EDIT: make examples consisten with the latest package update + improv…

…e code quality

.gitignore

@@ -5,6 +5,7 @@
 dist/*
 orcidpyclient.egg-info/*
 docs/_build/*
+generated/*
 
 # extensions
 *.pyc

README.md

@@ -8,7 +8,7 @@ A simple wrapper around the orcid.org API. Ready to run examples can be found in
 
 Install latest relased version
 ```
-pip install -i https://test.pypi.org/simple/ orcidpyclient
+pip install -i https://test.pypi.org/simple/ orcidpyclient --upgrade
 ```
 
 Install latest version from source code

docs/core.md

@@ -36,6 +36,15 @@ for key_word in orcid_res.keywords:
     print (key_word)
 ```
 
+#### Iterate over publications
+
+```python
+import orcidpyclient
+orcid_res = orcidpyclient.get('0000-0002-4510-0385')
+for value in obj.publications:
+    print(value)
+```
+
 #### Trying different author with a different ORCID
 
 ```python

docs/examples.md

@@ -12,10 +12,13 @@
 * Additional information
 	+ iterates through the list or ID's, extracts ORCID, creates bat file to compile bibtex into HTMLs with help of JabRef
 		- List should be in the python dict format, here is the example (I created file 'orcid-list.json')
-		```
+		```json
 		[
-		 { 'John Wilbanks' : '0000-0002-4510-0385'},
-        ]
+			{
+				"name": "John Wilbanks",
+				"orcid": "0000-0002-4510-0385"
+			}
+		]
 		```
     + **NOTE**: To make in run on Mac OS, it's better if you will copy JabRef into the 'generated' folder directly
 

docs/examples/extracting_bibtex.py

@@ -2,30 +2,28 @@
 import logging
 import os
 
-import orcidpyclient as orcid
+try:
+    import orcidpyclient
+except:
 
-logging.getLogger(__name__).setLevel(logging.INFO)
-
-# retrieve a profile from his ORCID
-me = orcid.get("0000-0001-5661-4587")
-
-TARGET_FODLER = "generated"
+    import os
+    import sys
+    from pathlib import Path
 
+    current_path = Path(os.path.abspath(os.path.dirname(__file__)))
+    _path_to_add = os.path.join(str(current_path.parent.parent))
+    print(f"[i] Try following path to load package: {_path_to_add})")
+    sys.path.append(_path_to_add)
 
-def print_keyword(obj):
-    """Printing author keywords"""
+    import orcidpyclient
 
-    print("[i] printing author keywords")
-    for key_word in obj.keywords:
-        print(key_word)
+    print(f"[i] Use dev version of package with version")
 
 
-def print_publications(obj):
-    """Printing author publications"""
+logging.getLogger(__name__).setLevel(logging.INFO)
 
-    print("[i] printing author publications")
-    for value in obj.publications:
-        print(value)
+TARGET_FODLER = "generated"
+ORCID_ID = "0000-0001-5661-4587"
 
 
 def save_bibtex(bibtex, file_name="orcid-bibtex-output.bib", encoding="utf-8"):
@@ -88,19 +86,19 @@ def extract_bibtex(obj):
 
     bibtex = {}
     for value in obj.publications:
-        if value.citation_type == "BIBTEX":
+        if value.citation_type.lower() == "bibtex":
             if value.publicationyear not in bibtex:
                 bibtex[value.publicationyear] = list()
                 bibtex[value.publicationyear].append(value.citation_value)
             else:
                 bibtex[value.publicationyear].append(value.citation_value)
         else:
-            print("[i] this publications is having no BIBTEX {0}".format(value))
+            print("[i] this publications is having NO BibTeX {0}".format(value))
 
     return bibtex
 
 
-def orcid_bibtex(obj):
+def extract_bibtex_orcid(orcid_profile):
