partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | RcaApp.get_ball_by_ball | match_key: key of the match
over_key : key of the over
Return:
json data: | src/pycricket.py | def get_ball_by_ball(self, match_key, over_key=None):
"""
match_key: key of the match
over_key : key of the over
Return:
json data:
"""
if over_key:
ball_by_ball_url = "{base_path}match/{match_key}/balls/{over_key}/".format(base_path=self.... | def get_ball_by_ball(self, match_key, over_key=None):
"""
match_key: key of the match
over_key : key of the over
Return:
json data:
"""
if over_key:
ball_by_ball_url = "{base_path}match/{match_key}/balls/{over_key}/".format(base_path=self.... | [
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train | RcaApp.get_recent_season_matches | Calling specific season recent matches.
Arg:
season_key: key of the season.
Return:
json date | src/pycricket.py | def get_recent_season_matches(self, season_key):
"""
Calling specific season recent matches.
Arg:
season_key: key of the season.
Return:
json date
"""
season_recent_matches_url = self.api_path + "season/" + season_key + "/recent_matches/"
r... | def get_recent_season_matches(self, season_key):
"""
Calling specific season recent matches.
Arg:
season_key: key of the season.
Return:
json date
"""
season_recent_matches_url = self.api_path + "season/" + season_key + "/recent_matches/"
r... | [
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"matches",
"."
] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L235-L247 | [
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train | RcaApp.get_recent_seasons | Calling the Recent Season API.
Return:
json data | src/pycricket.py | def get_recent_seasons(self):
"""
Calling the Recent Season API.
Return:
json data
"""
recent_seasons_url = self.api_path + "recent_seasons/"
response = self.get_response(recent_seasons_url)
return response | def get_recent_seasons(self):
"""
Calling the Recent Season API.
Return:
json data
"""
recent_seasons_url = self.api_path + "recent_seasons/"
response = self.get_response(recent_seasons_url)
return response | [
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] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L249-L259 | [
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] | fa47fe2e92915fc58db38898213e974742af55d4 |
train | RcaApp.get_schedule | Calling the Schedule API.
Return:
json data | src/pycricket.py | def get_schedule(self, date=None):
"""
Calling the Schedule API.
Return:
json data
"""
schedule_url = self.api_path + "schedule/"
params = {}
if date:
params['date'] = date
response = self.get_response(schedule_url, params)
... | def get_schedule(self, date=None):
"""
Calling the Schedule API.
Return:
json data
"""
schedule_url = self.api_path + "schedule/"
params = {}
if date:
params['date'] = date
response = self.get_response(schedule_url, params)
... | [
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"."
] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L261-L274 | [
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train | RcaApp.get_season_schedule | Calling specific season schedule
Arg:
season_key: key of the season
Return:
json data | src/pycricket.py | def get_season_schedule(self, season_key):
"""
Calling specific season schedule
Arg:
season_key: key of the season
Return:
json data
"""
schedule_url = self.api_path + "season/" + season_key + "/schedule/"
response = self.get_response(sched... | def get_season_schedule(self, season_key):
"""
Calling specific season schedule
Arg:
season_key: key of the season
Return:
json data
"""
schedule_url = self.api_path + "season/" + season_key + "/schedule/"
response = self.get_response(sched... | [
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] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L276-L288 | [
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train | RcaApp.get_season | Calling Season API.
Arg:
season_key: key of the season
card_type: optional, default to micro_card. Accepted values are
micro_card & summary_card
Return:
json data | src/pycricket.py | def get_season(self, season_key, card_type="micro_card"):
"""
Calling Season API.
Arg:
season_key: key of the season
card_type: optional, default to micro_card. Accepted values are
micro_card & summary_card
Return:
json data
"""
... | def get_season(self, season_key, card_type="micro_card"):
"""
Calling Season API.
Arg:
season_key: key of the season
card_type: optional, default to micro_card. Accepted values are
micro_card & summary_card
Return:
json data
"""
... | [
"Calling",
"Season",
"API",
"."
] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L290-L306 | [
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... | fa47fe2e92915fc58db38898213e974742af55d4 |
train | RcaApp.get_season_stats | Calling Season Stats API.
Arg:
season_key: key of the season
Return:
json data | src/pycricket.py | def get_season_stats(self, season_key):
"""
Calling Season Stats API.
Arg:
season_key: key of the season
Return:
json data
"""
season_stats_url = self.api_path + "season/" + season_key + "/stats/"
response = self.get_response(season_stats_u... | def get_season_stats(self, season_key):
"""
Calling Season Stats API.
