I want to scrape sample_info.csv file from https://depmap.org/portal/download/.
Since there is a React script on the website it's not that straightforward with BeautifulSoup and accessing the file via an appropriate tag. I did approach this from many angles and the one that gave me the best results looks like this and it returns the executed script where all downloaded files are listed together with other data. My then idea was to strip the tags and store the information in JSON. However, I think there must be some kind of mistake in the data because it is impossible to store it as JSON.
url = 'https://depmap.org/portal/download/'
html_content = requests.get(url).text
soup = BeautifulSoup(html_content, "lxml")
all_scripts = soup.find_all('script')
script = str(all_scripts[32])
last_char_index = script.rfind("}]")
first_char_index = script.find("[{")
script_cleaned = script[first_char_index:last_char_index+2]
script_json = json.loads(script_cleaned)
This code gives me an error
JSONDecodeError: Extra data: line 1 column 7250 (char 7249)
I know that my solution might not be elegant but it took me closest to the goal i.e. downloading the sample_info.csv file from the website. Not sure how to proceed here. If there are other options? I tried with selenium but this solution will not be feasible for the end-user of my script due to the driver path declaration
It is probably easier in this context to use regular expressions, since the string is invalid JSON.
This RegEx tool (https://pythex.org/) can be useful for testing expressions.
import re
re.findall(r'"downloadUrl": "(.*?)".*?"fileName": "(.*?)"', script_cleaned)
#[
# ('https://ndownloader.figshare.com/files/26261524', 'CCLE_gene_cn.csv'),
# ('https://ndownloader.figshare.com/files/26261527', 'CCLE_mutations.csv'),
# ('https://ndownloader.figshare.com/files/26261293', 'Achilles_gene_effect.csv'),
# ('https://ndownloader.figshare.com/files/26261569', 'sample_info.csv'),
# ('https://ndownloader.figshare.com/files/26261476', 'CCLE_expression.csv'),
# ('https://ndownloader.figshare.com/files/17741420', 'primary_replicate_collapsed_logfold_change_v2.csv'),
# ('https://gygi.med.harvard.edu/publications/ccle', 'protein_quant_current_normalized.csv'),
# ('https://ndownloader.figshare.com/files/13515395', 'D2_combined_gene_dep_scores.csv')
# ]
Edit: This also works by passing the html_content directly (no need to BeautifulSoup).
url = 'https://depmap.org/portal/download/'
html_content = requests.get(url).text
re.findall(r'"downloadUrl": "(.*?)".*?"fileName": "(.*?)"', html_content)
Related
I have very basic knowledge of python, so sorry if my question sounds dumb.
I need to query a website for a personal project I am doing, but I need to query it 500 times, and each time I need to change 1 specific part of the url, then take the data and upload it to gsheets.
(The () signifies what part of the url I need to change)
'https://www.alphavantage.co/query?function=BALANCE_SHEET&symbol=(symbol)&apikey=apikey'
I thought about using while and format {} to do it, but I was unsure how to change the string each time, bar writing out the names for variables by hand (defeating the whole purpose of this).
I already have a list of the symbols I need to use, but I don't know how to input them
Example of how I get 1 piece of data
import requests
url = 'https://www.alphavantage.co/query?function=BALANCE_SHEET&symbol=MMM&apikey=demo'
r = requests.get(url)
data = r.json()
Example of what I'd like to change it to
import requests
url = 'https://www.alphavantage.co/query?function=BALANCE_SHEET&symbol=AOS&apikey=demo'
r = requests.get(url)
data = r.json()
#then change it to
import requests
url = 'https://www.alphavantage.co/query?function=BALANCE_SHEET&symbol=ABT&apikey=demo'
r = requests.get(url)
data = r.json()
so on and so forth, 500 times.
