.gitignore

+**/__pycache__/

count_journal.py

+#!/usr/bin/env python3
+
+from input.interface import InputInterface as Input
+
+def count_journals(url: str):
+    inter = Input()
+    pub = inter.get_publication(url)
+
+    if pub.citations:
+        for citation in pub.citations:
+            journal = citation.journal
+            if journal in cit:
+                cit[journal] += 1
+            else:
+                cit[journal] = 1
+
+    if pub.references:
+        for reference in pub.references:
+            journal = reference.journal
+            if journal in cit:
+                cit[journal] += 1
+            else:
+                cit[journal] = 1
+
+if __name__ == "__main__":
+    cit = {}
+	
+    count_journals("https://doi.org/10.1021/acs.jcim.1c00203")
+    count_journals("https://doi.org/10.1021/acs.jcim.6b00561")
+    count_journals("https://doi.org/10.1021/acs.jcim.6b00613")
+    count_journals("https://doi.org/10.1021/acs.jcim.1c00917")
+    count_journals("https://doi.org/10.1021/acs.jmedchem.0c01332")
+		#count_journals("https://pubs.acs.org/doi/10.1021/acs.biochem.1c00290")
+		#count_journals("https://pubs.acs.org/doi/10.1021/acsenvironau.1c00007")
+		#count_journals("https://pubs.acs.org/doi/10.1021/acs.biochem.7b01162")
+
+    cit = dict(sorted(cit.items(), key=lambda item: item[1]))
+    for journal in cit:
+        if journal != "":
+            print(f'{journal}: {cit[journal]}')

example_input.py

+#!/usr/bin/env python3
+
+from input.interface import InputInterface as Input
+
+def main(url: str):
+    i = Input()
+    #print(i.get_publication(url))
+    print(i.get_pub_light(url))
+    # print(i.get_supported_fetchers()) Useless because all classes are called the same
+
+if __name__ == "__main__":
+	#main("https://doi.org/10.1021/acs.jcim.1c0023")
+    main("https://doi.org/10.1021/acs.jcim.5b00332")

input/README.md

 # Projekt CiS-Projekt 2021/22
-Input-Skripts
 
+Input-Package to fetch publication information with a given url.
+
+## Usage/Examples
+
+```python
+from input.interface import InputInterface as Input
+from input.publication import Publication
+
+def main(url):
+    inter = Input()
+    try:
+        pub = inter.get_publication(url)
+    except Exception as error:
+        raise error
+
+    print(pub)
+    pub.title = "Cool new Title"
+    print(pub)
+
+if __name__ == "__main__":
+    main("https://doi.org/10.1021/acs.chemrev.8b00728")
+```
+
+The expected results of calling this methode are:
+| Input-Url | Result    |
+|-----------|-----------|
+| supported & correct| A publication Instance |
+| supported & uncorrect| ValueError|
+| not supported | ValueError|
+
+Supported Url are urls, which comply with the url-pattern of supported Journals.  
+
+### Supported Journals:
+
+- ACS-Journals
+- (Nature-Journals)
+
+## 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
+- Julius Schenk
\ No newline at end of file