Arg:
season_key: key of the season
Return:
json data
"""
season_stats_url = self.api_path + "season/" + season_key + "/stats/"
response = self.get_response(season_stats_u... | [
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train | RcaApp.get_season_team | Calling Season teams API
Arg:
season_key: key of the season
Return:
json data | src/pycricket.py | def get_season_team(self, season_key, season_team_key,stats_type=None):
"""
Calling Season teams API
Arg:
season_key: key of the season
Return:
json data
"""
params = {"stats_type": stats_type}
season_team_url = self.api_path + 'season/' +... | def get_season_team(self, season_key, season_team_key,stats_type=None):
"""
Calling Season teams API
Arg:
season_key: key of the season
Return:
json data
"""
params = {"stats_type": stats_type}
season_team_url = self.api_path + 'season/' +... | [
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] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L322-L334 | [
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train | RcaApp.get_season_points | Calling Season Points API.
Arg:
season_key: key of the season
Return:
json data | src/pycricket.py | def get_season_points(self, season_key):
"""
Calling Season Points API.
Arg:
season_key: key of the season
Return:
json data
"""
season_points_url = self.api_path + "season/" + season_key + "/points/"
response = self.get_response(season_poi... | def get_season_points(self, season_key):
"""
Calling Season Points API.
Arg:
season_key: key of the season
Return:
json data
"""
season_points_url = self.api_path + "season/" + season_key + "/points/"
response = self.get_response(season_poi... | [
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train | RcaApp.get_season_player_stats | Calling Season Player Stats API.
Arg:
season_key: key of the season
player_key: key of the player
Return:
json data | src/pycricket.py | def get_season_player_stats(self, season_key, player_key):
"""
Calling Season Player Stats API.
Arg:
season_key: key of the season
player_key: key of the player
Return:
json data
"""
season_player_stats_url = self.api_path + "season/" + ... | def get_season_player_stats(self, season_key, player_key):
"""
Calling Season Player Stats API.
Arg:
season_key: key of the season
player_key: key of the player
Return:
json data
"""
season_player_stats_url = self.api_path + "season/" + ... | [
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train | RcaApp.get_overs_summary | Calling Overs Summary API
Arg:
match_key: key of the match
Return:
json data | src/pycricket.py | def get_overs_summary(self, match_key):
"""
Calling Overs Summary API
Arg:
match_key: key of the match
Return:
json data
"""
overs_summary_url = self.api_path + "match/" + match_key + "/overs_summary/"
response = self.get_response(overs_summ... | def get_overs_summary(self, match_key):
"""
Calling Overs Summary API
Arg:
match_key: key of the match
Return:
json data
"""
overs_summary_url = self.api_path + "match/" + match_key + "/overs_summary/"
response = self.get_response(overs_summ... | [
"Calling",
"Overs",
"Summary",
"API"
] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L365-L376 | [
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train | RcaApp.get_news_aggregation | Calling News Aggregation API
Return:
json data | src/pycricket.py | def get_news_aggregation(self):
"""
Calling News Aggregation API
Return:
json data
"""
news_aggregation_url = self.api_path + "news_aggregation" + "/"
response = self.get_response(news_aggregation_url)
return response | def get_news_aggregation(self):
"""
Calling News Aggregation API
Return:
json data
"""
news_aggregation_url = self.api_path + "news_aggregation" + "/"
response = self.get_response(news_aggregation_url)
return response | [
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] | fa47fe2e92915fc58db38898213e974742af55d4 |
train | RcaApp.get_fantasy_credits | Calling Fantasy Credit API
Arg:
match_key: key of the match
Return:
json data | src/pycricket.py | def get_fantasy_credits(self, match_key):
"""
Calling Fantasy Credit API
Arg:
match_key: key of the match
Return:
json data
"""
fantasy_credit_url = self.api_path_v3 + "fantasy-match-credits/" + match_key + "/"
response = self.get_respons... | def get_fantasy_credits(self, match_key):
"""
Calling Fantasy Credit API
Arg:
match_key: key of the match
Return:
json data
"""
fantasy_credit_url = self.api_path_v3 + "fantasy-match-credits/" + match_key + "/"
response = self.get_respons... | [
"Calling",
"Fantasy",
"Credit",
"API"
] | roanuz/py-cricket | python | https://github.com/roanuz/py-cricket/blob/fa47fe2e92915fc58db38898213e974742af55d4/src/pycricket.py#L390-L402 | [
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train | RcaApp.get_fantasy_points | Calling Fantasy Points API
Arg:
match_key: key of the match
Return:
json data | src/pycricket.py | def get_fantasy_points(self, match_key):
"""
Calling Fantasy Points API
Arg:
match_key: key of the match
Return:
json data
"""
fantasy_points_url = self.api_path_v3 + "fantasy-match-points/" + match_key + "/"
response = self.get_response(... | def get_fantasy_points(self, match_key):
"""
Calling Fantasy Points API
Arg:
match_key: key of the match
Return:
json data
"""
fantasy_points_url = self.api_path_v3 + "fantasy-match-points/" + match_key + "/"
response = self.get_response(... | [
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train | RedditPlugin.main | Generates an output string by replacing the keywords in the format
string with the corresponding values from a submission dictionary. | i3situation/plugins/reddit.py | def main(self):
"""
Generates an output string by replacing the keywords in the format
string with the corresponding values from a submission dictionary.
