added newest version of the input files

example_input.py

 #!/usr/bin/env python3
 
-from input.interface import InputInterface
-import input.publication
+from input.interface import InputInterface as Input
 
 def main(url: str):
-    #print(get_publication(url))
-    print(InputInterface.get_publication(url))
-    #pub.print_pub()
+    print(Input.get_publication(url))
 
 if __name__ == "__main__":
 	#main("https://doi.org/10.1021/acs.jcim.1c00203")
-	#main("https://doi.org/10.1021/acs.jcim.1c00917")
-	main("https://doi.org/10.1021/acs.jcim.5b00332")
+    main("https://pubs.acs.org/doi/10.1021/acs.jcim.5b00332")

input/README.md

@@ -5,12 +5,12 @@ Input-Package to fetch publication information with a given url.
 ## Usage/Examples
 
 ```python
-from input.interface import get_publication
+from input.interface import InputInterface as Input
 from input.publication import Publication
 
 def main(url):
     try:
-        pub = get_publication(url)
+        pub = Input.get_publication(url)
     except Exception as error:
         raise error
 
@@ -21,6 +21,14 @@ def main(url):
 if __name__=="__main__":
     main("https://doi.org/10.1021/acs.chemrev.8b00728")
 ```
+
+## Testing
+
+``` c
+python -m unittest input/test/<file.py> -v
+# for all tests in directory
+python -m unittest discover input/test -v
+```
 ## Authors
 - Florian Jochens
 - Sam Ockenden

input/get/acs.py

@@ -21,13 +21,16 @@ class Fetcher(JournalFetcher):
     SUPPORTED_JOURNALS = ['1021']
 
     @staticmethod
-    def can_use_url(url: str) -> bool:
+    def can_use_url(url: str) -> str:
         """
         Uses Regex to extract journal specific substrings in Doi.
         TODO: Support non Doi-urls
         """
-        matched_url = re.match(r'(https?://)?(doi.org/)?(10.(\d{4})/\w+.\S+)', url)
+        matched_url = re.match(r'^(https?://)?(doi.org/|pubs.acs.org/doi/)?(10.(\d{4})/\w+.\S+)', url.strip(". \t\r\n"))
+        if matched_url is not None:
             return matched_url[4] in Fetcher.SUPPORTED_JOURNALS
+        else:
+            return False
 
     @staticmethod
     def get_publication(url: str) -> Publication:
@@ -65,16 +68,19 @@ class Fetcher(JournalFetcher):
         references_soup = ref_cit_soup.select('ol#references')
         if references_soup != []:
             for reference in references_soup[0].select('li'):
-                ref_doi = "https://doi.org/{}".format(reference.select('.refDoi')[0].text.strip()[5:])\
-                        if reference.select('.refDoi') != [] else "None"
+                if reference.select('.refDoi') != []:
+                    ref_doi = "https://doi.org/{}".format(reference.select('.refDoi')[0].text.strip()[5:])
+                else: 
+        #           No Doi -> No Paper
+                    continue
                 ref_title = reference.select('.NLM_article-title')[0].text\
-                        if reference.select('.NLM_article-title') != [] else "None"
+                        if reference.select('.NLM_article-title') != [] else None
                 ref_journal = reference.select('i')[0].text\
-                        if reference.select('i') != [] else "None"
+                        if reference.select('i') != [] else None
                 
                 ref_contributors=[]
                 for author in reference.select('.NLM_contrib-group'):
-                    ref_contributors.append(author.text)
+                    ref_contributors.append(author.text.replace("\n", " ").replace("\r", ""))
 
                 references.append(Citation(ref_doi, ref_title, ref_journal, ref_contributors, cit_type="Reference"))
 
