tweaking orcid search (#48)

* not allowing orcid search without first and last name, and adding other-names to search
* moving reference to no longer used token
* adding basic tests for orcid
* removing parameters from search, worksbetter without
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
Signed-off-by: vsoch <vsochat@stanford.edu>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

.tributors

@@ -2,10 +2,9 @@
     "yarikoptic": {
         "name": "Yaroslav Halchenko",
         "blog": "www.onerussian.com",
-        "email": "debian@onerussian.com",
-        "bio": "Cheers!",
         "orcid": "0000-0003-3456-2493",
-        "affiliation": "Dartmouth College"
+        "affiliation": "Dartmouth College",
+        "bio": "Cheers!"
     },
     "vsoch": {
         "name": "Vanessasaurus",

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip.
 
 ## [0.0.x](https://github.com/con/tributors/tree/master) (0.0.x)
+ - searching orcid for other-names as final resort, requiring first/last (0.0.19)
  - searching for last, first and reverse for orcid lookup (0.0.18)
  - unicode characters allowed, and dont update users with orcids (0.0.17)
  - should allow for repository names with .git extension (0.0.15)

docs/_docs/getting-started.md

@@ -99,24 +99,12 @@ pip install tributors
 
 ### 2. Environment
 
-Especially if you need orcid ids in your metadata, for a first time go you
-should export an id and secret to interact with the Orcid API. It'a also recommended
-to export a GitHub token to increase your API limit:
+It's recommended to export a GitHub token to increase your API limit:
 
 ```bash
-export ORCID_ID=APP-XXXXXXX
-export ORCID_SECRET=12345678910111213141516171819202122
 export GITHUB_TOKEN=XXXXXXXXXXXXXXX
 ```
 
-Once you generate an orcid token, it will be written to a temporary file,
-and you can read the file and export the variable for later discovery (and you'll
-no longer need the ID and secret):
-
-```bash
-export ORCID_TOKEN=XXXXXXXXXXXXXXXXXXXXXXXX
-```
-
 ### 3. Update Lookups
 
 Before you update your contribution files, you probably want to update your .tributors
@@ -153,6 +141,36 @@ $ tributors update zenodo
 $ tributors update codemeta
 ```
 
+If the client finds more than one orcid identifier for a name, you'll be prompted
+to run in `--interactive` mode. Running in interactive mode will allow you
+to choose a number for each one:
+
+```bash
+$ tributors update zenodo --interactive
+INFO:    zenodo:Updating .zenodo.json
+INFO:    zenodo:Updating .tributors cache from .zenodo.json
+
+Meyer, Kyle
+======================================================
+[1]
+  Name: Meyer, Kyle
+  Orcid: 0000-0002-1933-2908
+  Institutions: University of California Davis, University of Michigan, University of Texas at Austin
+
+[2]
+  Name: Meyer, Kyle
+  Orcid: 0000-0001-8632-4425
+  Institutions: Kroger Co, Northeastern Ohio Medical University, University of Toledo, University of Toledo Medical Center
+
+[3]
+  Name: Meyer, Kyle
+  Orcid: 0000-0001-8846-7411
+  Institutions: University of Auckland, University of Oregon, University of Wisconsin Milwaukee
+
+Please enter a choice, or s to skip.
+[1:3 or s to skip] : 
+```
+
 ### 3. Init
 You can also create empty files if you don't have them yet:
 
@@ -411,30 +429,6 @@ export ZENODO_TOKEN=xxxxxx
 export GITHUB_TOKEN=xxxxxx
 ```
 