"""
self.manage_submissions()
out_string = self.options['format']
# Pop until we get something which len(titl... | def main(self):
"""
Generates an output string by replacing the keywords in the format
string with the corresponding values from a submission dictionary.
"""
self.manage_submissions()
out_string = self.options['format']
# Pop until we get something which len(titl... | [
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... | 3160a21006fcc6961f240988874e228a5ec6f18e |
train | RedditPlugin.login | Logs into Reddit in order to display a personalised front page. | i3situation/plugins/reddit.py | def login(self):
"""
Logs into Reddit in order to display a personalised front page.
"""
data = {'user': self.options['username'], 'passwd':
self.options['password'], 'api_type': 'json'}
response = self.client.post('http://www.reddit.com/api/login', data=data)
... | def login(self):
"""
Logs into Reddit in order to display a personalised front page.
"""
data = {'user': self.options['username'], 'passwd':
self.options['password'], 'api_type': 'json'}
response = self.client.post('http://www.reddit.com/api/login', data=data)
... | [
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train | RedditPlugin.manage_submissions | If there are no or only one submissions left, get new submissions.
This function manages URL creation and the specifics for front page
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If there are no or only one submissions left, get new submissions.
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"""
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train | RedditPlugin.get_submissions | Connects to Reddit and gets a JSON representation of submissions.
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url: A url that requests for submissions should be sent to. | i3situation/plugins/reddit.py | def get_submissions(self, url):
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Connects to Reddit and gets a JSON representation of submissions.
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url: A url that requests for submissions should be sent to.
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Connects to Reddit and gets a JSON representation of submissions.
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train | CmusPlugin.main | A compulsary function that gets the output of the cmus-remote -Q command
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A compulsary function that gets the output of the cmus-remote -Q command
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"""
try:
# Setting stderr to subprocess.STDOUT seems to stop the error
# mes... | def main(self):
"""
A compulsary function that gets the output of the cmus-remote -Q command
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train | CmusPlugin.convert_cmus_output | Change the newline separated string of output data into
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cmus_output: A string with information about cmus that is newline
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Change the newline separated string of output data into
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Change the newline separated string of output data into
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train | CmusPlugin.convert_time | A helper function to convert seconds into hh:mm:ss for better
readability.
time: A string representing time in seconds. | i3situation/plugins/cmus.py | def convert_time(self, time):
"""
A helper function to convert seconds into hh:mm:ss for better
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time: A string representing time in seconds.
"""
time_string = str(datetime.timedelta(seconds=int(time)))
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A helper function to convert seconds into hh:mm:ss for better
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time: A string representing time in seconds.
"""
time_string = str(datetime.timedelta(seconds=int(time)))
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train | Plugin.output | Output all of the options and data for a segment.
full_text: A string representing the data that should be output to i3bar.
short_text: A more concise version of full_text, in case there is minimal
room on the i3bar. | i3situation/plugins/_plugin.py | def output(self, full_text, short_text):
"""
Output all of the options and data for a segment.
full_text: A string representing the data that should be output to i3bar.
short_text: A more concise version of full_text, in case there is minimal
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"""
... | def output(self, full_text, short_text):
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Output all of the options and data for a segment.
