dcicutils 8.8.6.1b11__tar.gz → 8.8.6.1b13__tar.gz

{dcicutils-8.8.6.1b11 → dcicutils-8.8.6.1b13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.6.1b11
+Version: 8.8.6.1b13
 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-8.8.6.1b11 → dcicutils-8.8.6.1b13}/dcicutils/command_utils.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import contextlib
 import functools
 import glob
@@ -7,7 +8,7 @@ import re
 import requests
 import subprocess
 
-from typing import Optional
+from typing import Callable, Optional
 from .exceptions import InvalidParameterError
 from .lang_utils import there_are
 from .misc_utils import INPUT, PRINT, environ_bool, print_error_message, decorator
@@ -384,3 +385,70 @@ def script_catch_errors():
                 message = str(e)  # Note: We ignore the type, which isn't intended to be shown.
                 PRINT(message)
             exit(1)
+
+
+class Question:
+    """
+    Supports asking the user (via stdin) a yes/no question, possibly repeatedly; and after
+    some maximum number times of the same answer in a row (consecutively), then asks them
+    if they want to automatically give that same answer to any/all subsequent questions.
+    Supports static/global list of such Question instances, hashed (only) by the question text.
+    """
+    _static_instances = {}
+
+    @staticmethod
+    def instance(question: Optional[str] = None,
+                 max: Optional[int] = None, printf: Optional[Callable] = None) -> Question:
+        question = question if isinstance(question, str) else ""
+        if not (instance := Question._static_instances.get(question)):
+            Question._static_instances[question] = (instance := Question(question, max=max, printf=printf))
+        return instance
+
+    @staticmethod
+    def yes(question: Optional[str] = None,
+            max: Optional[int] = None, printf: Optional[Callable] = None) -> bool:
+        return Question.instance(question, max=max, printf=printf).ask()
+
+    def __init__(self, question: Optional[str] = None,
+                 max: Optional[int] = None, printf: Optional[Callable] = None) -> None:
+        self._question = question if isinstance(question, str) else ""
+        self._max = max if isinstance(max, int) and max > 0 else None
+        self._print = printf if callable(printf) else print
+        self._yes_consecutive_count = 0
+        self._no_consecutive_count = 0
+        self._yes_automatic = False
+        self._no_automatic = False
+
+    def ask(self, question: Optional[str] = None) -> bool:
+
+        def question_automatic(value: str) -> bool:
+            nonlocal self
+            RARROW = "▶"
+            LARROW = "◀"
+            if yes_or_no(f"{RARROW}{RARROW}{RARROW}"
+                         f" Do you want to answer {value} to all such questions?"
+                         f" {LARROW}{LARROW}{LARROW}"):
+                return True
+            self._yes_consecutive_count = 0
+            self._no_consecutive_count = 0
+
+        if self._yes_automatic:
+            return True
+        elif self._no_automatic:
+            return False
+        elif yes_or_no((question if isinstance(question, str) else "") or self._question or "Undefined question"):
+            self._yes_consecutive_count += 1
+            self._no_consecutive_count = 0
+            if (self._no_consecutive_count == 0) and self._max and (self._yes_consecutive_count >= self._max):
+                # Have reached the maximum number of consecutive YES answers; ask if YES to all subsequent.
+                if question_automatic("YES"):
+                    self._yes_automatic = True
+            return True
+        else:
+            self._no_consecutive_count += 1
+            self._yes_consecutive_count = 0
+            if (self._yes_consecutive_count == 0) and self._max and (self._no_consecutive_count >= self._max):
+                # Have reached the maximum number of consecutive NO answers; ask if NO to all subsequent.
+                if question_automatic("NO"):
+                    self._no_automatic = True
+            return False

{dcicutils-8.8.6.1b11 → dcicutils-8.8.6.1b13}/dcicutils/structured_data.py

@@ -11,7 +11,6 @@ from webtest.app import TestApp
 from dcicutils.common import OrchestratedApp
 from dcicutils.data_readers import CsvReader, Excel, RowReader
 from dcicutils.datetime_utils import normalize_date_string, normalize_datetime_string
-from dcicutils.file_utils import search_for_file
 from dcicutils.misc_utils import (create_dict, create_readonly_object, is_uuid, load_json_if,
                                   merge_objects, remove_empty_properties, right_trim, split_string,
                                   to_boolean, to_enum, to_float, to_integer, VirtualApp)
@@ -209,14 +208,6 @@ class StructuredDataSet:
                             result.append({"type": type_name, "file": file_name})
         return result
 
-    def upload_files_located(self,
-                             location: Union[str, Optional[List[str]]] = None, recursive: bool = False) -> List[str]:
-        upload_files = copy.deepcopy(self.upload_files)
-        for upload_file in upload_files:
-            if file_path := search_for_file(upload_file["file"], location, recursive=recursive, single=True):
-                upload_file["path"] = file_path
-        return upload_files
-
     @property
     def nrows(self) -> int:
         return self._nrows
@@ -351,20 +342,22 @@ class StructuredDataSet:
 
     def _load_json_file(self, file: str) -> None:
         with open(file) as f:
-            item = json.load(f)
+            data = json.load(f)
+            import pdb ; pdb.set_trace()  # noqa
+            pass
             if ((schema_name_inferred_from_file_name := Schema.type_name(file)) and
                 (self._portal.get_schema(schema_name_inferred_from_file_name) is not None)):  # noqa
                 # If the JSON file name looks like a schema name then assume it
                 # contains an object or an array of object of that schema type.
                 if self._merge:
-                    item = self._merge_with_existing_portal_object(item, schema_name_inferred_from_file_name)
-                self._add(Schema.type_name(file), item)
-            elif isinstance(item, dict):
+                    data = self._merge_with_existing_portal_object(data, schema_name_inferred_from_file_name)
+                self._add(Schema.type_name(file), data)
+            elif isinstance(data, dict):
                 # Otherwise if the JSON file name does not look like a schema name then
                 # assume it a dictionary where each property is the name of a schema, and
                 # which (each property) contains a list of object of that schema type.
-                for schema_name in item:
-                    item = item[schema_name]
+                for schema_name in data:
+                    item = data[schema_name]
                     if self._merge:
                         item = self._merge_with_existing_portal_object(item, schema_name)
                     self._add(schema_name, item)

{dcicutils-8.8.6.1b11 → dcicutils-8.8.6.1b13}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.6.1b11"
+version = "8.8.6.1b13"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"