def __init__(self, root_directory):

# saves current directory in a string

self.root_directory = root_directory

self.start_time = Timer.timeNow()

self.end_time = Timer.timeNow()

self.manager = None

self.list_authors: List[Autor] = []

self.list_articles: List[Artigo] = []

self.input_search = ''

self.input_pages = 0

self.gui = None

self.index_progress_bar = 1

def update_search_parameters(self, input_search, input_pages):

self.input_search = input_search

self.input_pages = input_pages

# extract the type of the article from the BibText cite text and returns it as a single word string

# TODO: extract it from "publicationTypes" attribute

def return_type_cite(self, string_cite):

list_cite = string_cite.split('{')

type_cite = list_cite[0][1:]

return type_cite

def start_search(self):

self.start_time = Timer.timeNow()

# loads files for the inputted search if they exist, otherwise, the files are created

self.manager = Gerenciador(self.input_search, self.root_directory)

self.list_authors = self.manager.loadAutores()

self.list_articles = set(self.manager.loadArtigos())

# runs the following code 3 times, one for each type os search

# for k in range(0, 2):

# TODO: replicate old functionality with API,

# i.e., search in different ways.

for k in range(0,2):

# label gui

self.gui.app.queueFunction(self.gui.app.setLabel, 'progress_bar_label', 'Crawling with '

+ str(k+1) + '/2 parameter...')

# + str(k+1) + '/3 parameter...')

#self.gui.app.queueFunction(self.gui.app.setMeter, 'progress_bar', 0)

# access switched to api calls,

# input now sent directly via request url,

# with extra whitespace striped

_search_query = re.sub(r"\s+", " ", self.input_search.strip())

_article_count = self.input_pages

_articles_query_params = {

"query": _search_query,

"fields": "abstract,authors,citationCount,citationStyles,title,url,venue,year",

"offset": 0,

"limit": _article_count

}

if k == 1:

_articles_query_params["year"] = str(datetime.date.today().year - 5) + '-'

# TODO: model expected JSON object types

# e.g., search :: String -> [Paper]

# Paper :: { title: String, Author: Author, ...}

_articles_endpoint = 'https://api.semanticscholar.org/graph/v1/paper/search'

with requests.get(_articles_endpoint, params=_articles_query_params) as articles_res:

_articles_res = articles_res.json()

# search for now happens only once

# TODO: mimic the old behavior,

# i.e., searching with different filters applied:

# results from the last five years;

# results with Reviews marked.

# runs the code for the amount of articles desired

self.index_progress_bar = 1

# no need for pagination yet,

# as number of articles is explicitly set,

# in API request.

# TODO: sync progress bar to other inputs,

# previously was number of pages crawled.

# for pag in range(0, self.input_pages):

# progress bar

# self.gui.app.queueFunction(self.gui.app.setMeter, 'progress_bar',

# (100 * self.index_progress_bar)/self.input_pages)

# self.index_progress_bar += 1

# from API response,

# iterates over each article in the articles list

if "data" in _articles_res.keys():

for item in _articles_res["data"]:

# now takes it directly from JSON

# saves the article title as a string

title = item["title"]

# now authors field is present in API response

_paper_authors = item["authors"]

# TODO: get html links for authors who have it,

# probably will require another API call.

# creates a set list of the authors for the article

list_authors_in_article: Set[Autor] = set()

self.list_authors = set(self.list_authors)

# iterates over each author in the list.

for temp in _paper_authors:

# author name now comes in "name" field

name = temp["name"]

# saves the author name as a string

# no link comes with author from Papers API

# TODO: fetch their link somehow.

link = None

# saves the author page html link as a string

# creates temporary author

author = Autor(name, link)

# adds new authors to the set lists

self.list_authors.add(author)

list_authors_in_article.add(author)

self.list_authors = list(self.list_authors)

self.list_authors.sort()

list_authors_in_article = list(list_authors_in_article)

list_authors_in_article.sort()

# origin comes as "venue" in API response.

_venue = item["venue"]

origin = _venue if _venue else "-"

# saves the article origin as a string

# TODO: log when field comes empty,

# print paper id, field name and its value.

# date comes as "year" in API response.

_year = item["year"]

# TODO: log when field comes empty,

# print paper id, field name and its value.

date = str(_year) if _year else "0"

# saves the article date as a string

# citationCount comes as a number in API response.

_citationCount = item["citationCount"]

citationCount = str(int(_citationCount if _citationCount else "0"))

# saves the article total citations as a string

# TODO: log when field comes empty,

# print paper id, field name and its value.

# link comes as "url" in API response.

_url = item["url"]

link = _url if _url else "-"

# saves the article html link as a string

# TODO: log when field comes empty,

# print paper id, field name and its value.

# currently no type comes in API response.

_citationStyles = item["citationStyles"]

_bibtex = _citationStyles["bibtex"] if _citationStyles else _citationStyles

bibtex = '-'

cite = '-'

if _bibtex:

bibtex = _bibtex

# TODO: format bibtex,

# it comes in a weird list-like style,

# e.g., @["Journal Article", "Review"]{...}

cite = self.return_type_cite(bibtex)

# saves the article type as a string

# TODO: get type from "publicationTypes" field.

# synopsis comes as "abstract" in API response.

_abstract = item["abstract"]

synopsis = _abstract.replace(" Expand", "") if _abstract else "No synopsis"

synopsis = synopsis.replace("TLDR\n", "")

qualis_score = find_similar_journal(target_text=origin)

# creates a new instance of a Article object

new_article = Artigo(title, list_authors_in_article, origin, date,

citationCount, link, cite, bibtex, synopsis, qualis_score)

# adds new article to set list (set list does not allow duplicates)

before = len(self.list_articles)

self.list_articles.add(new_article)

after = len(self.list_articles)

# add article to the author's article list if the article is not repeated

if before is not after:

for autorTemp in list_authors_in_article:

autorTemp.addArtigo(new_article)

# no need to switch pages when using API.

# TODO: add pagination to API calls.

else:

print("From Semantic Scholar API:", file=sys.stderr)

for k in _articles_res.keys():

print(k, ": ", _articles_res[k], sep="", file=sys.stderr)

self.end_time = Timer.timeNow()

self.list_articles = list(self.list_articles)

# saves the list of articles and authors as .pkl files

self.list_authors = list(self.list_authors)

self.manager.saveArtigos(self.list_articles)

self.manager.saveAutores(self.list_authors)

self.gui.show_search_done_alert(Timer.totalTime(self.start_time, self.end_time), str(len(self.list_articles)))

def saves_excel(self, parameter):

# creates the excel file

os.chdir(self.root_directory)

excelExporter = ExcelExporter(self.input_search, self.gui.single_or_merge, self.root_directory)

excelExporter.gui = self.gui

excelExporter.order_type(parameter)