dcicutils 8.8.3__py3-none-any.whl → 8.8.3.1b2__py3-none-any.whl

dcicutils/captured_output.py

@@ -9,7 +9,7 @@ _real_stderr = sys.stderr
 
 
 @contextmanager
-def captured_output(capture: bool = True):
+def captured_output(capture: bool = True, encoding: Optional[str] = None):
     """
     Context manager to capture any/all output to stdout or stderr, and not actually output it to stdout
     or stderr. Yields and object with a get_captured_output() method to get the output captured thus far,
@@ -24,7 +24,7 @@ def captured_output(capture: bool = True):
 
     original_stdout = _real_stdout
     original_stderr = _real_stderr
-    captured_output = io.StringIO()
+    captured_output = io.StringIO() if not encoding else _EncodedStringIO(encoding)
 
     def set_original_output() -> None:
         sys.stdout = original_stdout
@@ -68,3 +68,19 @@ def uncaptured_output():
     finally:
         sys.stdout = original_stdout
         sys.stderr = original_stderr
+
+
+class _EncodedStringIO:
+    def __init__(self, encoding: str = "utf-8"):
+        self.encoding = encoding
+        self.buffer = io.BytesIO()
+    def write(self, s):  # noqa
+        self.buffer.write(s.encode(self.encoding))
+    def flush(self):  # noqa
+        self.buffer.flush()
+    def getvalue(self):  # noqa
+        return self.buffer.getvalue().decode(self.encoding)
+    def __str__(self):  # noqa
+        return self.getvalue()
+    def __repr__(self):  # noqa
+        return repr(self.getvalue())

dcicutils/progress_bar.py

@@ -5,7 +5,7 @@ import threading
 import time
 from tqdm import tqdm
 from types import FrameType as frame
-from typing import Callable, Optional, Union
+from typing import Callable, List, Optional, Union
 from contextlib import contextmanager
 from dcicutils.command_utils import yes_or_no
 
@@ -54,12 +54,11 @@ class ProgressBar:
                  interrupt_exit: bool = False,
                  interrupt_exit_message: Optional[Union[Callable, str]] = None,
                  interrupt_message: Optional[str] = None,
-                 printf: Optional[Callable] = None,
-                 tidy_output_hack: bool = True) -> None:
+                 tidy_output_hack: bool = True,
+                 capture_output_for_testing: bool = False) -> None:
         self._bar = None
         self._disabled = False
         self._done = False
-        self._printf = printf if callable(printf) else print
         self._tidy_output_hack = (tidy_output_hack is True)
         self._started = time.time()
         self._stop_requested = False
@@ -90,7 +89,7 @@ class ProgressBar:
             self._tidy_output_hack = self._define_tidy_output_hack()
         self._total = total if isinstance(total, int) and total >= 0 else 0
         self._description = self._format_description(description)
-        # self._initialize()
+        self._captured_output_for_testing = [] if capture_output_for_testing else None
 
     def _initialize(self) -> bool:
         # Do not actually create the tqdm object unless/until we have a positive total.
@@ -197,6 +196,10 @@ class ProgressBar:
     def duration(self) -> None:
         return time.time() - self._started
 