-If you want to link emails with Orcid id's, it is suggested to generate and export an `ORCID_TOKEN` to ensure that you can look up these identifiers based on email addresses. 
-However to disable this, simply export the token as "disabled"
-
-```bash
-export ORCID_TOKEN=disabled
-```
-
-In order to generate this token
-for the first time, you should export an `ORCID_ID` and `ORCID_SECRET` that you need to 
-generate in the [developer tools](https://orcid.org/developer-tools). The callback
-uri can be either one of the defaults that they provide (we don't use it).
-Once you have your id and secret, export them to the environment.
-
-```bash
-export ORCID_ID=xxxxxxxx
-export ORCID_SECRET=xxxxx
-```
-
-The `ORCID_TOKEN` and `ORCID_REFRESH_TOKEN` will be written to a temporary file,
-and you can export these in the future to be discovered by the tributors client.
-Subsequent requests use the token to interact with the [public search API](https://members.orcid.org/api/tutorial/search-orcid-registry). Note that we haven't
-yet implemented using the refresh token to request a new one, so if you
-hit this use case, please [open an issue](https://github.com/con/tributors/issues).
-
 ### 2. Generate
 
 Generate means that you don't have a particular metadata file for a service,

tests/test_orcid.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+"""
+
+Copyright (C) 2020 Vanessa Sochat.
+
+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/.
+
+"""
+
+import os
+import pytest
+
+
+def test_queries(tmp_path):
+    """test that changing order of First Last and Last, First returns same result
+    """
+    from tributors.main.orcid import get_orcid, record_search
+
+    orcid_id = "0000-0003-3456-2493"
+
+    # Test different orders of name
+    result = get_orcid(email=None, name="Yaroslav Halchenko")
+    assert result == orcid_id
+    result = get_orcid(email=None, name="Halchenko, Yaroslav")
+    assert result == orcid_id
+
+    # Test lookup by email
+    result = get_orcid(email="debian@onerussian.com")
+    assert result == orcid_id
+
+    # Test search for other name
+    result = get_orcid(email=None, name="Ярослав Олеговіч Гальченко")
+    assert result == orcid_id
+
+    # Test returning None
+    result = get_orcid(email=None, name="Zumbudda")
+    assert not result
+
+    # Test find by other-names (can't do because more than one result)
+    result = get_orcid(email=None, name="Horea Christian")
+    assert result == "0000-0001-7037-2449"

tributors/client/__init__.py

@@ -90,6 +90,13 @@ def get_parser():
     )
 
     for command in [update, init]:
+        command.add_argument(
+            "--interactive",
+            dest="interactive",
+            help="Allow interactive selection of orcid ids.",
+            default=False,
+            action="store_true",
+        )
         command.add_argument(
             "parsers",
             help="Metadata file parsers to update or initialize.",

tributors/client/init.py

@@ -22,6 +22,7 @@ def main(args, extra):
 
     # Parse extra arguments
     extra = parse_extra(extra)
+    extra["--interactive"] = args.interactive
 
     # Skip users, if a space separated list is defined
     skip_users = []

tributors/client/update.py

@@ -20,6 +20,7 @@ def main(args, extra):
 
     # Parse extra arguments
     extra = parse_extra(extra)
+    extra["--interactive"] = args.interactive
 
     # Start with user provided parsers
     parsers = args.parsers

tributors/main/__init__.py

@@ -10,7 +10,6 @@
 
 from tributors.main.parsers import get_named_parser
 from tributors.utils.file import write_json, read_json
-from .orcid import get_orcid_token
 from .github import GitHubRepository
 import logging
 import os
@@ -114,18 +113,17 @@ def update(
            from GitHub or a cache.
         """
         parsers = parsers or []
-        self.orcid_token = get_orcid_token()
 
         # Generate a shared repository object
         repo = GitHubRepository(repo, skip_users=skip_users)
+        bot.debug(f"Found repository {repo}")
 
         # Get resource lookup ids (emails, orcids, logins)
         resources = self.get_resource_lookups(from_resources, params)
 
         # Update each metadata file via its parser
         for parser in parsers:
             client = get_named_parser(name=parser, repo=repo, params=params)
-            client.orcid_token = self.orcid_token
             client.cache = self.cache
             client.update(thresh=thresh, from_resources=resources)
             self.cache.update(client.cache)