dcicutils 8.8.3.1b15__tar.gz → 8.8.3.1b17__tar.gz

{dcicutils-8.8.3.1b15 → dcicutils-8.8.3.1b17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.3.1b15
+Version: 8.8.3.1b17
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.8.3.1b15 → dcicutils-8.8.3.1b17}/dcicutils/captured_output.py

@@ -24,6 +24,8 @@ def captured_output(capture: bool = True, encoding: Optional[str] = None):
 
     original_stdout = _real_stdout
     original_stderr = _real_stderr
+    # FYI: This encoding business with _EncodedStringIO was introduced (circa April 2024)
+    # when ran into issues unit testing progress_bar which outputs those funny block characters.
     captured_output = io.StringIO() if not encoding else _EncodedStringIO(encoding)
 
     def set_original_output() -> None:

{dcicutils-8.8.3.1b15 → dcicutils-8.8.3.1b17}/dcicutils/progress_bar.py

@@ -335,7 +335,15 @@ class ProgressBar:
             nonlocal sys_stdout_write
             if sys_stdout_write is not None:
                 sys.stdout.write = sys_stdout_write
+        def ascii_spinners() -> list:  # noqa
+            # Fun with ASCII spinners.
+            return list("⠋⠙⠹⠸⠼⠴⠦⠧⠇⠏")  # borrowed from rich python package
+            # return list("⣾⣽⣻⢿⡿⣟⣯⣷")  # borrowed from rich python package
+            # return list("⠿⠻⠽⠾⠷⠯⠟")
+            # return list("⠏⠛⠹⠼⠶⠧")
+            # return list("⠻⠽⠾⠷⠯⠟")
+            # return list("|/—◦\\")
         sys.stdout.write = tidy_stdout_write
-        spina = ["|", "/", "—", "◦", "\\"] ; spini = 0 ; spinn = len(spina)  # noqa
+        spina = ascii_spinners() ; spini = 0 ; spinn = len(spina)  # noqa
         sentinel = "[progress]" ; sentinel_internal = f"{sentinel}:"  # noqa
         return namedtuple("tidy_output_hack", ["restore", "sentinel"])(restore_stdout_write, sentinel)

{dcicutils-8.8.3.1b15 → dcicutils-8.8.3.1b17}/dcicutils/structured_data.py

@@ -174,6 +174,18 @@ class StructuredDataSet:
         result = []
         if self._norefs:
             for ref in self._resolved_refs:
+                # The structure of this self._resolved_refs is setup in Schema._map_function_ref,
+                # which is called whenever a reference (linkTo) is encountered. It is a set of
+                # tuples containing three items: [0] the ref path, [1] its uuid (if applicable),
+                # and [2] its src. The src identifies the place where this ref occurred and is a
+                # dictionary containing file, type, column, and row properties. For this case, of
+                # norefs (i.e. unchecked refs), the uuid ([1]) is None because we are skipping
+                # ref resolution. But the src is actually a *string* dump of the dictionary, only
+                # because dictionaries cannot be put in a set (which is what _resolved_refs is);
+                # this dump is also done in Schema._map_function_ref (should probably change this
+                # to be a list to avoid this - TODO); we only even store this src info for this
+                # norefs case, as not really needed otherwise. This is just to support the
+                # useful-for-troublehsooting options --info --refs for smaht-submitr.
                 if len(ref) >= 3 and (ref_path := ref[0]) and (ref_src := load_json(ref[2])):
                     if existing_ref := [item for item in result if item.get("path") == ref_path]:
                         existing_ref[0]["srcs"].append(ref_src)
@@ -681,9 +693,11 @@ class Schema(SchemaBase):
                 # Here the caller has specified the (StructuredDataSet) norefs option
                 # which means we do not check for the existence of references at all.
                 if value:
-                    # Dump the src as a JSON string because a dictionary cannot be added to a set; note
-                    # that this is ONLY used for smaht-submitr/submit-metadata-bundle --info --refs.
-                    # This info can be gotten at using StructureDataSet.unchecked_refs.
+                    # Dump the src as a JSON string because a dictionary cannot be added to a set;
+                    # this is ONLY used for smaht-submitr/submit-metadata-bundle --info --refs.
+                    # This info exposed via StructureDataSet.unchecked_refs. TODO: Should probably
+                    # make this not a set type so we dont' have to do this dump (and corresponding
+                    # load, in StructureDataSet.unchecked_refs).
                     self._resolved_refs.add((f"/{link_to}/{value}", None,
                                              json.dumps(src) if isinstance(src, dict) else None))
                 return value

{dcicutils-8.8.3.1b15 → dcicutils-8.8.3.1b17}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.3.1b15"  # TODO: To become 8.8.4
+version = "8.8.3.1b17"  # TODO: To become 8.8.4
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"