You might combine .format with for loop, consider following simple example
symbols = ["abc","xyz","123"]
for s in symbols:
url = 'https://www.example.com?symbol={}'.format(s)
print(url)
output
https://www.example.com?symbol=abc
https://www.example.com?symbol=xyz
https://www.example.com?symbol=123
You might also elect to use any other way of formatting, e.g. f-string (requires python3.6 or newer) in which case code would be
symbols = ["abc","xyz","123"]
for s in symbols:
url = f'https://www.example.com?symbol={s}'
print(url)
Alternatively you might params optional argument of requests.get function as follows
import requests
symbols = ["abc","xyz","123"]
for s in symbols:
r = requests.get('https://www.example.com', params={'symbol':s})
print(r.url)
output
https://www.example.com/?symbol=abc
https://www.example.com/?symbol=xyz
https://www.example.com/?symbol=123
I've been tinkering with Python using Pythonista on my iPad. I decided to write a simple script that pulls song lyrics in Japanese from one website, and makes post requests to another website that basically annotates the lyrics with extra information.
When I use Python 2 and the module mechanize for the second website, everything works fine, but when I use Python 3 and requests, the resulting text is nonsense.
This is a minimal script that doesn't exhibit the issue:
#!/usr/bin/env python2
from bs4 import BeautifulSoup
import requests
import mechanize
def main():
# Get lyrics from first website (lyrical-nonsense.com)
url = 'https://www.lyrical-nonsense.com/lyrics/bump-of-chicken/hello-world/'
html_raw_lyrics = BeautifulSoup(requests.get(url).text, "html5lib")
raw_lyrics = html_raw_lyrics.find("div", id="Lyrics").get_text()
# Use second website to anotate lyrics with fugigana
browser = mechanize.Browser()
browser.open('http://furigana.sourceforge.net/cgi-bin/index.cgi')
browser.select_form(nr=0)
browser.form['text'] = raw_lyrics
request = browser.submit()
# My actual script does more stuff at this point, but this snippet doesn't need it
annotated_lyrics = BeautifulSoup(request.read().decode('utf-8'), "html5lib").find("body").get_text()
print annotated_lyrics
if __name__ == '__main__':
main()
The truncated output is:
扉(とびら)開(ひら)けば捻(ねじ)れた昼(ひる)の夜(よる)昨日(きのう)どうやって帰(かえ)った体(からだ)だけが確(たし)かおはよう これからまた迷子(まいご)の続(つづ)き見慣(みな)れた知(し)らない景色(けしき)の中(なか)でもう駄目(だめ)って思(おも)ってから わりと何(なん)だかやれている死(し)にきらないくらいに丈夫(じょうぶ)何(なに)かちょっと恥(は)ずかしいやるべきことは忘(わす)れていても解(わか)るそうしないと とても苦(くる)しいから顔(かお)を上(あ)げて黒(くろ)い目(め)の人(にん)君(くん)が見(み)たから光(ひかり)は生(う)まれた選(えら)んだ色(しょく)で塗(ぬ)った世界(せかい)に [...]
This is a minimal script that exhibits the issue:
#!/usr/bin/env python3
from bs4 import BeautifulSoup
import requests
def main():
# Get lyrics from first website (lyrical-nonsense.com)
url = 'https://www.lyrical-nonsense.com/lyrics/bump-of-chicken/hello-world/'
html_raw_lyrics = BeautifulSoup(requests.get(url).text, "html5lib")
raw_lyrics = html_raw_lyrics.find("div", id="Lyrics").get_text()
# Use second website to anotate lyrics with fugigana
url = 'http://furigana.sourceforge.net/cgi-bin/index.cgi'
data = {'text': raw_lyrics, 'state': 'output'}
html_annotated_lyrics = BeautifulSoup(requests.post(url, data=data).text, "html5lib")
annotated_lyrics = html_annotated_lyrics.find("body").get_text()
print(annotated_lyrics)
if __name__ == '__main__':
main()
whose truncated output is:
IQp{_<n(åiFcf0c_S`QLºKJoFSK~_÷PnMc_åjDorn-gFÄîcfcfKhU`KfD{kMjDOD+UKacheZKWDyMSho،fDfã]FWjDhhfæWDKTRfÒDînºL_KIo~_x`rgWc_Lkò~fxyjD·nsoiS`FTê`QLÒüíüLn [...]