input/get/acs.py

+#!/usr/bin/env python3
+
+"""
+Child class of JournalFetcher
+Usage: Check if Url can be used with 'can_use_url'
+       and then fetch publication with 'get_publication'
+"""
+
+import re
+
+from input.get.journal_fetcher import JournalFetcher
+from input.publication import Publication, Citation
+
+
+class Fetcher(JournalFetcher):
+    """
+    Specific Fetcher for the ACS journals.
+    """
+
+    # Constant for the abbreviations of the supported Journals
+    SUPPORTED_JOURNALS = ['1021']
+
+    @staticmethod
+    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/|pubs.acs.org/doi/)?(10.(\d{4})/\w+.\S+)', url.strip(". \t\r\n"))
+        
+        #Checks if match exists
+        if matched_url is not None:
+            return matched_url[4] in Fetcher.SUPPORTED_JOURNALS
+        else:
+            return False
+
+    @staticmethod
+
+
+    def get_pub_light(url: str) -> Publication:
+        """
+        Fetches html and creates Beatifulsoup-instance in parent class.
+        Specific css-searches for ACS-Journals and creates Publication-instance.
+        """
+
+        # Creation of Soup
+        try:
+            soup = JournalFetcher.get_soup(url)
+        except Exception as error:
+            raise error
+        
+        # Raise Error if re recognizes Pattern, but url isnt correct:
+        #   For other Urls
+        if soup.text.strip(" \t\n")=="Missing resource null":
+            raise ValueError("'{}' matches Pattern for 'ACS', but doesnt link to Paper.".format(url))
+
+        #   For Dois
+        if soup.title is not None:
+            if soup.title.text == "Error: DOI Not Found":
+                raise ValueError("'{}' matches Pattern for 'ACS', but doesnt link to Paper.".format(url))
+
+        
+        soup_header = soup.select('.article_header')[0]
+        
+        # Creates Publication
+        doi_url = soup_header.select('a[title="DOI URL"]')[0].string
+        title = soup_header.select(".hlFld-Title")[0].text
+
+        contributors = []
+        for author in soup_header.select(".hlFld-ContribAuthor"):
+            contributors.append(author.text)
+
+        journal = soup_header.select(".cit-title")[0].text
+
+        # Replaces abbreviation with whole name
+        if journal in JournalFetcher.abbrev_dict:
+            journal = JournalFetcher.abbrev_dict[journal]
+                
+
+        published = soup_header.select(".pub-date-value")[0].text
+
+        subjects = []
+        subject_soup = soup_header.select('.article_header-taxonomy')[0]
+        for subject in subject_soup.select('a'):
+            subjects.append(subject.text)
+
+        return Publication(doi_url, title, contributors, journal, published, 
+                           subjects)
+
+    def get_publication(url: str) -> Publication:
+        """
+        Fetches html and creates Beatifulsoup-instance in parent class.
+        Specific css-searches for ACS-Journals and creates Publication-instance.
+        """
+
+        # Creation of Soup
+        try:
+            soup = JournalFetcher.get_soup(url)
+        except Exception as error:
+            raise error
+        
+        # Raise Error if re recognizes Pattern, but url isnt correct:
+        #   For other Urls
+        if soup.text.strip(" \t\n")=="Missing resource null":
+            raise ValueError("'{}' matches Pattern for 'ACS', but doesnt link to Paper.".format(url))
+
+        #   For Dois
+        if soup.title is not None:
+            if soup.title.text == "Error: DOI Not Found":
+                raise ValueError("'{}' matches Pattern for 'ACS', but doesnt link to Paper.".format(url))
+
+        
+        soup_header = soup.select('.article_header')[0]
+        
+        #Could be used for more specific search
+        ref_cit_soup = soup
+
+        # Creates Publication
+        doi_url = soup_header.select('a[title="DOI URL"]')[0].string
+        title = soup_header.select(".hlFld-Title")[0].text
+
+        contributors = []
+        for author in soup_header.select(".hlFld-ContribAuthor"):
+            contributors.append(author.text)
+
+        journal = soup_header.select(".cit-title")[0].text
+
+        # Replaces abbreviation with whole name
+        if journal in JournalFetcher.abbrev_dict:
+            journal = JournalFetcher.abbrev_dict[journal]
+                
+
+        published = soup_header.select(".pub-date-value")[0].text
+
+        subjects = []
+        subject_soup = soup_header.select('.article_header-taxonomy')[0]
+        for subject in subject_soup.select('a'):
+            subjects.append(subject.text)
+
+
+        references = []
+        references_soup = ref_cit_soup.select('ol#references')
+        if references_soup != []:
+            for reference in references_soup[0].select('li'):
+                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
+                ref_journal = reference.select('i')[0].text\
+                        if reference.select('i') != [] else None
+
+                # Replaces abbreviation with whole name
+                if ref_journal in JournalFetcher.abbrev_dict:
+                    ref_journal = JournalFetcher.abbrev_dict[ref_journal]
+                
+                ref_contributors=[]
+                for author in reference.select('.NLM_contrib-group'):
+                    ref_contributors.append(author.text.replace("\n", " ").replace("\r", ""))
+
+                references.append(Citation(ref_doi, ref_title, ref_journal, ref_contributors, cit_type="Reference"))
+
+        citations = []
+        citation_soup = ref_cit_soup.select('.cited-content_cbyCitation')
+        if citation_soup != []:
+            for citation in citation_soup[0].select('li'):
+                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
+
+                # Replaces abbreviation with whole name
+                if cit_journal in JournalFetcher.abbrev_dict:
+                    cit_journal = JournalFetcher.abbrev_dict[cit_journal]
+                cit_contributors =[]
+                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 != '':
+                    cit_contributors.append(cit_contributors_last)  
+                citations.append(Citation(cit_doi, cit_title, cit_journal, cit_contributors, cit_type = "Citation"))
+
+        return Publication(doi_url, title, contributors, journal, published
+                            , subjects, references, citations)

input/get/journal_fetcher.py

+#!/usr/bin/env python3
+
+"""
+Parent class for specific Journal
+"""
+
+from abc import ABCMeta, abstractmethod
+from bs4 import BeautifulSoup
+import requests
+from input.publication import Publication
+
+
+class JournalFetcher(metaclass=ABCMeta):
+    """
+    This is a abstract-class for fetcher modules
+    """
+    
+    @staticmethod
+    def get_soup(url: str) -> BeautifulSoup:
+        """
+        Retrieves webside-html and returns a BeautifulSoup-instance
+
+        Parameters:
+        -----------
+        :type url: str
+        :param url: doi-url to a publication
+        :return: BeatifulSoup-instance
+        """
+        try:
+            req = requests.get(url)
+        except  requests.exceptions.HTTPError as err:
+            raise SystemExit(err)
+
+        return BeautifulSoup(req.content, 'html.parser')
+
+
+    @staticmethod
+    @abstractmethod
+    def can_use_url(url: str) -> bool:
+        """
+        Abstract-function to be implemented in subclass.
+        Checks if given url links to a supported journal
+        """
+        raise AttributeError("JournalFetcher for '{}' hasnt implemented 'can_use_url()'".format(url))
+
+
+    @staticmethod
+    @abstractmethod
+    def get_publication(url: str) -> Publication:
+        """
+        Abstract-function to be implemented in subclass.
+        Creates a Publication-instance.
+        """
+        raise AttributeError("JournalFetcher for '{}' hasnt implemented 'get_publication()'".format(url))
+
+
+    # A Dictionary, which connects abbreviation to whole journal-name
+    abbrev_dict = {
+          "Nat. Protoc.":"Journal of Natural Products"
+        ,"PLoS Comput. Biol.":"PLoS Computational Biology"
+        ,"PLoS One":"PLoS One"
+        ,"Protein Sci.":"Protein Science"
+        ,"J. Am. Chem. Soc.":"Journal of the American Chemical Society"
+        ,"J. Chem. Phys.":"Journal of Chemical Physics"
+        ,"Appl. Sci.":"Applied Science"
+        ,"Comput. Sci. Eng.":"Computing in Science & Engineering"
+        ,"Beilstein J. Org. Chem.":"Beilstein Journal of Organic Chemistry"
+        ,"Biol. Chem.":"Biological Chemistry"
+        ,"Isr. J. Chem.":"Israel Journal of Chemistry"
+        ,"Nat. Methods":"Nature Methods"
+        ,"Proc. Natl. Acad. Sci. U. S. A.":"Proceedings of the National Academy of Sciences of the United States of America"
+        ,"J. Phys. Chem. B":"Journal of Physical Chemistry B"
+        ,"Carbohydr. Res.":"Carbohydrate Research"
+        ,"J. Chem. Theory Comput.":"Journal of Chemical Theory and Computation"
+        ,"J. Mol. Biol.":"Journal of Molecular Biology"
+        ,"Nucleic Acids Res.":"Nucleic Acids Research"
+        ,"J. Comput. Chem.":"Journal of Computational Chemistry"
+        ,"J. Cheminf.":"Journal of Cheminformatics"
+        ,"J. Med. Chem.":"Journal of Medicinal Chemistry"
+        ,"J. Comput.-Aided Mol. Des.":"Journal of Computer-Aided Molecular Design"
+        ,"J. Chem. Inf. Model.":"Journal of Chemical Information and Modeling"
+        ,"Mol. Cell":"Molecular Cell"
+        ,"J. Cell Biolog.":"Journal of Cell Biology"
+        ,"Mol. Cell Biol.":"Molecular and Cellular Biology"
+        ,"J. Cell Sci.":"Journal of Cell Science"
+        ,"Nat. Cell Biol.":"Nature Cell Biology"
+        ,"J. Aerosol Sci. Technol.":"Aerosol Science and Technology"
+        ,"Mol. Biol. Cell":"Molecular Biology of the Cell"
+        ,"Build. Environ.":"Building and Environment"
+        ,"Sci. Rep.":"Scientific Reports"
+        ,"Nat. Chem.":"Nature Chemistry"
+        ,"Nat. Med.":"Nature Medicine"
+        ,"Nat. Commun.":"Nature Communications"
+        ,"Exp. Cell Res.":"Experimental Cell Research"
+        ,"Nat. Chem. Biol.":"Nature Chemical Biology"
+        }
\ No newline at end of file