+    @property
+    def captured_output_for_testing(self) -> Optional[List[str]]:
+        return self._captured_output_for_testing
+
     def _format_description(self, value: str) -> str:
         if not isinstance(value, str):
             value = ""
@@ -209,7 +212,7 @@ class ProgressBar:
             nonlocal self
             def handle_secondary_interrupt(signum: int, frame: frame) -> None:  # noqa
                 nonlocal self
-                self._printf("\nEnter 'yes' or 'no' or CTRL-\\ to completely abort ...")
+                print("\nEnter 'yes' or 'no' or CTRL-\\ to completely abort ...")
             self.disable()
             self._interrupt(self) if self._interrupt else None
             set_interrupt_handler(handle_secondary_interrupt)
@@ -226,7 +229,7 @@ class ProgressBar:
                         restore_interrupt_handler()
                         if self._interrupt_exit_message:
                             if isinstance(interrupt_exit_message := self._interrupt_exit_message(self), str):
-                                self._printf(interrupt_exit_message)
+                                print(interrupt_exit_message)
                         exit(1)
                     elif interrupt_stop is False or ((interrupt_stop is None) and (self._interrupt_exit is False)):
                         set_interrupt_handler(handle_interrupt)
@@ -261,6 +264,12 @@ class ProgressBar:
             nonlocal self, sys_stdout_write, sentinel_internal, spina, spini, spinn
             def replace_first(value: str, match: str, replacement: str) -> str:  # noqa
                 return value[:i] + replacement + value[i + len(match):] if (i := value.find(match)) >= 0 else value
+            def remove_extra_trailing_spaces(text: str) -> str:  # noqa
+                while text.endswith("  "):
+                    text = text[:-1]
+                return text
+            if not text:
+                return
             if (self._disabled or self._done) and sentinel_internal in text:
                 # Another hack to really disable output on interrupt; in this case we set
                 # tqdm.disable to True, but output can still dribble out, so if the output
@@ -270,11 +279,14 @@ class ProgressBar:
                 spinc = spina[spini % spinn] if not ("100%|" in text) else "| ✓" ; spini += 1  # noqa
                 text = replace_first(text, sentinel_internal, f" {spinc}")
                 text = replace_first(text, "%|", "% ◀|")
+                text = remove_extra_trailing_spaces(text)
                 # Another oddity: for the rate sometimes tqdm intermittently prints
                 # something like "1.54s/" rather than "1.54/s"; something to do with
                 # the unit we gave, which is empty; idunno; just replace it here.
                 text = replace_first(text, "s/ ", "/s ")
             sys_stdout_write(text)
+            if self._captured_output_for_testing is not None:
+                self._captured_output_for_testing.append(text)
             sys.stdout.flush()
         def restore_stdout_write() -> None:  # noqa
             nonlocal sys_stdout_write

dcicutils/structured_data.py

@@ -653,7 +653,10 @@ class Schema(SchemaBase):
         def map_ref(value: str, link_to: str, portal: Optional[Portal], src: Optional[str]) -> Any:
             nonlocal self, typeinfo
             if self._norefs:
-                self._resolved_refs.add((f"/{link_to}/{value}", None))
+                if value:
+                    # Dump the src because this cannot add dictionary to a set; note that
+                    # this is ONLY used for smaht-submitr/submit-metadata-bundle --info --refs.
+                    self._resolved_refs.add((f"/{link_to}/{value}", json.dumps(src) if isinstance(src, dict) else None))
                 return value
             if not value:
                 if (column := typeinfo.get("column")) and column in self.data.get("required", []):

{dcicutils-8.8.3.dist-info → dcicutils-8.8.3.1b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.3
+Version: 8.8.3.1b2
 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.dist-info → dcicutils-8.8.3.1b2.dist-info}/RECORD