     """
     (Class) -> None
 
@@ -111,7 +109,7 @@ def orcid_bibtex(obj):
         os.makedirs(TARGET_FODLER)
 
     # extracting bibtex
-    orcid_bibtex = extract_bibtex(me)
+    orcid_bibtex = extract_bibtex(orcid_profile)
 
     # saving bibtex to file
     save_bibtex(orcid_bibtex)
@@ -120,6 +118,7 @@ def orcid_bibtex(obj):
     save_nocite(orcid_bibtex)
 
 
-# print_keyword(me)
-# print_publications(me)
-orcid_bibtex(me)
+if __name__ == "__main__":
+    # retrieve a profile from his ORCID
+    orcid_profile = orcidpyclient.get(ORCID_ID, debug=False)
+    extract_bibtex_orcid(orcid_profile)

docs/examples/orcid_bibtex_to_html.py

@@ -6,7 +6,23 @@
 import traceback
 import uuid
 
-import orcidpyclient as orcid
+try:
+    import orcidpyclient
+except:
+
+    import os
+    import sys
+    from pathlib import Path
+
+    current_path = Path(os.path.abspath(os.path.dirname(__file__)))
+    _path_to_add = os.path.join(str(current_path.parent.parent))
+
+    print(f"[i] Try following path to load package: {_path_to_add})")
+    sys.path.append(_path_to_add)
+
+    import orcidpyclient
+
+    print(f"[i] Use dev version of package with version")
 
 logging.getLogger(__name__).setLevel(logging.INFO)
 
@@ -160,7 +176,7 @@ def extract_bitex(obj, author):
     for value in obj.publications:
         try:
             if hasattr(value, "citation_type"):
-                if value.citation_type == "BIBTEX":
+                if value.citation_type.lower() == "bibtex":
                     if value.publicationyear not in bibtex:
                         bibtex[value.publicationyear] = list()
                         bibtex[value.publicationyear].append(value.citation_value)
@@ -184,7 +200,8 @@ def extract_bitex(obj, author):
     return bibtex
 
 
-def load_list(fname: str = "orcid-list.json"):
+def load_list(fname: str):
+
     if not os.path.exists(fname):
         raise Exception("JSON file was not found: {fname}")
 
@@ -200,12 +217,15 @@ def main():
 
     Extrating bibtex from ORCID, saving it to the file
     """
-
+    orcid_file_name_ = "orcid-list.json"
     separate_by_year = False
     try:
-        orcid_list = load_list()
-    except:
-        print("No py file with ORCIDS to work with was found")
+        orcid_list = load_list(fname=orcid_file_name_)
+        print(orcid_list)
+    except Exception as ex:
+        print(f"[e] JSON file with ORCIDs was NOT found: {orcid_file_name_}")
+        _, _, ex_traceback = sys.exc_info()
+        log_traceback(ex, ex_traceback)
         exit(0)
 
     orcid_extracted = list()
@@ -215,13 +235,12 @@ def main():
 
     years = {}
     # extracting bibtex
-    for key in orcid_list:
+    for item in orcid_list:
 
-        name = key
+        name, orcidid = item["name"], item["orcid"]
         years[name] = list()
-        orcidid = orcid_list[key]
         print("[i] extracting bibtex for {0}".format(name))
-        orcid_obj = orcid.get(orcidid)
+        orcid_obj = orcidpyclient.get(orcidid)
 
         # extracting bibtex
         try:
@@ -230,7 +249,8 @@ def main():
             # years
             tmp_list = list()
             for key in orcid_bibtex:
-                tmp_list.append(key)
+                tmp_list.append(int(key))
+
             years[name] = sorted(tmp_list, reverse=True)
 
             # saving bibtex into separated files

docs/examples/search_authors.py

@@ -0,0 +1,7 @@
+# importing module located in parent folder
+import sys
+