input/get/nature.py

+#!/usr/bin/env python3
+
+"""
+Child class of JournalFetcher
+Usage: Check if Url can be used with 'can_use_url'
+       and then fetch publication with 'get_publication'
+"""
+
+# import re
+from input.get.journal_fetcher import JournalFetcher
+from input.publication import Publication
+
+
+class Fetcher(JournalFetcher):
+
+    """
+    scrapes publication metadata from a provided url
+    """
+
+    #   TODO: List of Compatable Journals
+    #   NOTE: nature does not use journal names in doi links, must match by 10.xxxx identifier instead
+    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 False
+
+    @staticmethod
+    def get_publication(url: str) -> Publication:
+        """
+        Creates a Publication-instance.
+        """
+
+        soup = JournalFetcher.get_soup(url)
+
+        _doi_url = "https://doi.org/" + soup.head.find(attrs={"name": "DOI"}).get("content")
+        _title = soup.head.find(attrs={"name": "citation_title"}).get("content")
+        _journal = soup.head.find(attrs={"name": "citation_journal_title"}).get("content")
+        _published = soup.head.find(attrs={"name": "prism.publicationDate"}).get("content")
+        _contributors = []
+        _subjects = []
+
+        for creator in soup.head.findAll(attrs={"name": "dc.creator"}):
+            _contributors.append(creator.get("content"))
+
+        for subject in soup.head.findAll(attrs={"name": "dc.subject"}):
+            _subjects.append(subject.get("content"))
+
+        return Publication(_doi_url, _title, _contributors, _journal, _published, _subjects)
+
+        # TODO: Exceptions-handling
+        #   raise ValueException("Cant Fetch: '{}'".format(error))
+        # return None

input/get/template_.py

+#!/usr/bin/env python3
+
+"""
+Child class of JournalFetcher
+Usage: None, this is just a template and should be ignored
+"""
+
+# import re
+from input.get.journal_fetcher import JournalFetcher
+from input.publication import Publication
+
+
+class Fetcher(JournalFetcher):
+
+    """
+    This is only a template and therefore has no functionality
+    """
+
+    # TODO: Naming-Convention:
+    #   Class: 'Fetcher'
+    #   file: [journal-/organisation-name]
+    #       format = "[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
+        #   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
+    def get_publication(url: str) -> Publication:
+        """
+        Creates a Publication-instance.
+        """
+
+        # TODO: Fetch data from the HTML
+        #   soup = JournalFetcher.get_soup(url)
+        #   doi,title,contributors[],journal,publication_date,subjects[],references[],citations[] 
+        # TODO: Create new Publication-instance
+        #   return Publication(doi_url, title, contributors = [], journal
+        #           , publication_date, subjects = [], references = [], citations = [])
+        return None
\ No newline at end of file

input/interface.py

+#!/usr/bin/env python3
+
+"""
+Interface for the Input-Package only this should be accessed from outside this Package.
+
+"""
+from os import walk
+import importlib
+import pathlib
+import re
+from input.publication import Publication
+
+class InputInterface:
+    """
+    Singleton which dynamically imports and manages fetchers
+    """
+
+    instance = None
+    get_path = None
+    fetcher_classes=[]
+
+    # '__new__' is called before '__init__' and gives us an instance
+    def __new__(cls, *args, **kwargs):
+        
+        # checks if an instance exists and if it doesnt creates one
+        if cls.instance == None:
+            cls.instance = super(InputInterface, cls).__new__(cls,*args, **kwargs)
+        
+        return cls.instance
+
+    def __init__(self):
+        # imports all modules
+
+        if self.fetcher_classes ==[]:
+            self.import_fetcher_classes()
+            if self.fetcher_classes ==[]:
+                raise AttributeError("No specific Fetchers where found at: '{}'"
+                                    .format(self.get_path))
+        
+
+    def get_publication(self, url: str) -> Publication:
+        """
+        The interface-method to get a Publication-instance
+        (including it's citations and references)
+
+        Parameters
+        ----------
+        :param url: url to a Publication
+        :type url: str
+        :return: Publication instance or None if not supported
+        """
+        
+        # Checks if module supports the 'url' and 
+        # returns a Publication if it does.
+        for fetcher_class in InputInterface.fetcher_classes:
+            if fetcher_class.can_use_url(url):
+                return fetcher_class.get_publication(url)
+            
+        # No Module for given url was found
+        raise ValueError("'{}' is not supported".format(url))
+        
+    def get_pub_light(self, url: str) -> Publication:
+        """
+        The interface-method to get a Publication-instance 
+        (only for main article)
+
+        Parameters
+        ----------
+        :param url: url to a Publication
+        :type url: str
+        :return: Publication instance or None if not supported
+        """
+        
+        # Checks if module supports the 'url' and 
+        # returns a Publication if it does.
+        for fetcher_class in InputInterface.fetcher_classes:
+            if fetcher_class.can_use_url(url):
+                return fetcher_class.get_pub_light(url)
+            
+        # No Module for given url was found
+        raise ValueError("'{}' is not supported".format(url))
+    
+    def get_supported_fetchers(self):
+        # print(self.fetcher_classes[0].__name__) Useless right now, 
+        # because all classes are called the same
+        return [a.__name__ for a in self.fetcher_classes]
+
+    def import_fetcher_classes(self):
+        """
+        Searches in 'get', if there are [a-z]*.py modules (specific Fetchers)
+        and tries to import them.
+        Saves found modules in 'fetcher_files'.
+        """
+
+        # Path to 'get'-package
+        self.get_path = '{}/get'.format(pathlib.Path(__file__).parent.resolve())
+        
+        # Searches for modules with given Pattern
+        fetcher_file_names=[]
+        for file in next(walk(self.get_path), (None, None, []))[2]:
+            if re.match(r'[a-z]+.py', file) is not None:
+                fetcher_file_names.append(file)
+
+        # Tries to import those modules and saves their 'Fetcher'-class
+        for file in fetcher_file_names:
+            try:
+                fetcher_class = importlib.import_module("input.get.{}".format(file[:-3]))
+                try:
+                    self.fetcher_classes.append(fetcher_class.__getattribute__('Fetcher'))
+                except Exception as error:
+                    ImportError("Module '{}' does not have a 'Fetcher'-class".format(file[:-3]))
+            except Exception:
+                raise ImportError("Module '{}' can not be imported".format(file[:-3]))