@@ -82,14 +88,18 @@ class Fetcher(JournalFetcher):
         citation_soup = ref_cit_soup.select('.cited-content_cbyCitation')
         if citation_soup != []:
             for citation in citation_soup[0].select('li'):
-                cit_doi = citation.select('a[title="DOI URL"]')[0].text\
-                        if citation.select('a[title="DOI URL"]') != [] else "None"
+                if citation.select('a[title="DOI URL"]') != []: 
+                    cit_doi = citation.select('a[title="DOI URL"]')[0].text
+                else:
+        #           No Doi -> No Paper
+                    continue
                 cit_title = citation.select('.cited-content_cbyCitation_article-title')[0].text\
                         if citation.select('.cited-content_cbyCitation_article-title')!= [] else "None"
                 cit_journal = citation.select('.cited-content_cbyCitation_journal-name')[0].text\
                         if citation.select('.cited-content_cbyCitation_journal-name') != [] else "None"
                 cit_contributors =[]
-                cit_contributors = citation.select('.cited-content_cbyCitation_article-contributors')[0].text.split(', ')
+                cit_contributors = citation.select('.cited-content_cbyCitation_article-contributors')[0]\
+                    .text.replace("\n", " ").replace("\r", "").split(', ')
         #           clean up of the last Entry
                 cit_contributors_last = cit_contributors.pop().strip(". ")
                 if cit_contributors_last != '':
@@ -98,8 +108,3 @@ class Fetcher(JournalFetcher):
 
         return Publication(doi_url, title, contributors, journal, published
                             , subjects, num_citations, references, citations)
-
-
-    @staticmethod
-    def test_fetcher():
-        pass

input/get/acs_fj.py

-#!/usr/bin/env python3
-
-"""
-Child class of JournalFetcher
-JCIM
-"""
-
-# import re
-from input.get.journal_fetcher import JournalFetcher
-from input.publication import Publication, Citation, Reference
-import requests as req
-from bs4 import BeautifulSoup as bs
-
-class Fetcher(JournalFetcher):
-
-    """
-    """
-
-    # TODO: Naming-Convention:
-    #   Class: 'Fetcher'
-    #   file: input_get_[journal-/organisation-name]
-    #       format = "input_get_[a-z]*.py" allowed
-    #   TODO: List of Compatable Journals
-    _SUPPORTED_JOURNALS = []
-
-    @staticmethod
-    def can_use_url(url: str) -> bool:
-        """
-        Checks if given url links to a supported journal.
-        """
-
-        # TODO: Check the URL for compatability
-        #   re.match in _SUPPORTED_JOURNALS
-        return True 
-
-    @staticmethod
-    def get_publication(url: str) -> Publication:
-        return input(url)
-        
-
-    @staticmethod
-    def test_fetcher():
-        pass
-
-def get_article_info(soup):
-    header = soup.find('div', class_ = 'article_header-left pull-left')
-    article_title = header.find('span', class_ = 'hlFld-Title').text
-    publication_date = header.find('span', class_ = 'pub-date-value').text
-    for link in header.find('div', class_ = 'article_header-doiurl'):
-        doi_url = link.get('href')
-    subs = header.find('div', class_ = 'article_header-taxonomy')
-    subjects = []
-    for sub in subs.find_all('a'):
-        subjects.append(sub.get('title'))
-    cons = header.find('ul', class_ = 'loa')
-    contributors = []
-    for con in cons.find_all('span', class_ = 'hlFld-ContribAuthor'):
-        contributors.append(con.text)
-    numc = header.find('div', class_ = 'articleMetrics_count')
-    if not numc.a:
-        num_citations = 0
-    else:
-        num_citations = numc.a.text
-    pub = Publication(doi_url, article_title, contributors, "JCIM",
-                      publication_date, subjects, num_citations)
-    #pub = Publication(article_title, publication_date, contributors, doi_url,
-    #                  subjects, num_citations)
-    return pub
-
-
-def get_citation_info(pub, num_citations, soup):
-    details = soup.find('ol', class_ = 'cited-content_cbyCitation')
-    titles = [] 
-    for title in details.find_all('span', 
-            class_ = 'cited-content_cbyCitation_article-title'):
-        titles.append(title.text.replace('.', ''))
-    journal_names = []
-    for name in details.find_all('span',
-            class_ = 'cited-content_cbyCitation_journal-name'):
-        journal_names.append(name.text)
-    doi_urls = []
-    for url in details.find_all('a'):
-        doi_urls.append(url.get('href'))
-    # TODO: There are a few diffrent types how Contributors are listed
-    contributors = []
-    for contrib in details.find_all('span', 
-            class_ = 'cited-content_cbyCitation_article-contributors'):
-        contributors.append(contrib.text)
-    for i in range(0, int(num_citations)):
-        pub.citations.append(Citation(doi_urls[i], titles[i], journal_names[i], \
-                             contributors[i]))
-
-def input(url):
-    html_text = req.get(url).text
-    soup = bs(html_text, 'html.parser')
-    
-    pub = get_article_info(soup)
-    if int(pub.num_citations) > 0:
-        get_citation_info(pub, int(pub.num_citations), soup)
-    return pub