It's worth noting that if I just try to get the HTML of the second request, like so:
# Use second website to anotate lyrics with fugigana
url = 'http://furigana.sourceforge.net/cgi-bin/index.cgi'
data = {'text': raw_lyrics, 'state': 'output'}
annotated_lyrics = requests.post(url, data=data).content.decode('utf-8')
A embedded null character error occurs when printing annotated_lyrics. This issue can be circumvented by passing truncated lyrics to the post requests. In the current example, only one character can be passed.
However, with
url = 'https://www.lyrical-nonsense.com/lyrics/aimer/brave-shine/'
I can pass up to 51 characters, like so:
data = {'text': raw_lyrics[0:51], 'state': 'output'}
before triggering the embedded null character error.
I've tried using urllib instead of requests, decoding and encoding to utf-8 the resulting HTML of the post request, or the data passed as an argument to this request. I've also checked that the encoding of the website is utf-8, which matches the encoding of the post requests:
r = requests.post(url, data=data)
print(r.encoding)
prints utf-8.
I think the problem has to do with how Python 3 is more strict in how it treats strings vs bytes, but I've been unable to pinpoint the exact cause.
While I'd appreciate a working code sample in Python 3, I'm more interested in what exactly I'm doing wrong, in what is the code doing that results in failure.
I'm able to get the lyrics properly with this code in python3.x:
url = 'https://www.lyrical-nonsense.com/lyrics/bump-of-chicken/hello-world/'
resp = requests.get(url)
print(BeautifulSoup(resp.text).find('div', class_='olyrictext').get_text())
Printing (truncated)
>>> BeautifulSoup(resp.text).find('div', class_='olyrictext').get_text()
'扉開けば\u3000捻れた昼の夜\r\n昨日どうやって帰った\u3000体だけ...'
A few things strike me as odd there, notably the \r\n (windows line ending) and \u3000 (IDEOGRAPHIC SPACE) but that's probably not the problem
The one thing I noticed that's odd about the form submission (and why the browser emulator probably succeeds) is the form is using multipart instead of urlencoded form data. (signified by enctype="multipart/form-data")
Sending multipart form data is a little bit strange in requests, I had to poke around a bit and eventually found this which helps show how to format the multipart data in a way that the backing server understands. To do this you have to abuse files but have a "None" filename. "for humans" hah!
url2 = 'http://furigana.sourceforge.net/cgi-bin/index.cgi'
resp2 = requests.post(url2, files={'text': (None, raw_lyrics), 'state': (None, 'output')})
And the text is not mangled now!
>>> BeautifulSoup(resp2.text).find('body').get_text()
'\n扉(とびら)開(ひら)けば捻(ねじ)れた昼(ひる)...'
(Note that this code should work in either python2 or python3)
I'm new to Python, just get started with it today.
My system environment are Python 3.5 with some libraries on Windows10.
I want to extract football player data from site below as CSV file.
Problem: I can not extract data from soup.find_all('script')[17] to my expected CSV format. How to extract those data as I want ?
My code is shown as below.
from bs4 import BeautifulSoup
import re
from urllib.request import Request, urlopen
req = Request('http://www.futhead.com/squad-building-challenges/squads/343', headers={'User-Agent': 'Mozilla/5.0'})
webpage = urlopen(req).read()
soup = BeautifulSoup(webpage,'html.parser') #not sure if i need to use lxml
soup.find_all('script')[17] #My target data is in 17th
My expected output would be similar to this
position,slot_position,slug
ST,ST,paulo-henrique
LM,LM,mugdat-celik
As #josiah Swain said, it's not going to be pretty. For this sort of thing it's more recommended to use JS as it can understand what you have.