input/publication.py

+#!/usr/bin/env python3
+
+# this is needed for typing pre python 3.9, this maybe as an large Overhead
+from typing import Any, List
+
+
+class Publication:
+    """
+        Represents a Publications
+    """
+    def __init__(self, doi_url: str, title: str \
+                 , contributors: List[str], journal: str \
+                 , publication_date: str, subjects: List[str]\
+                 , references: List[Any] = None, citations: List[Any] = None ):
+        """
+        Parameters
+        ----------
+        :param doi_url: doi_url of the publication
+        :type doi_url: str
+        :param title: title of the publication
+        :type title: str
+        :param contributors:list of all contributors
+        :type contributors: list[]
+        :param published: date of release
+        :type published: str
+        :param subjects: the subject of the Publication
+        :type subjects: List[str]
+        :param references: the Citation which is been referenced by this Publication 
+        :type references: List[Any]
+        :param citations: the Citation which references this Publication
+        :type citations: List[Any]
+        :return: None
+        """
+        self.doi_url = doi_url
+        self.title = title
+        self.contributors = contributors
+        self.journal = journal
+        self.publication_date = publication_date
+        self.subjects = subjects
+        if references is None:
+            self.references = []
+        else:
+            self.references = references
+        if citations is None:
+            self.citations = []
+        else: 
+            self.citations = citations
+        
+        # For the 'Verarbeitungsgruppe'
+        self.group = None
+
+    def __str__(self) -> str:
+        return ("Title:        {}\n"
+                "Doi-url:      {}\n"
+                "Authors:      {}\n"
+                "Journal:      {}\n"
+                "Published on: {}\n"
+                "Subjects:     {}\n"
+                "References:   \n{}\n"
+                "Citations:    \n{}")\
+                .format(self.title, self.doi_url, ", ".join(self.contributors)
+                        , self.journal, self.publication_date
+                        , ", ".join(self.subjects)
+                        , "\n".join(self.get_citation_string(self.references))
+                        , "\n".join(self.get_citation_string(self.citations)))
+
+    @staticmethod
+    def get_citation_string(citations):
+        if citations == []:
+            return ["None"]
+        else:
+            citation_string = []
+            for citation in citations:
+                citation_string.append(citation.__str__())
+        return citation_string
+
+    def add_citations(self, citation) -> None:
+        """
+        Appends a list of Citations or Citation to self.citations.
+
+        Parameter
+        ---------
+        :param citation: Citation or Reference of the Publication
+        :type citation: Citation or list[Citation]
+        :return: self.citations
+        """
+        if type(citation) is Citation:
+            self.citations.append(citation)
+
+        # Checks if 'citation' is a list of Citations
+        elif type(citation) is list:
+            for _cit in citation:
+                if type(_cit) is Citation:
+                    self.citations.append(_cit)
+                else:
+                    raise TypeError("_set_citation expects Citations or List of Citations, not: '{}'"
+                                    .format(type(_cit)))
+        else:
+            raise TypeError("_set_citation expects Citations or List of Citations, not: '{}'"
+                            .format(type(citation)))
+
+        return self.citations
+
+    def __eq__(self, other) -> bool:
+        """ Compares the unique doi_url of two Publications"""
+        if type(self)==type(other):
+            return self.doi_url == other.doi_url
+        return False
+
+
+class Citation:
+    def __init__(self, doi_url: str, title: str \
+                , journal: str, contributors: List[str] \
+                , cit_type: str = "Citation"):
+        """
+        Parameters
+        ----------
+        :param doi_url: doi_url of the publication
+        :type doi_url: str
+        :param title: title of the publication
+        :type title: str
+        :param contributors: list of all contributors
+        :type contributors: List[str]
+        :param cit_type: Specifies if Reference or Citation
+        :type cit_type: str
+        :return: None
+        """
+
+        self.title = title
+        self.doi_url = doi_url
+        self.journal = journal
+        self.contributors = contributors
+        self.cit_type = cit_type
+
+    def __str__(self) -> str:
+        return ("\t{}-Title:        {}\n"
+                "\t{}-Doi:          {}\n"
+                "\t{}-Journal:      {}\n"
+                "\t{}-Contributors: {}\n")\
+                .format(self.cit_type, self.title
+                      , self.cit_type, self.doi_url
+                      , self.cit_type, self.journal
+                      , self.cit_type, ", ".join(self.contributors))