input/get/journal_fetcher.py

@@ -14,6 +14,7 @@ class JournalFetcher(metaclass=ABCMeta):
     """
     This is a abstract-class for fetcher modules
     """
+    
     @staticmethod
     def get_soup(url: str) -> BeautifulSoup:
         """
@@ -32,6 +33,7 @@ class JournalFetcher(metaclass=ABCMeta):
 
         return BeautifulSoup(req.content, 'html.parser')
 
+
     @staticmethod
     @abstractmethod
     def can_use_url(url: str) -> bool:
@@ -41,6 +43,7 @@ class JournalFetcher(metaclass=ABCMeta):
         """
         raise AttributeError("JournalFetcher for '{}' hasnt implemented 'can_use_url()'".format(url))
 
+
     @staticmethod
     @abstractmethod
     def get_publication(url: str) -> Publication:
@@ -49,12 +52,3 @@ class JournalFetcher(metaclass=ABCMeta):
         Creates a Publication-instance.
         """
         raise AttributeError("JournalFetcher for '{}' hasnt implemented 'get_publication()'".format(url))
-
-    @staticmethod
-    @abstractmethod
-    def test_fetcher():
-        """
-        Abstract-function to be implemented in subclass.
-        Unit-test for the class.
-        """
-        raise AttributeError("JournalFetcher: Subclass hasnt implemented 'test_fetcher()'")

input/get/nature.py

@@ -57,7 +57,3 @@ class Fetcher(JournalFetcher):
         # TODO: Exceptions-handling
         #   raise ValueException("Cant Fetch: '{}'".format(error))
         # return None
-
-    @staticmethod
-    def test_fetcher():
-        pass

input/get/template_.py

@@ -31,7 +31,9 @@ class Fetcher(JournalFetcher):
 
         # TODO: Check the URL for compatability
         #   url_re = re.match(r'(https?://)?(doi.org/)?(10.(\d{4})/\w+.\S+)', url)
+        #   if url_re is not None:
         #       return   url_re[4] in SUPPORTED_JOURNALS
+        #   else:
         return False
 
     @staticmethod
@@ -46,7 +48,3 @@ class Fetcher(JournalFetcher):
         # TODO: Create new Publication-instance
         #   return Publication(doi,title,contributors[],journal,publication_date,subjects[],num_citation=None ,references[],citations[])
         return None
\ No newline at end of file
-
-    @staticmethod
-    def test_fetcher():
-        pass

input/publication.py

@@ -4,10 +4,10 @@ class Publication:
     """
         Represents a Publications
     """
-    def __init__(self, doi_url: str, title: str
-                 , contributors: str, journal: str
-                 , publication_date: str, subjects = None, num_citations = None
-                 , references = None, citations = None ):
+    def __init__(self, doi_url: str, title: str \
+                 , contributors: list[str], journal: str \
+                 , publication_date: str, subjects: list[str], num_citations: int = None \
+                 , references: list[any] = None, citations: list[any] = None ):
         """
         Parameters
         ----------
@@ -72,7 +72,7 @@ class Publication:
                 citation_string.append(citation.__str__())
         return citation_string
 
-    def citations(self, citation) -> None:
+    def add_citations(self, citation) -> None:
         """
         Appends a list of Citations or Citation to self.citations.
 
