Merge pull request #86 from con/enh-orcid

Various little enhancements while dealing with interactive ORCID entry + add final empty line in pretty json dump

tributors/main/orcid.py

@@ -9,7 +9,7 @@
 """
 
 from tributors.utils.file import write_file, get_tmpfile
-from tributors.utils.prompt import choice_prompt
+from tributors.utils.prompt import choice_prompt, entry_prompt
 import logging
 import os
 import requests
@@ -193,16 +193,34 @@ def record_search(url, email, interactive=False, search_type=""):
 
     # If interactive, ask for choice prompt
     if interactive:
-        choices = [str(i) for i, _ in enumerate(results, 1)] + ["s", "S", "skip"]
-        prefix = "1:%s or s to skip" % min(10, len(results))
+        skip_choices = ["s", "S", "skip"]
+        enter_choices = ["e", "E", "enter"]
+        quit_choices = ["q"]
+        choices = (
+            [str(i) for i, _ in enumerate(results, 1)]
+            + skip_choices
+            + enter_choices
+            + quit_choices
+        )
+        prefix = "1:%s or s to skip, e to enter, q to quit the loop" % min(
+            10, len(results)
+        )
         choice = choice_prompt(
-            "Please enter a choice, or s to skip.",
+            "Please enter a choice, or s to skip, e to enter.",
             choices=choices,
             choice_prefix=prefix,
             multiple=False,
         )
+        if choice in quit_choices:
+            raise StopIteration("Requested by user")
+
+        if choice in enter_choices:
+            return entry_prompt(
+                f"Please enter the ORCID for {email}.",
+                regex="[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$",
+            )
 
-        if not choice or choice in ["s", "S", "skip"]:
+        if not choice or choice in skip_choices:
             return
 
         # Return the orcid identifier

tributors/main/parsers/base.py

@@ -142,23 +142,26 @@ def update_cache(self, update_lookup=True):
 
         # Then add an Orcid lookup
         for login, entry in self.cache.items():
-            # If we have an email, and orcid isn't defined
-            if "orcid" not in entry:
-                orcid = get_orcid(
-                    entry.get("email"), entry.get("name"), interactive=interactive
-                )
-                if orcid:
-                    entry["orcid"] = orcid
-                    cli = OrcidIdentifier(orcid)
-
-                    # If we found the record, update metadata
-                    if (
-                        cli.found
-                        and not entry.get("name")
-                        or entry.get("name") == login
-                    ):
-                        entry["name"] = "%s %s" % (cli.firstName, cli.lastName)
-                    if cli.affiliation and not entry.get("affiliation"):
-                        entry["affiliation"] = cli.affiliation
-
-            self.cache[login] = entry
+            try:
+                # If we have an email, and orcid isn't defined
+                if "orcid" not in entry:
+                    orcid = get_orcid(
+                        entry.get("email"), entry.get("name"), interactive=interactive
+                    )
+                    if orcid:
+                        entry["orcid"] = orcid
+                        cli = OrcidIdentifier(orcid)
+
+                        # If we found the record, update metadata
+                        if (
+                            cli.found
+                            and not entry.get("name")
+                            or entry.get("name") == login
+                        ):
+                            entry["name"] = "%s %s" % (cli.firstName, cli.lastName)
+                        if cli.affiliation and not entry.get("affiliation"):
+                            entry["affiliation"] = cli.affiliation
+
+                self.cache[login] = entry
+            except StopIteration:
+                break

tributors/utils/file.py

@@ -20,15 +20,13 @@ def write_json(json_obj, filename, pretty=True):
      - json_obj (dict) : the dict to print to json
      - filename (str)  : the output file to write to
     """
+    kw = dict(indent=4, separators=(",", ": ")) if pretty else {}
     with open(filename, "w", encoding="utf8") as filey:
-        if pretty:
-            filey.writelines(
-                json.dumps(
-                    json_obj, indent=4, ensure_ascii=False, separators=(",", ": ")
-                )
-            )
-        else:
-            filey.writelines(json.dumps(json_obj), ensure_ascii=False)
+        dump = json.dumps(json_obj, ensure_ascii=False, **kw)
+        if pretty and not dump.endswith(os.linesep):
+            # Add newline as it is typically desired
+            dump += os.linesep
+        filey.write(dump)
     return filename
 
 

tributors/utils/prompt.py

@@ -1,31 +1,15 @@
 """
 
 Copyright (C) 2020-2022 Vanessa Sochat.
+              2024      Yaroslav O. Halchenko
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
 with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 """
 
-
-enter_input = getattr(__builtins__, "raw_input", input)
-
-
-def request_input():
-    """Wait for the user to input some string, optionally with multiple lines."""
-    lines = []
-
-    # The message can be multiple lines
-    while True:
-        try:
-            line = enter_input()
-        except EOFError:
-            break
-        if line:
-            lines.append(line)
-
-    return "\n".join(lines)
+import re
 
 
 def choice_prompt(prompt, choices, choice_prefix=None, multiple=False):
@@ -41,15 +25,12 @@ def choice_prompt(prompt, choices, choice_prefix=None, multiple=False):
     choice = None
     print(prompt)
 
-    # Support for Python 2 (raw_input)
-    get_input = getattr(__builtins__, "raw_input", input)
-
     if not choice_prefix:
         choice_prefix = "/".join(choices)
     message = "[%s] : " % (choice_prefix)
 
     while choice not in choices:
-        choice = get_input(message).strip()
+        choice = input(message).strip()
 
         # If multiple allowed, add selection to choices if includes all valid
         if multiple is True:
@@ -58,3 +39,22 @@ def choice_prompt(prompt, choices, choice_prefix=None, multiple=False):
                 choices.append(choice)
         message = "Please enter a valid option in [%s]" % choice_prefix
     return choice
+
+
+def entry_prompt(prompt, regex=None):
+    """Ask the user for a prompt, and only return when a valid entry is provided.
+
+    Parameters
+    ==========
+    prompt: the prompt to ask the user
+    regex: a regular expression to match the entry
+    """
+    entry = None
+    print(prompt)
+    message = "Please enter a value. Empty to skip: "
+    while not entry:
+        entry = input(message).strip()
+        if entry and regex is not None and not re.match(regex, entry):
+            entry = None
+            message = r"Please enter a valid response. Should match regex {regex!r}"
+    return entry