input/requirements.txt

+beautifulsoup4
+requests
\ No newline at end of file

input/test/test_acs.py

+#!/usr/bin/env python
+
+from input.get.acs import Fetcher as Acs
+from input.publication import Publication, Citation
+from input.test.test_input import FetcherTestCase
+
+
+class AcsTestCase(FetcherTestCase):
+    """
+    Methods with test_* will be detected by unittest and run.
+    """
+
+    def test_acs_url(self):
+        # Positive Testing
+        self.can_use_url_test(Acs, "https://doi.org/10.1021/acs.jcim.1c00203"           , True)
+        self.can_use_url_test(Acs, "doi.org/10.1021/acs.jcim.1c00203"                   , True)
+        self.can_use_url_test(Acs, "10.1021/acs.jcim.1c00203"                           , True)
+        self.can_use_url_test(Acs, " 10.1021/acs.jcim.1c00203"                          , True)
+        self.can_use_url_test(Acs, "10.1021/acs.jcim.1c00203 "                          , True)
+        self.can_use_url_test(Acs, "\t 10.1021/acs.jcim.1c00203  \t\n"                  , True)
+        self.can_use_url_test(Acs, "https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203"  , True)
+
+        # Negative Testing
+        self.can_use_url_test(Acs, ""                                                   , False)
+        self.can_use_url_test(Acs, "https://doi.org/10.1038/219021a0"                   , False)
+        self.can_use_url_test(Acs, "https://www.nature.com/articles/219021a0"           , False)
+        self.can_use_url_test(Acs, "https://pubs.acs.org/doi/doi.org/10.1021/acs.jcim.1c00203", False)
+        
+
+
+    def test_acs_publication(self):
+        url = "https://doi.org/10.1021/acs.jcim.1c00203"
+        self.get_publication_test(Acs, url, self.expectedPubs[url])
+
+    def test_acs_exceptions(self):
+        test_url= "https://doi.org/10.1021/acs.jcim.1c002"
+        self.get_publication_exception_test(Acs, test_url)
+        
+    # Dictionary of Expected Results, with url
+    expectedPubs = {
+       "https://doi.org/10.1021/acs.jcim.1c00203":
+        Publication(
+           doi_url = "https://doi.org/10.1021/acs.jcim.1c00203",
+           title = "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings",
+           contributors = ["Jerome Eberhardt", "Diogo Santos-Martins", "Andreas F. Tillack", "Stefano Forli"],
+           journal="Journal of Chemical Information and Modeling",
+           publication_date = "July 19, 2021",
+           subjects = ["Algorithms","Ligands","Molecules","Receptors","Macrocycles"],
+           references = [
+            Citation(doi_url = "https://doi.org/10.1002/jcc.21334"
+                , title ="AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading"
+                , journal="Journal of Computational Chemistry"
+                , contributors=["Trott, O.", "Olson, A. J."]
+                , cit_type="Reference")
+            , Citation(doi_url = "https://doi.org/10.1038/nprot.2016.051"
+                , title ="Computational protein-ligand docking and virtual drug screening with the AutoDock suite"
+                , journal="Journal of Natural Products"
+                , contributors=["Forli, S.","Huey, R.","Pique, M. E.","Sanner, M. F.","Goodsell, D. S.","Olson, A. J."]
+                , cit_type="Reference")
+            , Citation(title = "A semiempirical free energy force field with charge-based desolvation"
+                , doi_url = "https://doi.org/10.1002/jcc.20634"
+	            , journal="Journal of Computational Chemistry"
+                , contributors=["Huey, R.","Morris, G. M.","Olson, A. J.","Goodsell, D. S."]
+                , cit_type="Reference")
+            , Citation(title="Accelerating autodock4 with gpus and gradient-based local search"
+                , doi_url="https://doi.org/10.1021/acs.jctc.0c01006"
+                , journal="Journal of Chemical Theory and Computation"
+                , contributors=["Santos-Martins, D.","Solis-Vasquez, L.","Tillack, A. F.","Sanner, M. F.","Koch, A.","Forli, S."]
+                , cit_type="Reference")
+            , Citation(title="AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility"
+                , doi_url="https://doi.org/10.1371/journal.pcbi.1004586"
+                , journal="PLoS Computational Biology"
+                , contributors=["Ravindranath, P. A.","Forli, S.","Goodsell, D. S.","Olson, A. J.","Sanner, M. F."]
+                , cit_type="Reference")
+            , Citation(title="Docking flexible cyclic peptides with AutoDock CrankPep"
+                , doi_url="https://doi.org/10.1021/acs.jctc.9b00557"
+                , journal="Journal of Chemical Theory and Computation"
+                , contributors=["Zhang, Y.","Sanner, M. F."]
+                , cit_type="Reference")
+            , Citation(title="Fast, accurate, and reliable molecular docking with QuickVina 2"
+                , doi_url="https://doi.org/10.1093/bioinformatics/btv082"
+                , journal="Bioinformatics"
+                , contributors=["Alhossary, A.","Handoko, S. D.","Mu, Y.","Kwoh, C.-K."]
+                , cit_type="Reference")
+            , Citation(title="Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise"
+                , doi_url="https://doi.org/10.1021/ci300604z"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Koes, D. R.","Baumgartner, M. P.","Camacho, C. J."]
+                , cit_type="Reference")
+            , Citation(title="Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking"
+                , doi_url="https://doi.org/10.1021/acs.jctc.5b00834"
+                , journal="Journal of Chemical Theory and Computation"
+                , contributors=["Nivedha, A. K.","Thieker, D. F.","Makeneni, S.","Hu, H.","Woods, R. J."]
+                , cit_type="Reference")
+            , Citation(title="AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina"
+                , doi_url="https://doi.org/10.1186/s13321-016-0139-1"
+                , journal="Journal of Cheminformatics"
+                , contributors=["Koebel, M. R.","Schmadeke, G.","Posner, R. G.","Sirimulla, S."]
+                , cit_type="Reference")
+            , Citation(title="Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening"
+                , doi_url="https://doi.org/10.1371/journal.pone.0155183"
+                , journal="PLoS One"
+                , contributors=["Quiroga, R.","Villarreal, M. A."]
+                , cit_type="Reference")
+            , Citation(title="Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems"
+                , doi_url="https://doi.org/10.1021/ci700036j"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Forli, S.","Botta, M."]
+                , cit_type="Reference")
+            , Citation(title="AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins"