@@ -132,9 +132,9 @@ Subjects:''')
 
 
 class Citation:
-    def __init__(self, doi_url: str, title: str
-                , journal: str, contributors = None
-                , cit_type = "Citation"):
+    def __init__(self, doi_url: str, title: str \
+                , journal: str, contributors: list[str] \
+                , cit_type: str = "Citation"):
         """
         Parameters
         ----------
@@ -168,7 +168,7 @@ class Citation:
 
 # This is just a replica of Citations 
 class Reference:
-    def __init__(self, doi_url, title, journal, contributors):
+    def __init__(self, doi_url: str, title: str, journal: str, contributors: list[str]):
         self.title = title
         self.doi_url = doi_url
         self.journal = journal

input/tempdir/input_fj.py

-#!/usr/bin/env python3
-"""
-Functions for information retrieval of articles from the ACS journal JCIM
-
-"""
-
-__author__ = "Florian Jochens"
-__email__ = "fj@andaco.de"
-__status__ = "Production"
-#__copyright__ = ""
-#__credits__ = ["", "", "", ""]
-#__license__ = ""
-#__version__ = ""
-#__maintainer__ = ""
-
-from bs4 import BeautifulSoup as bs
-import requests as req
-import sys  
-from pathlib import Path
-
-class Publication:
-    #_registry = []
-    _citations = []
-    
-    def __init__(self, title, publication_date, contributors, doi_url, 
-                 subjects, num_citations):
-        #self._registry.append(self)
-        self.title = title
-        self.publication_date = publication_date
-        self.contributors = contributors
-        self.doi_url = doi_url
-        self.subjects = subjects
-        self.num_citations = num_citations
-
-class Citation:
-    def __init__(self, title, journal, contributors, doi_url):
-        self.title = title
-        self.journal = journal
-        self.contributors = contributors
-        self.doi_url = doi_url
-
-def get_article_info(soup):
-    header = soup.find('div', class_ = 'article_header-left pull-left')
-    article_title = header.find('span', class_ = 'hlFld-Title').text
-    publication_date = header.find('span', class_ = 'pub-date-value').text
-    for link in header.find('div', class_ = 'article_header-doiurl'):
-        doi_url = link.get('href')
-    subs = header.find('div', class_ = 'article_header-taxonomy')
-    subjects = []
-    for sub in subs.find_all('a'):
-        subjects.append(sub.get('title'))
-    cons = header.find('ul', class_ = 'loa')
-    contributors = []
-    for con in cons.find_all('span', class_ = 'hlFld-ContribAuthor'):
-        contributors.append(con.text)
-    numc = header.find('div', class_ = 'articleMetrics_count')
-    if not numc.a:
-        num_citations = 0
-    else:
-        num_citations = numc.a.text
-
-    pub = Publication(article_title, publication_date, contributors, doi_url,
-                      subjects, num_citations)
-    return pub
-
-def get_download_url():
-    export = soup.find('div', class_ = 'cit-download-dropdown_content')
-    url = 'https://pubs.acs.org'
-    for link in export.find_all('a'):
-        if link.get('title') == 'Citation and references':
-            url += link.get('href')     
-    print(url)
-    return url
-
-def download(url): # Download citation and references file
-    if url.find('='):
-        filename = url.rsplit('=', 1)[1]
-    path = Path(('./files/' + filename))
-    if path.is_file():
-        print("File already exists")
-    else:
-        print("File does not exist")
-
-def get_citation_info(pub, num_citations, soup):
-    pub._citations = []
-    details = soup.find('ol', class_ = 'cited-content_cbyCitation')
-    titles = [] 
-    for title in details.find_all('span', 
-            class_ = 'cited-content_cbyCitation_article-title'):
-        titles.append(title.text.replace('.', ''))
-    journal_names = []
-    for name in details.find_all('span',
-            class_ = 'cited-content_cbyCitation_journal-name'):
-        journal_names.append(name.text)
-    doi_urls = []
-    for url in details.find_all('a'):
-        doi_urls.append(url.get('href'))
-    contributors = []
-    for contrib in details.find_all('span', 
-            class_ = 'cited-content_cbyCitation_article-contributors'):
-        contributors.append(contrib.text)
-    for i in range(0, int(num_citations)):
-        pub._citations.append(Citation(titles[i], journal_names[i], 
-                              contributors[i], doi_urls[i]))
-def print_pub_info(pub):
-    print(f'''Article title:    {pub.title}
-Publication date: {pub.publication_date}
-DOI-URL:          {pub.doi_url}
-
-Subjects:''')
-    print(*(pub.subjects), sep = ", ")
-    print('\nContributors:')
-    print(*(pub.contributors), sep = ", ")
-
-    if int(pub.num_citations) > 0:
-        if int(pub.num_citations) == 1:
-            print(f'\nThis publication is cited by the following publication:\n')
-        else:
-            print(f'\nThis publication is cited by the following {pub.num_citations} publications:\n')
-        for citation in pub._citations:
-            print(f'''
-    Title:        {citation.title}
-    Journal:      {citation.journal}
-    Contributors: {citation.contributors}
-    DOI-URL:      {citation.doi_url}
-            ''')
-    else:
-        print('\nThis publication is not cited by any other publication.')
-
-def input(url):
-    html_text = req.get(url).text
-    soup = bs(html_text, 'html.parser')
-    
-    pub = get_article_info(soup)
-    if int(pub.num_citations) > 0:
-        get_citation_info(pub, int(pub.num_citations), soup)
-    return pub
-
-#if len(sys.argv) != 2:
-#    sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
-#    exit(1)
-#url = sys.argv[1]
-#pub = input(url)
-#print_pub_info(pub)