Saying that, python is awesome and here is you solution!
#Same imports as before
from bs4 import BeautifulSoup
import re
from urllib.request import Request, urlopen
#And one more
import json
# The code you had
req = Request('http://www.futhead.com/squad-building-challenges/squads/343',
headers={'User-Agent': 'Mozilla/5.0'})
webpage = urlopen(req).read()
soup = BeautifulSoup(webpage,'html.parser')
# Store the script
script = soup.find_all('script')[17]
# Extract the oneline that stores all that JSON
uncleanJson = [line for line in script.text.split('\n')
if line.lstrip().startswith('squad.register_players($.parseJSON') ][0]
# The easiest way to strip away all that yucky JS to get to the JSON
cleanJSON = uncleanJson.lstrip() \
.replace('squad.register_players($.parseJSON(\'', '') \
.replace('\'));','')
# Extract out that useful info
data = [ [p['position'],p['data']['slot_position'],p['data']['slug']]
for p in json.loads(cleanJSON)
if p['player'] is not None]
print('position,slot_position,slug')
for line in data:
print(','.join(line))
The result I get for copying and pasting this into python is:
position,slot_position,slug
ST,ST,paulo-henrique
LM,LM,mugdat-celik
CAM,CAM,soner-aydogdu
RM,RM,petar-grbic
GK,GK,fatih-ozturk
CDM,CDM,eray-ataseven
LB,LB,kadir-keles
CB,CB,caner-osmanpasa
CB,CB,mustafa-yumlu
RM,RM,ioan-adrian-hora
GK,GK,bora-kork
Edit: On reflection this is not the easiest code to read for a beginner. Here is a easier to read version
# ... All that previous code
script = soup.find_all('script')[17]
allScriptLines = script.text.split('\n')
uncleanJson = None
for line in allScriptLines:
# Remove left whitespace (makes it easier to parse)
cleaner_line = line.lstrip()
if cleaner_line.startswith('squad.register_players($.parseJSON'):
uncleanJson = cleaner_line
cleanJSON = uncleanJson.replace('squad.register_players($.parseJSON(\'', '').replace('\'));','')
print('position,slot_position,slug')
for player in json.loads(cleanJSON):
if player['player'] is not None:
print(player['position'],player['data']['slot_position'],player['data']['slug'])
So my understanding is that beautifulsoup is better for HTML parsing, but you are trying to parse javascript nested in the HTML.
So you have two options
Simply create a function that takes the result of soup.find_all('script')[17], loop and search the string manually for the data and extract it. You can even use ast.literal_eval(string_thats_really_a_dictionary) to make it even easier. This is may not be the best a approach but if you are new to python you might want to do it this just for practice.
Use the json library like in this example. or alternatively like this way. This is probably the better way to do.
I'm currently working on an arcbot and I'm trying to make a command "!urbandictionary", it should scrape the meaning of a term, the first one which is provided by urbandictionary, if there's another solution, e.g. another dictionary site with a better api that's also good. Here's my code:
if Command.lower() == '!urban':
dictionary = Argument[1] #this is the term which the user provides, e.g. "scrape"
dictionaryscrape = urllib2.urlopen('http://www.urbandictionary.com/define.php?term='+dictionary).read() #plain html of the site
scraped = getBetweenHTML(dictionaryscrape, '<div class="meaning">','</div>') #Here's my problem, i'm not sure if it scrapes the first meaning or not..
messages.main(scraped,xSock,BotID) #Sends the meaning of the provided word (Argument[0])
How do I correctly scrape a meaning of a word in urbandictionary?
Just get the text from the meaning class:
import requests
from bs4 import BeautifulSoup
word = "scrape"
r = requests.get("http://www.urbandictionary.com/define.php?term={}".format(word))
soup = BeautifulSoup(r.content)
print(soup.find("div",attrs={"class":"meaning"}).text)
Gassing and breaking your car repeatedly really fast so that the front and rear bumpers "scrape" the pavement; while going hyphy
There is an unofficial api here apparently
`http://api.urbandictionary.com/v0/define?term={word}`
From https://github.com/zdict/zdict/wiki/Urban-dictionary-API-documentation
So I have a data retrieval/entry project and I want to extract a certain part of a webpage and store it in a text file. I have a text file of urls and the program is supposed to extract the same part of the page for each url.
