blob@(?P<store>[a-z]\w*)$',
+    EXTERNAL_BLOB=r'blob@(?P<store>[a-z][\-\w]*)$',
     INTERNAL_ATTACH=r'attach$',
-    EXTERNAL_ATTACH=r'attach@(?P<store>[a-z]\w*)$',
-    FILEPATH=r'filepath@(?P<store>[a-z]\w*)$',
+    EXTERNAL_ATTACH=r'attach@(?P<store>[a-z][\-\w]*)$',
+    FILEPATH=r'filepath@(?P<store>[a-z][\-\w]*)$',
     UUID=r'uuid$',
     ADAPTED=r'<.+>$'
 ).items()}

docs-parts/intro/Releases_lang1.rst

@@ -1,6 +1,7 @@
 0.13.4 -- TBA
 ----------------------
 * Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995
+* Bugfix - Fix external store key name doesn't allow '-' (#1005) PR #1006
 
 0.13.3 -- Feb 9, 2022
 ----------------------

tests/schema_adapted.py

@@ -8,7 +8,7 @@
 from . import PREFIX, CONN_INFO, S3_CONN_INFO
 
 stores_config = {
-    'repo_s3': dict(
+    'repo-s3': dict(
         S3_CONN_INFO,
         protocol='s3',
         location='adapted/repo',
@@ -59,7 +59,7 @@ class LayoutToFilepath(dj.AttributeAdapter):
     An adapted data type that saves a graph layout into fixed filepath
     """
 
-    attribute_type = 'filepath@repo_s3'
+    attribute_type = 'filepath@repo-s3'
 
     @staticmethod
     def get(path):
@@ -68,7 +68,7 @@ def get(path):
 
     @staticmethod
     def put(layout):
-        path = Path(dj.config['stores']['repo_s3']['stage'], 'layout.json')
+        path = Path(dj.config['stores']['repo-s3']['stage'], 'layout.json')
         with open(str(path), "w") as f:
             json.dump(layout, f)
         return path

tests/schema_external.py

@@ -22,7 +22,7 @@
         protocol='file',
         location=tempfile.mkdtemp()),
 
-    'repo_s3': dict(
+    'repo-s3': dict(
         S3_CONN_INFO,
         protocol='s3',
         location='dj/repo',
@@ -130,7 +130,7 @@ class FilepathS3(dj.Manual):
     # table for file management 
     fnum : int 
     ---
-    img : filepath@repo_s3  # managed files 
+    img : filepath@repo-s3  # managed files 
     """
 
 dj.errors._switch_filepath_types(False)

tests/test_filepath.py

@@ -91,7 +91,7 @@ def test_filepath(store="repo"):
 
 def test_filepath_s3():
     """ test file management with s3 """
-    test_filepath(store="repo_s3")
+    test_filepath(store="repo-s3")
 
 
 def test_duplicate_upload(store="repo"):
@@ -107,7 +107,7 @@ def test_duplicate_upload(store="repo"):
 
 
 def test_duplicate_upload_s3():
-    test_duplicate_upload(store="repo_s3")
+    test_duplicate_upload(store="repo-s3")
 
 
 @raises(dj.DataJointError)
@@ -128,7 +128,7 @@ def test_duplicate_error(store="repo"):
 
 
 def test_duplicate_error_s3():
-    test_duplicate_error(store="repo_s3")
+    test_duplicate_error(store="repo-s3")
 
 
 def test_filepath_class(table=Filepath(), store="repo"):
@@ -176,12 +176,12 @@ def test_filepath_class_again():
 
 
 def test_filepath_class_s3():
-    test_filepath_class(FilepathS3(), "repo_s3")
+    test_filepath_class(FilepathS3(), "repo-s3")
 
 
 def test_filepath_class_s3_again():
     """test_filepath_class_s3 again to deal with existing remote files"""
-    test_filepath_class(FilepathS3(), "repo_s3")
+    test_filepath_class(FilepathS3(), "repo-s3")
 
 
 def test_filepath_cleanup(table=Filepath(), store="repo"):
@@ -218,7 +218,7 @@ def test_filepath_cleanup(table=Filepath(), store="repo"):
 
 def test_filepath_cleanup_s3():
     """test deletion of filepath entries from external table """
-    store = "repo_s3"
+    store = "repo-s3"
     test_filepath_cleanup(FilepathS3(), store)