+                , doi_url="https://doi.org/10.1021/ci500209e"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Santos-Martins, D.","Forli, S.","Ramos, M. J.","Olson, A. J."]
+                , cit_type="Reference")
+            , Citation(title="A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking"
+                , doi_url="https://doi.org/10.1021/jm2005145"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Forli, S.","Olson, A. J."]
+                , cit_type="Reference")
+            , Citation(title="Directional phosphorylation and nuclear transport of the splicing factor SRSF1 is regulated by an RNA recognition motif"
+                , doi_url="https://doi.org/10.1016/j.jmb.2016.04.009"
+                , journal="Journal of Molecular Biology"
+                , contributors=["Serrano, P.","Aubol, B. E.","Keshwani, M. M.","Forli, S.","Ma, C.-T.","Dutta, S. K.","Geralt, M.","Wüthrich, K.","Adams, J. A."]
+                , cit_type="Reference")
+            , Citation(title="Covalent docking using autodock: Two-point attractor and flexible side chain methods"
+                , doi_url="https://doi.org/10.1002/pro.2733"
+                , journal="Protein Science"
+                , contributors=["Bianco, G.","Forli, S.","Goodsell, D. S.","Olson, A. J."]
+                , cit_type="Reference")
+            , Citation(title="Consensus docking: improving the reliability of docking in a virtual screening context"
+                , doi_url="https://doi.org/10.1021/ci300399w"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Houston, D. R.","Walkinshaw, M. D."]
+                , cit_type="Reference")
+            , Citation(title="DockBench: an integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations"
+                , doi_url="https://doi.org/10.3390/molecules20069977"
+                , journal="Molecules"
+                , contributors=["Cuzzolin, A.","Sturlese, M.","Malvacio, I.","Ciancetta, A.","Moro, S."]
+                , cit_type="Reference")
+            , Citation(title="A new force field for molecular mechanical simulation of nucleic acids and proteins"
+                , doi_url="https://doi.org/10.1021/ja00315a051"
+                , journal="Journal of the American Chemical Society"
+                , contributors=["Weiner, S. J.","Kollman, P. A.","Case, D. A.","Singh, U. C.","Ghio, C.","Alagona, G.","Profeta, S.","Weiner, P."]
+                , cit_type="Reference")
+            , Citation(title="AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions"
+                , doi_url="https://doi.org/10.1093/bioinformatics/btz152"
+                , journal="Bioinformatics"
+                , contributors=["Arcon, J. P.","Modenutti, C. P.","Avendaño, D.","Lopez, E. D.","Defelipe, L. A.","Ambrosio, F. A.","Turjanski, A. G.","Forli, S.","Marti, M. A."]
+                , cit_type="Reference")
+            , Citation(title="Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory"
+                , doi_url="https://doi.org/10.1021/jp9723574"
+                , journal="Journal of Physical Chemistry B"
+                , contributors=["Lazaridis, T."]
+                , cit_type="Reference")
+            , Citation(title="Inhomogeneous fluid approach to solvation thermodynamics. 2. Applications to simple fluids"
+                , doi_url="https://doi.org/10.1021/jp972358w"
+                , journal="Journal of Physical Chemistry B"
+                , contributors=["Lazaridis, T."]
+                , cit_type="Reference")
+            , Citation(title="Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril"
+                , doi_url="https://doi.org/10.1063/1.4733951"
+                , journal="Journal of Chemical Physics"
+                , contributors=["Nguyen, C. N.","Young, T. K.","Gilson, M. K."]
+                , cit_type="Reference")
+            , Citation(title="AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking"
+                , doi_url="https://doi.org/10.3390/molecules21111604"
+                , journal="Molecules"
+                , contributors=["Uehara, S.","Tanaka, S."]
+                , cit_type="Reference")
+            , Citation(title="ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery"
+                , doi_url="https://doi.org/10.1021/acs.jcim.0c00675"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Irwin, J. J.","Tang, K. G.","Young, J.","Dandarchuluun, C.","Wong, B. R.","Khurelbaatar, M.","Moroz, Y. S.","Mayfield, J.","Sayle, R. A."]
+                , cit_type="Reference")
+            , Citation(title="Structural biology-inspired discovery of novel KRAS–PDEδ inhibitors"
+                , doi_url="https://doi.org/10.1021/acs.jmedchem.7b01243"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Jiang, Y.","Zhuang, C.","Chen, L.","Lu, J.","Dong, G.","Miao, Z.","Zhang, W.","Li, J.","Sheng, C."]
+                , cit_type="Reference")
+            , Citation(title="D3R grand challenge 2015: evaluation of protein–ligand pose and affinity predictions"
+                , doi_url="https://doi.org/10.1007/s10822-016-9946-8"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["Gathiaka, S.","Liu, S.","Chiu, M.","Yang, H.","Stuckey, J. A.","Kang, Y. N.","Delproposto, J.","Kubish, G.","Dunbar, J. B.","Carlson, H. A.","Burley, S. K.","Walters, W. P.","Amaro, R. E.","Feher, V. A.","Gilson, M. K."]
+                , cit_type="Reference")
+            , Citation(title="D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies"
+                , doi_url="https://doi.org/10.1007/s10822-020-00289-y"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["Parks, C. D.","Gaieb, Z.","Chiu, M.","Yang, H.","Shao, C.","Walters, W. P.","Jansen, J. M.","McGaughey, G.","Lewis, R. A.","Bembenek, S. D.","Ameriks, M. K.","Mirzadegan, T.","Burley, S. K.","Amaro, R. E.","Gilson, M. K."]
+                , cit_type="Reference")
+            , Citation(title="D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU"
+                , doi_url="https://doi.org/10.1007/s10822-019-00241-9"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["Santos-Martins, D.","Eberhardt, J.","Bianco, G.","Solis-Vasquez, L.","Ambrosio, F. A.","Koch, A.","Forli, S."]
+                , cit_type="Reference")
+            , Citation(title="Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4"
+                , doi_url="https://doi.org/10.1007/s10822-019-00240-w"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["El Khoury, L.","Santos-Martins, D.","Sasmal, S.","Eberhardt, J.","Bianco, G.","Ambrosio, F. A.","Solis-Vasquez, L.","Koch, A.","Forli, S.","Mobley, D. L."]
+                , cit_type="Reference")
+            , Citation(title="Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4"
+                , doi_url="https://doi.org/10.1007/s10822-019-00225-9"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["Lam, P. C.-H.","Abagyan, R.","Totrov, M."]
+                , cit_type="Reference")