@@ -2,7 +2,7 @@ dcicutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dcicutils/base.py,sha256=gxNEv3DSVUfoX3NToWw7pcCdguxsJ75NDqsPi3wdFG4,5115
 dcicutils/beanstalk_utils.py,sha256=nHMWfFnZAXFiJh60oVouwbAPMKsQfHnDtkwz_PDE6S4,51434
 dcicutils/bundle_utils.py,sha256=ZVQcqlt7Yly8-YbL3A-5DW859_hMWpTL6dXtknEYZIw,34669
-dcicutils/captured_output.py,sha256=9UorUoA-RSGf7fUILHy73JiZ-mJ1IV-or_JGMyncaMs,2522
+dcicutils/captured_output.py,sha256=2pzkq7vtC47zwsSeXS6cJNxC_LXpUbw6ArudKlJHdb0,3108
 dcicutils/cloudformation_utils.py,sha256=MtWJrSTXyiImgbPHgRvfH9bWso20ZPLTFJAfhDQSVj4,13786
 dcicutils/codebuild_utils.py,sha256=CKpmhJ-Z8gYbkt1I2zyMlKtFdsg7T8lqrx3V5ieta-U,1155
 dcicutils/command_utils.py,sha256=JExll5TMqIcmuiGvuS8q4XDUvoEfi2oSH0E2FVF6suU,15285
@@ -48,7 +48,7 @@ dcicutils/obfuscation_utils.py,sha256=fo2jOmDRC6xWpYX49u80bVNisqRRoPskFNX3ymFAmj
 dcicutils/opensearch_utils.py,sha256=V2exmFYW8Xl2_pGFixF4I2Cc549Opwe4PhFi5twC0M8,1017
 dcicutils/portal_object_utils.py,sha256=gDXRgPsRvqCFwbC8WatsuflAxNiigOnqr0Hi93k3AgE,15422
 dcicutils/portal_utils.py,sha256=Xm0IqL2dA9C2gx98cPEbvlo81V76bEmpUpxb_8S3VqM,30480
-dcicutils/progress_bar.py,sha256=tGhqjONjDIjniqKUb8ATQuZmnJjG61XEu-EiY4uKMK4,13554
+dcicutils/progress_bar.py,sha256=sLX0_L1JRrtGSABOkNS-Y5prcWvZqsyxis_oTYbaLk0,14091
 dcicutils/project_utils.py,sha256=qPdCaFmWUVBJw4rw342iUytwdQC0P-XKpK4mhyIulMM,31250
 dcicutils/qa_checkers.py,sha256=cdXjeL0jCDFDLT8VR8Px78aS10hwNISOO5G_Zv2TZ6M,20534
 dcicutils/qa_utils.py,sha256=TT0SiJWiuxYvbsIyhK9VO4uV_suxhB6CpuC4qPacCzQ,160208
@@ -63,7 +63,7 @@ dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
 dcicutils/snapshot_utils.py,sha256=ymP7PXH6-yEiXAt75w0ldQFciGNqWBClNxC5gfX2FnY,22961
 dcicutils/ssl_certificate_utils.py,sha256=F0ifz_wnRRN9dfrfsz7aCp4UDLgHEY8LaK7PjnNvrAQ,9707
-dcicutils/structured_data.py,sha256=_Rqc_T6iO36lD3B1WqJeDSiNVFfkzpC1inkbH4B1XtA,58188
+dcicutils/structured_data.py,sha256=YCLGtjsCMXCm5ZM96aiTRQ9OPUuj0lK8O9vSkLx1gv8,58450
 dcicutils/submitr/progress_constants.py,sha256=5bxyX77ql8qEJearfHEvsvXl7D0GuUODW0T65mbRmnE,2895
 dcicutils/submitr/ref_lookup_strategy.py,sha256=Js2cVznTmgjciLWBPLCvMiwLIHXjDn3jww-gJPjYuFw,3467
 dcicutils/task_utils.py,sha256=MF8ujmTD6-O2AC2gRGPHyGdUrVKgtr8epT5XU8WtNjk,8082
@@ -72,8 +72,8 @@ dcicutils/trace_utils.py,sha256=g8kwV4ebEy5kXW6oOrEAUsurBcCROvwtZqz9fczsGRE,1769
 dcicutils/validation_utils.py,sha256=cMZIU2cY98FYtzK52z5WUYck7urH6JcqOuz9jkXpqzg,14797
 dcicutils/variant_utils.py,sha256=2H9azNx3xAj-MySg-uZ2SFqbWs4kZvf61JnK6b-h4Qw,4343
 dcicutils/zip_utils.py,sha256=rnjNv_k6L9jT2SjDSgVXp4BEJYLtz9XN6Cl2Fy-tqnM,2027
-dcicutils-8.8.3.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.8.3.dist-info/METADATA,sha256=aG6CCpyI525cQXOiUXz0PMEAGDdcHwtr7Wl9bekTNfc,3352
-dcicutils-8.8.3.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.8.3.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
-dcicutils-8.8.3.dist-info/RECORD,,
+dcicutils-8.8.3.1b2.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.8.3.1b2.dist-info/METADATA,sha256=nOF-Y3McrAK89qI09YdZEMAlJ_IsoquS9KBZAj_YXr4,3356
+dcicutils-8.8.3.1b2.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.8.3.1b2.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
+dcicutils-8.8.3.1b2.dist-info/RECORD,,