Specifically, the program copies the legal statute following "Legal Authority:" on pages such as this. As you can see, there is only one statute listed. However, some of the urls also look like this, meaning that there are multiple separated statutes.
My code works for pages of the first kind:
from sys import argv
from urllib2 import urlopen
script, urlfile, legalfile = argv
input = open(urlfile, "r")
output = open(legalfile, "w")
def get_legal(page):
# this is where Legal Authority: starts in the code
start_link = page.find('Legal Authority:')
start_legal = page.find('">', start_link+1)
end_link = page.find('<', start_legal+1)
legal = page[start_legal+2: end_link]
return legal
for line in input:
pg = urlopen(line).read()
statute = get_legal(pg)
output.write(get_legal(pg))
Giving me the desired statute name in the "legalfile" output .txt. However, it cannot copy multiple statute names. I've tried something like this:
def get_legal(page):
# this is where Legal Authority: starts in the code
end_link = ""
legal = ""
start_link = page.find('Legal Authority:')
while (end_link != '</a> '):
start_legal = page.find('">', start_link+1)
end_link = page.find('<', start_legal+1)
end2 = page.find('</a> ', end_link+1)
legal += page[start_legal+2: end_link]
if
break
return legal
Since every list of statutes ends with '</a> ' (inspect the source of either of the two links) I thought I could use that fact (having it as the end of the index) to loop through and collect all the statutes in one string. Any ideas?
I would suggest using BeautifulSoup to parse and search your html. This will be much easier than doing basic string searches.
Here's a sample that pulls all the <a> tags found within the <td> tag that contains the <b>Legal Authority:</b> tag. (Note that I'm using requests library to fetch page content here - this is just a recommended and very easy to use alternative to urlopen.)
import requests
from BeautifulSoup import BeautifulSoup
# fetch the content of the page with requests library
url = "http://www.reginfo.gov/public/do/eAgendaViewRule?pubId=200210&RIN=1205-AB16"
response = requests.get(url)
# parse the html
html = BeautifulSoup(response.content)
# find all the <a> tags
a_tags = html.findAll('a', attrs={'class': 'pageSubNavTxt'})
def fetch_parent_tag(tags):
# fetch the parent <td> tag of the first <a> tag
# whose "previous sibling" is the <b>Legal Authority:</b> tag.
for tag in tags:
sibling = tag.findPreviousSibling()
if not sibling:
continue
if sibling.getText() == 'Legal Authority:':
return tag.findParent()
# now, just find all the child <a> tags of the parent.
# i.e. finding the parent of one child, find all the children
parent_tag = fetch_parent_tag(a_tags)
tags_you_want = parent_tag.findAll('a')
for tag in tags_you_want:
print 'statute: ' + tag.getText()
If this isn't exactly what you needed to do, BeautifulSoup is still the tool you likely want to use for sifting through html.
They provide XML data over there, see my comment. If you think you can't download that many files (or the other end could dislike so many HTTP GET requests), I'd recommend asking their admins if they would kindly provide you with a different way of accessing the data.
I have done so twice in the past (with scientific databases). In one instance the sheer size of the dataset prohibited a download; they ran a SQL query of mine and e-mailed the results (but had previously offered to mail a DVD or hard disk). In another case, I could have done some million HTTP requests to a webservice (and they were ok) each fetching about 1k bytes. This would have taken long, and would have been quite inconvenient (requiring some error-handling, since some of these requests would always time out) (and non-atomic due to paging). I was mailed a DVD.
I'd imagine that the Office of Management and Budget could possibly be similar accomodating.