+            , Citation(title="Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking"
+                , doi_url="https://doi.org/10.1021/jm300687e"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Mysinger, M. M.","Carchia, M.","Irwin, J. J.","Shoichet, B. K."]
+                , cit_type="Reference")
+            , Citation(title="Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark"
+                , doi_url="https://doi.org/10.1021/acs.jcim.8b00312"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Gaillard, T."]
+                , cit_type="Reference")
+            , Citation(title="Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity"
+                , doi_url="https://doi.org/10.1021/acs.jcim.9b00778"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Nguyen, N. T.","Nguyen, T. H.","Pham, T. N. H.","Huy, N. T.","Bay, M. V.","Pham, M. Q.","Nam, P. C.","Vu, V. V.","Ngo, S. T."]
+                , cit_type="Reference")
+            , Citation(title="Development and validation of a genetic algorithm for flexible docking"
+                , doi_url="https://doi.org/10.1006/jmbi.1996.0897"
+                , journal="Journal of Molecular Biology"
+                , contributors=["Jones, G.","Willett, P.","Glen, R. C.","Leach, A. R.","Taylor, R."]
+                , cit_type="Reference")
+            , Citation(title="Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy"
+                , doi_url="https://doi.org/10.1021/jm0306430"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Friesner, R. A.","Banks, J. L.","Murphy, R. B.","Halgren, T. A.","Klicic, J. J.","Mainz, D. T.","Repasky, M. P.","Knoll, E. H.","Shelley, M.","Perry, J. K."]
+                , cit_type="Reference")
+            , Citation(title="Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine"
+                , doi_url="https://doi.org/10.1021/jm020406h"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Jain, A. N."]
+                , cit_type="Reference")
+            , Citation(title="A fast flexible docking method using an incremental construction algorithm"
+                , doi_url="https://doi.org/10.1006/jmbi.1996.0477"
+                , journal="Journal of Molecular Biology"
+                , contributors=["Rarey, M.","Kramer, B.","Lengauer, T.","Klebe, G."]
+                , cit_type="Reference")
+            , Citation(title="EDock: blind protein–ligand docking by replica-exchange monte carlo simulation"
+                , doi_url="https://doi.org/10.1186/s13321-020-00440-9"
+                , journal="Journal of Cheminformatics"
+                , contributors=["Zhang, W.","Bell, E. W.","Yin, M.","Zhang, Y."]
+                , cit_type="Reference")
+            , Citation(title="DOCK 6: Impact of new features and current docking performance"
+                , doi_url="https://doi.org/10.1002/jcc.23905"
+                , journal="Journal of Computational Chemistry"
+                , contributors=["Allen, W. J.","Balius, T. E.","Mukherjee, S.","Brozell, S. R.","Moustakas, D. T.","Lang, P. T.","Case, D. A.","Kuntz, I. D.","Rizzo, R. C."]
+                , cit_type="Reference")
+            , Citation(title="Improving scoring-docking-screening powers of protein–ligand scoring functions using random forest"
+                , doi_url="https://doi.org/10.1002/jcc.24667"
+                , journal="Journal of Computational Chemistry"
+                , contributors=["Wang, C.","Zhang, Y."]
+                , cit_type="Reference")
+            , Citation(title="ID-Score: a new empirical scoring function based on a comprehensive set of descriptors related to protein–ligand interactions"
+                , doi_url="https://doi.org/10.1021/ci300493w"
+                , journal="Journal of Chemical Information and Modeling"
+                , contributors=["Li, G.-B.","Yang, L.-L.","Wang, W.-J.","Li, L.-L.","Yang, S.-Y."]
+                , cit_type="Reference")
+            , Citation(title="Further development and validation of empirical scoring functions for structure-based binding affinity prediction"
+                , doi_url="https://doi.org/10.1023/a:1016357811882"
+                , journal="Journal of Computer-Aided Molecular Design"
+                , contributors=["Wang, R.","Lai, L.","Wang, S."]
+                , cit_type="Reference")
+            , Citation(title="A knowledge-based energy function for protein- ligand, protein- protein, and protein- DNA complexes"
+                , doi_url="https://doi.org/10.1021/jm049314d"
+                , journal="Journal of Medicinal Chemistry"
+                , contributors=["Zhang, C.","Liu, S.","Zhu, Q.","Zhou, Y."]
+                , cit_type="Reference")
+            , Citation(title="DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state"
+                , doi_url="https://doi.org/10.1186/s13321-019-0373-4"
+                , journal="Journal of Cheminformatics"
+                , contributors=["Chen, P.","Ke, Y.","Lu, Y.","Du, Y.","Li, J.","Yan, H.","Zhao, H.","Zhou, Y.","Yang, Y."]
+                , cit_type="Reference")
+            , Citation(title="Comparing AutoDock and Vina in ligand/decoy discrimination for virtual screening"
+                , doi_url="https://doi.org/10.3390/app9214538"
+                , journal="Applied Science"
+                , contributors=["Vieira, T. F.","Sousa, S. F."]
+                , cit_type="Reference")
+            , Citation(title="Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance"
+                , doi_url="https://doi.org/10.1186/s13321-016-0167-x"
+                , journal="Journal of Cheminformatics"
+                , contributors=["Chaput, L.","Martinez-Sanz, J.","Quiniou, E.","Rigolet, P.","Saettel, N.","Mouawad, L."]
+                , cit_type="Reference")
+            , Citation(title="Array programming with NumPy"
+                , doi_url="https://doi.org/10.1038/s41586-020-2649-2"
+                , journal="Nature"
+                , contributors=["Harris, C. R."]
+                , cit_type="Reference")
+            , Citation(title="Matplotlib: A 2D graphics environment"
+                , doi_url="https://doi.org/10.1109/mcse.2007.55"
+                , journal="Computing in Science & Engineering"
+                , contributors=["Hunter, J. D."]
+                , cit_type="Reference")
+           ], citations = [
+            Citation(doi_url = "https://doi.org/10.1021/acsomega.1c04320"
+            , title ="Novel Anti-Hepatitis B Virus Activity of Euphorbia schimperi and Its Quercetin and Kaempferol Derivatives"
+            , journal="ACS Omega"
+            , contributors=["Mohammad K. Parvez","Sarfaraz Ahmed","Mohammed S. Al-Dosari","Mazin A. S. Abdelwahid","Ahmed H. Arbab","Adnan J. Al-Rehaily","Mai M. Al-Oqail"],cit_type="Citation"),
+           
+           ]
+       )
+    }
\ No newline at end of file