input/tempdir/pub.py

-class Publication:
-    #_registry = []
-    #_citations = []
-    #_references = []
-    
-    def __init__(self, title, publication_date, contributors, doi_url, 
-                 subjects, num_citations):
-        #self._registry.append(self)
-        self.title = title
-        self.publication_date = publication_date
-        self.contributors = contributors
-        self.doi_url = doi_url
-        self.subjects = subjects
-        self.num_citations = num_citations
-        self.num_references = num_references
-    	self._citations = []
-    	self._references = []
-
-class Citation:
-    def __init__(self, title, journal, contributors, doi_url):
-        self.title = title
-        self.journal = journal
-        self.contributors = contributors
-        self.doi_url = doi_url
-
-class References:
-    def __init__(self, title, journal, contributors, doi_url):
-        self.title = title
-        self.journal = journal
-        self.contributors = contributors
-        self.doi_url = doi_url
-

input/tempdir/test.py

-#!/usr/bin/env python3
-
-from input_fj import input, print_pub_info
-import sys
-
-if len(sys.argv) != 3:
-    sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
-    exit(1)
-url = sys.argv[1]
-url2 = sys.argv[2]
-pub = input(url)
-print_pub_info(pub)
-pub2 = input(url2)
-print_pub_info(pub2)
-

input/test_input_get_publication.py

-import unittest 
-"""
-Testing the Publication fetcher
-
-Publication 1: 'https://doi.org/10.1021/acs.jcim.1c00203'
-Publication 2: 'doi.org/10.1021/acs.jcim.1c00917'
-Publication 3: '10.1038/nchem.1781'
-Publication 4: '11.12/jaj'
-Publication 5: '11.12/'
-Publication 6: 'https://doi.org/10.1021/acs.jmedchem.0c01332' # Paper is a PDF
-"""
-
-
-class TestGetPublication(unittest.TestCase):
-
-    def test_publication1(self):
-        pass
-
-    def test_publication2(self):
-        pass
-
-    def test_publication3(self):
-        pass
-
-
-if __name__=="__main__":
-    print("test")
-    unittest.main()
\ No newline at end of file