deploy: 7ccb7a5

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 550f7f9527fc2ff399da4e3fa545fe42
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/3d907fdca1dd51a08f24f311bec8d522/orcid_bibtex_to_html.py

@@ -0,0 +1,295 @@
+import codecs
+import json
+import logging
+import os
+import sys
+import traceback
+import uuid
+
+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)
+
+TARGET_FODLER = "generated"
+
+
+def log_traceback(ex, ex_traceback=None):
+    print("[i] exception happened, check log file")
+
+    if ex_traceback is None:
+        ex_traceback = ex.__traceback__
+
+    tb_lines = [
+        line.rstrip("\n")
+        for line in traceback.format_exception(ex.__class__, ex, ex_traceback)
+    ]
+
+    logging.exception(tb_lines)
+
+
+def generate_bat(
+    orcid_list, bat_name="buildall.{0}", separate=False, years=[], encoding="utf-8"
+):
+    """
+    (list, str, str) -> None
+
+    Generate BAT file with commands
+    """
+
+    cmd_comment = "REM"
+    cmd_file_name = bat_name.format("bat")
+    cmd_env = "set"
+    cmd_path = "%PATH%;"
+    path = "C:\\Soft\\JabRef\\;"
+    cmd_jabref = "JabRef-2.10.jar"
+
+    merge_files = 'copy /Y {0} "{1}".html\n'
+    merge_file_internal = '"{0}-{1}.html"+'
+
+    if os.name != "nt":
+        cmd_file_name = bat_name.format("sh")
+        cmd_comment = "#"
+        cmd_env = "export"
+        cmd_path = "$PATH;"
+        path = "~/JabRef/"
+        cmd_jabref = "java -jar JabRef-2.10.jar"
+        merge_files = 'cat {0} > "{1}".html\n'
+        merge_file_internal = '"{0}-{1}.html" '
+
+    cmd_header = "{0} SETTING PATH to JabRef\n".format(cmd_comment)
+    cmd_header += "{0} PATH={1}{2} \n\n".format(cmd_env, cmd_path, path)
+
+    # template = 'java -jar JabRef-2.10.jar -o "{0}".html,htmlvlba -n true "{0}".bib\n'
+    if not separate:
+        template = '{0} -o "{1}.html",htmlvlba -n true "{1}.bib"\n'
+    else:
+        template = '{0} -o "{1}-{2}.html",htmlvlba -n true "{1}-{2}.bib"\n'
+
+    cmd = ""
+    cmd_merge = ""
+
+    for key in orcid_list:
+
+        if not separate:
+            cmd += template.format(cmd_jabref, key)
+        else:
+            merge_tmp = ""
+
+            for x in years[key]:
+                cmd += template.format(cmd_jabref, key, x)
+                merge_tmp += merge_file_internal.format(key, x)
+
+            cmd_merge += merge_files.format(merge_tmp[:-1], key)
+
+    file_name = "{0}/{1}".format(TARGET_FODLER, cmd_file_name)
+    _file = codecs.open(file_name, "w", encoding)
+    _file.write(cmd_header)
+    _file.write(cmd)
+    _file.write("\n")
+
+    # to merge htmls
+    _file.write(cmd_merge)
+    _file.close()
+
+
+def save_bibtex(
+    bibtex, file_prefix="orcid-bibtex-output", separate=False, encoding="utf-8"
+):
+    """
+    (dict, str, str) -> None
+
+    Saves BibTeX to the files, if required separates them by year.