input/test/test_input.py

+import unittest
+from input.get.journal_fetcher import JournalFetcher
+from input.interface import InputInterface
+from input.publication import Publication
+
+"""
+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
+"""
+# TODO: Testcases for:
+#       - Specific Journals: Inherit from FetcherTestCase
+#       - interface module-importer (test case)
+#       - Error detection
+#           - wrong/no Journal_fetchers
+#           - wrong urls
+#           - correct Types in publication
+#       - Edgecases (i.e. paper as pdf, no connection, etc)
+
+
+class InterfaceTestCase(unittest.TestCase):
+    def setUp(self):
+        self.assertEqual(InputInterface.instance, None)
+        self.interface = InputInterface()
+
+    def test_singleton(self):
+        # interface should already be made in setUp()
+        self.assertNotEqual(self.interface.instance, None)
+        new_interface = InputInterface()
+        self.assertEqual(self.interface, new_interface)
+    
+    # def test_imported_modules(self):
+    #    fetchers = self.interface.get_supported_fetchers
+
+class FetcherTestCase(unittest.TestCase):
+
+
+    def can_use_url_test(self, fetcher : JournalFetcher, test_url: str, expected_res: bool):
+        # Tests the 'can_use_url'-method
+        self.assertEqual(fetcher.can_use_url(test_url), expected_res)
+
+
+    def get_publication_test(self, fetcher : JournalFetcher, test_url: str, expected_res: Publication):
+        """
+        this test asserts that every variable is equals to the expected result
+        """
+        actual_res = fetcher.get_publication(test_url)
+        self.assertEqual(actual_res.doi_url, expected_res.doi_url)
+        self.assertEqual(actual_res.title, expected_res.title)
+        self.assertEqual(actual_res.contributors, expected_res.contributors)
+        self.assertEqual(actual_res.journal, expected_res.journal)
+        self.assertEqual(actual_res.publication_date, expected_res.publication_date)
+        self.assertEqual(actual_res.subjects, expected_res.subjects)
+
+        # Checking for all references
+        self.assertEqual(len(actual_res.references), len(expected_res.references))
+        num_references = len(expected_res.references)
+        for i in range(num_references):
+            self.assertEqual(actual_res.references[i].doi_url,      expected_res.references[i].doi_url)
+            self.assertEqual(actual_res.references[i].journal,      expected_res.references[i].journal)
+            self.assertEqual(actual_res.references[i].contributors, expected_res.references[i].contributors)
+            self.assertEqual(actual_res.references[i].cit_type,     expected_res.references[i].cit_type)
+
+        # Checking for all citations
+        self.assertEqual(len(actual_res.citations), len(expected_res.citations))
+        num_citations = len(expected_res.citations)
+        for i in range(num_citations):
+            self.assertEqual(actual_res.citations[i].doi_url,      expected_res.citations[i].doi_url)
+            self.assertEqual(actual_res.citations[i].journal,      expected_res.citations[i].journal)
+            self.assertEqual(actual_res.citations[i].contributors, expected_res.citations[i].contributors)
+            self.assertEqual(actual_res.citations[i].cit_type,     expected_res.citations[i].cit_type)
+
+
+    def get_publication_exception_test(self, fetcher: JournalFetcher, test_url: str):
+        # Ckecks 
+        with self.assertRaises(ValueError):
+            fetcher.get_publication(test_url)
\ No newline at end of file

input_old/README.md

+# Projekt CiS-Projekt 2021/22
+Input-Skripts
+

input_old/example_urls

+https://pubs.acs.org/doi/10.1021/acs.jcim.5b00332
+https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709

input/input_fj.py → input_old/input_fj.py

@@ -21,9 +21,10 @@ from pathlib import Path
 class Publication:
     #_registry = []
     _citations = []
+    _references = []
     
     def __init__(self, title, publication_date, contributors, doi_url, 
-                 subjects, num_citations):
+                 subjects = None, num_citations = None):
         #self._registry.append(self)
         self.title = title
         self.publication_date = publication_date
@@ -31,6 +32,8 @@ class Publication:
         self.doi_url = doi_url
         self.subjects = subjects
         self.num_citations = num_citations
+        #self._citations = []
+        #self._references = []
 
 class Citation:
     def __init__(self, title, journal, contributors, doi_url):
@@ -39,6 +42,13 @@ class Citation:
         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
+    
 def get_article_info(soup):
     header = soup.find('div', class_ = 'article_header-left pull-left')
     article_title = header.find('span', class_ = 'hlFld-Title').text