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short_text: A more concise version of full_text, in case there is minimal
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train | Plugin.on_click | A function that should be overwritten by a plugin that wishes to react
to events, if it wants to perform any action other than running the
supplied command related to a button.
event: A dictionary passed from i3bar (after being decoded from JSON)
that has the folowing format:
e... | i3situation/plugins/_plugin.py | def on_click(self, event):
"""
A function that should be overwritten by a plugin that wishes to react
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supplied command related to a button.
event: A dictionary passed from i3bar (after being decoded from JSON)
... | def on_click(self, event):
"""
A function that should be overwritten by a plugin that wishes to react
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event: A dictionary passed from i3bar (after being decoded from JSON)
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train | url_reverse | Reverse the requested URL (passed via GET / POST as `url_name` parameter)
:param request: Request object
:return: The reversed path | ckeditor_filebrowser_filer/views.py | def url_reverse(request):
"""
Reverse the requested URL (passed via GET / POST as `url_name` parameter)
:param request: Request object
:return: The reversed path
"""
if request.method in ('GET', 'POST'):
data = getattr(request, request.method)
url_name = data.get('url_name')
... | def url_reverse(request):
"""
Reverse the requested URL (passed via GET / POST as `url_name` parameter)
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:return: The reversed path
"""
if request.method in ('GET', 'POST'):
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train | url_image | Converts a filer image ID in a complete path
:param request: Request object
:param image_id: Filer image ID
:param thumb_options: ThumbnailOption ID
:param width: user-provided width
:param height: user-provided height
:return: JSON serialized URL components ('url', 'width', 'height') | ckeditor_filebrowser_filer/views.py | def url_image(request, image_id, thumb_options=None, width=None, height=None):
"""
Converts a filer image ID in a complete path
:param request: Request object
:param image_id: Filer image ID
:param thumb_options: ThumbnailOption ID
:param width: user-provided width
:param height: user-provi... | def url_image(request, image_id, thumb_options=None, width=None, height=None):
"""
Converts a filer image ID in a complete path
:param request: Request object
:param image_id: Filer image ID
:param thumb_options: ThumbnailOption ID
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train | thumbnail_options | Returns the requested ThumbnailOption as JSON
:param request: Request object
:return: JSON serialized ThumbnailOption | ckeditor_filebrowser_filer/views.py | def thumbnail_options(request):
"""
Returns the requested ThumbnailOption as JSON
:param request: Request object
:return: JSON serialized ThumbnailOption
"""
response_data = [{'id': opt.pk, 'name': opt.name} for opt in ThumbnailOption.objects.all()]
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Returns the requested ThumbnailOption as JSON
:param request: Request object
:return: JSON serialized ThumbnailOption
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response_data = [{'id': opt.pk, 'name': opt.name} for opt in ThumbnailOption.objects.all()]
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train | serve_image | returns the content of an image sized according to the parameters
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:param image_id: Filer image ID
:param thumb_options: ThumbnailOption ID
:param width: user-provided width
:param height: user-provided height
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"""
returns the content of an image sized according to the parameters
:param request: Request object
:param image_id: Filer image ID
:param thumb_options: ThumbnailOption ID
:param width: user-provided width
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:param image_id: Filer image ID
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train | Config._touch_dir | A helper function to create a directory if it doesn't exist.
path: A string containing a full path to the directory to be created. | i3situation/core/config.py | def _touch_dir(self, path):
"""
A helper function to create a directory if it doesn't exist.
path: A string containing a full path to the directory to be created.
"""
try:
os.makedirs(path)
except OSError as e:
if e.errno != errno.EEXIST:
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A helper function to create a directory if it doesn't exist.
path: A string containing a full path to the directory to be created.
"""
try:
os.makedirs(path)
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train | Config.reload | Reload the configuration from the file. This is in its own function
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"""
Reload the configuration from the file. This is in its own function
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self._conf = configparser.ConfigParser()
# Preserve the case of sections and keys.
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Reload the configuration from the file. This is in its own function
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self._conf = configparser.ConfigParser()
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train | Config._replace_data_types | Replaces strings with appropriate data types (int, boolean).
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dictionary: A dictionary returned from the config file. | i3situation/core/config.py | def _replace_data_types(dictionary):
"""
Replaces strings with appropriate data types (int, boolean).
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Replaces strings with appropriate data types (int, boolean).
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train | main | Command line interface for the ``rotate-backups`` program. | rotate_backups/cli.py | def main():
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coloredlogs.install(syslog=True)
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rotation_scheme = {}
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parallel = False
use_sudo = False
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selected_locations = []
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"""Command line interface for the ``rotate-backups`` program."""
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train | BatteryPlugin.get_battery_state | Return the first line from the file located at battery_path/prop as a
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"""
Return the first line from the file located at battery_path/prop as a
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"""
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Return the first line from the file located at battery_path/prop as a
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train | coerce_location | Coerce a string to a :class:`Location` object.
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:param options: Any keyword arguments are passed on to
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"""
Coerce a string to a :class:`Location` object.