+sys.path.insert(0, "../")
+
+import sys
+import pyorcid

orcidpyclient/__init__.py

@@ -1,3 +1,3 @@
-__all__ = ('get', 'search', 'orcid_api_version')
+__all__ = ("get", "search", "orcid_api_version")
 
-from .rest import get, search, orcid_api_version
+from .functions import get, orcid_api_version, search

orcidpyclient/constants.py

@@ -1,4 +1,5 @@
-ORCID_API_VERSION = '3.0'
-ORCID_PUBLIC_BASE_URL = f'https://pub.orcid.org/v{ORCID_API_VERSION}/'
-ORCID_SANDBOX_BASE_URL = 'https://pub.orcid.org/'
+ORCID_API_VERSION = "3.0"
+ORCID_PUBLIC_BASE_URL = f"https://pub.orcid.org/v{ORCID_API_VERSION}/"
+ORCID_SANDBOX_BASE_URL = "https://pub.orcid.org/"
 
+BASE_HEADERS = {"Accept": "application/orcid+json", "Content-Type": "application/json;charset=UTF-8"}

orcidpyclient/exceptions.py

@@ -1,5 +1,6 @@
 class ORCIDException(Exception):
     pass
 
+
 class NotFoundException(ORCIDException):
     pass

orcidpyclient/functions.py

@@ -0,0 +1,76 @@
+import json
+import logging
+import sys
+
+import requests
+
+from .constants import BASE_HEADERS, ORCID_API_VERSION, ORCID_PUBLIC_BASE_URL
+from .logger_config import logger, stdout_sh
+from .rest import Author
+
+
+def _set_logger_debug(debug: bool = False):
+    """_summary_
+
+    Args:
+        debug (bool, optional): _description_. Defaults to False.
+    """
+
+    if debug:
+        logger.setLevel(logging.DEBUG)
+        stdout_sh.setLevel(logging.DEBUG)
+
+
+def get(orcid_id: str, debug: bool = False):
+    """Get an author based on an ORCID identifier."""
+
+    _set_logger_debug(debug)
+
+    if sys.version_info[0] < 3:
+        raise Exception("Python 2 is not supported")
+
+    _url = f"{ORCID_PUBLIC_BASE_URL}{orcid_id}"
+    _res = requests.get(_url, headers=BASE_HEADERS)
+
+    json_body = _res.json()
+
+    logger.debug("RESPONSE (BASE): {0}".format(json.dumps(json_body, sort_keys=True, indent=4, separators=(",", ": "))))
+
+    return Author(json_body)
+
+
+def search(query, debug: bool = False):
+    """Search the ORCID by sending a query to API
+
+       API documentation:
+        https://info.orcid.org/documentation/api-tutorials/api-tutorial-searching-the-orcid-registry/
+
+        api_example_query = {'q':'family-name:Malavolti+AND+given-names:Marco'}
+
+    Args:
+        query (_type_): query string
+        debug (bool, optional): option for the logging. Defaults to False.
+
+    Returns:
+        _type_: iterator of the results
+    """
+
+    _set_logger_debug(debug)
+
+    if sys.version_info[0] < 3:
+        raise Exception("Python 2 is not supported")
+
+    _url = f"{ORCID_PUBLIC_BASE_URL}search?q={query}"
+    resp = requests.get(_url, headers=BASE_HEADERS)
+    logger.debug(resp.url)
+    json_body = resp.json()
+    logger.debug(json_body)
+    if json_body.get("result") is not None:
+        return (get(res.get("orcid-identifier", {}).get("path")) for res in json_body.get("result", {}))
+    else:
+        return iter(list())
+
+
+def orcid_api_version():
+    """Provides version of ORCID API that is used"""
+    return ORCID_API_VERSION

orcidpyclient/logger_config.py

@@ -0,0 +1,13 @@
+import logging
+import sys
+
+_logger_depth = "INFO"
+
+logger = logging.getLogger("#orcid#")
+logger.setLevel(getattr(logging, _logger_depth))
+
+stdout_sh = logging.StreamHandler(sys.stdout)
+stdout_sh.setLevel(getattr(logging, _logger_depth))
+stdout_sh.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
+
+logger.addHandler(stdout_sh)