+    """
+
+    file_name = "{0}/{1}".format(TARGET_FODLER, file_prefix)
+
+    if not separate:
+        _file = codecs.open(file_name + ".bib", "w", encoding)
+
+    for key in bibtex:
+
+        if separate:
+            _file = codecs.open(file_name + "-" + str(key) + ".bib", "w", encoding)
+
+        _file.write("%%%%%%%% \n% {0} \n%%%%%%%%\n\n".format(key))
+
+        bibtex_group = ""
+        for value in bibtex[key]:
+            bibtex_group += value + "\n\n"
+        _file.write(bibtex_group)
+
+        if separate:
+            _file.close()
+
+    if not separate:
+        _file.close()
+
+    print("[i] file with bibtex was created, check it here: {0}".format(file_name))
+
+
+def form_bibtex(authors, title, year):
+    """Forms custom BibTeX entry"""
+
+    UMLAUT_TO_LATEX = {
+        "Ö": '\\"{O}',
+        "ö": '\\"{o}',
+        "Ä": '\\"{A}',
+        "ä": '\\"{a}',
+        "Ü": '\\"{U}',
+        "ü": '\\"{u}',
+        "ß": "{\\ss}",
+    }
+
+    template = "@InProceedings{0}{2} , \n\t Title = {0}{3}{1}, \n\t Author = {0}{4}{1}, \n\t Year = {0}{5}{1}\n{1}"
+    _authors = " and ".join(authors)
+    try:
+        _title = title
+        for x in UMLAUT_TO_LATEX:
+            _title = _title.replace(x, UMLAUT_TO_LATEX[x])
+    except Exception as ex:
+        _, _, ex_traceback = sys.exc_info()
+        log_traceback(ex, ex_traceback)
+        _title = title
+
+    return template.format("{", "}", str(uuid.uuid1())[:13], _title, _authors, year)
+
+
+def extract_bitex(obj, author):
+    """
+    (Class) -> dict()
+
+    Method takes as an input object with all publications from ORCID and forms dict with it.
+    """
+
+    bibtex = {}
+    nobibtex = list()
+
+    for value in obj.publications:
+        try:
+            if hasattr(value, "citation_type"):
+                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:
+                    nobibtex.append(
+                        form_bibtex([author], value.title, value.publicationyear)
+                    )
+                    print(
+                        "[i] this publications is having no BIBTEX, new BIBTEX was generated {0}".format(
+                            value.title
+                        )
+                    )
+            else:
+                nobibtex.append(
+                    form_bibtex([author], value.title, value.publicationyear)
+                )
+                print(
+                    "[i] this publications is having no BIBTEX, new BIBTEX was generated {0}".format(
+                        value.title
+                    )
+                )
+        except Exception as ex:
+            _, _, ex_traceback = sys.exc_info()
+            log_traceback(ex, ex_traceback)
+            year = 0
+            nobibtex.append(form_bibtex([author], value.title, year))
+
+    if nobibtex:
+        bibtex[99999] = nobibtex
+
+    return bibtex
+
+
+def load_list(fname: str):
+
+    if not os.path.exists(fname):
+        raise Exception("JSON file was not found: {fname}")
+
+    with open(fname, "r") as f:
+        json_data = json.load(f)
+
+    return json_data
+
+
+def main():
+    """
+    (list) -> None
+
+    Extrating bibtex from ORCID, saving it to the file
+    """
+    orcid_file_name_ = "orcid-list.json"
+    separate_by_year = False
+    try:
+        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()
+
+    if not os.path.exists(TARGET_FODLER):
+        os.makedirs(TARGET_FODLER)
+
+    years = {}
+    # extracting bibtex
+    for item in orcid_list:
+
+        name, orcidid = item["name"], item["orcid"]
+        years[name] = list()
+        print("[i] extracting bibtex for {0}".format(name))
+        orcid_obj = orcidpyclient.get(orcidid)
+
+        # extracting bibtex
+        try:
+            orcid_bibtex = extract_bitex(orcid_obj, author=name)
+
+            # years
+            tmp_list = list()
+            for key in orcid_bibtex:
+                tmp_list.append(int(key))
+
+            years[name] = sorted(tmp_list, reverse=True)
+
+            # saving bibtex into separated files
+            save_bibtex(
+                bibtex=orcid_bibtex, file_prefix=name, separate=separate_by_year
+            )
+            orcid_extracted.append(name)
+        except Exception as ex:
+            _, _, ex_traceback = sys.exc_info()
+            log_traceback(ex, ex_traceback)
+
+    print(years)
+    generate_bat(orcid_extracted, separate=separate_by_year, years=years)
+
+
+if __name__ == "__main__":
+
+    # setting system default encoding to the UTF-8
+    # reload(sys)
+    # sys.setdefaultencoding("UTF8")
+
+    # initiating main processing
+    main()