:param value: The value to coerce (a string or :class:`Location` object).
:param options: Any keyword arguments are passed on to
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"""
Coerce a string to a :class:`Location` object.
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train | coerce_retention_period | Coerce a retention period to a Python value.
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Coerce a retention period to a Python value.
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Coerce a retention period to a Python value.
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train | load_config_file | Load a configuration file with backup directories and rotation schemes.
:param configuration_file: Override the pathname of the configuration file
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Load a configuration file with backup directories and rotation schemes.
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Load a configuration file with backup directories and rotation schemes.
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train | rotate_backups | Rotate the backups in a directory according to a flexible rotation scheme.
.. note:: This function exists to preserve backwards compatibility with
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do... | rotate_backups/__init__.py | def rotate_backups(directory, rotation_scheme, **options):
"""
Rotate the backups in a directory according to a flexible rotation scheme.
.. note:: This function exists to preserve backwards compatibility with
older versions of the `rotate-backups` package where all of the
logic... | def rotate_backups(directory, rotation_scheme, **options):
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Rotate the backups in a directory according to a flexible rotation scheme.
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:param kw: Any keyword arguments are passed on to :func:`rotate_backups()`.
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Rotate the backups in the given locations concurrently.
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Rotate the backups in the given locations concurrently.
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train | RotateBackups.rotate_backups | Rotate the backups in a directory according to a flexible rotation scheme.
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Rotate the backups in a directory according to a flexible rotation scheme.
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Rotate the backups in a directory according to a flexible rotation scheme.
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Group backups collected by :func:`collect_backups()` by rotation frequencies.
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train | RotateBackups.apply_rotation_scheme | Apply the user defined rotation scheme to the result of :func:`group_backups()`.
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Apply the user defined rotation scheme to the result of :func:`group_backups()`.
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train | RotateBackups.find_preservation_criteria | Collect the criteria used to decide which backups to preserve.
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Collect the criteria used to decide which backups to preserve.
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train | Status.reload | Reload the installed plugins and the configuration file. This is called
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Reload the installed plugins and the configuration file. This is called
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train | ThreadManager.add_thread | Creates a thread, starts it and then adds it to the thread pool.
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train | PluginLoader._compile_files | Compiles python plugin files in order to be processed by the loader.
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Compiles python plugin files in order to be processed by the loader.
It compiles the plugins if they have been updated or haven't yet been
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"""
for f in glob.glob(os.path.join(self.dir_path, '*.py')):
# Check for compiled... | def _compile_files(self):
"""
Compiles python plugin files in order to be processed by the loader.
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for f in glob.glob(os.path.join(self.dir_path, '*.py')):
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train | PluginLoader._load_compiled | Accepts a path to a compiled plugin and returns a module object.
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"""
name = os.path.splitext(os.path.split(file_path)[-1])[0]
plugin_directory ... | def _load_compiled(self, file_path):
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"""
Matches the plugins that have been specified in the config file
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"""
objects = []
for settings in self._config:
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Matches the plugins that have been specified in the config file
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train | ModelDatabrowse.root | Handles main URL routing for the databrowse app.
`url` is the remainder of the URL -- e.g. 'objects/3'. | django_databrowse/sites.py | def root(self, request, url):
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# Delegate to the appropriate method, based on the URL.
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train | DatabrowseSite.register | Registers the given model(s) with the given databrowse site.
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train | DatabrowseSite.unregister | Unregisters the given model(s).
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Unregisters the given model(s).
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Unregisters the given model(s).
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train | DatabrowseSite.root | Handles main URL routing for the databrowse app.
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Handles main URL routing for the databrowse app.
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"""
self.root_url = request.path[:len(request.path) - len(url)]
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... | def root(self, request, url):
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Handles main URL routing for the databrowse app.
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self.root_url = request.path[:len(request.path) - len(url)]
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train | DatabrowseSite.model_page | Handles the model-specific functionality of the databrowse site,
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Handles the model-specific functionality of the databrowse site,
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Handles the model-specific functionality of the databrowse site,
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train | EasyInstanceField.values | Returns a list of values for this field for this instance. It's a list
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Returns a list of values for this field for this instance. It's a list
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train | EasyInstanceField.urls | Returns a list of (value, URL) tuples. | django_databrowse/datastructures.py | def urls(self):
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plugin_urls = []
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urls = plugin.urls(plugin_name, self)
... | def urls(self):
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plugin_urls = []
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train | CalendarPlugin.field_dict | Helper function that returns a dictionary of all DateFields or
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it takes that into account when building the dictionary. | django_databrowse/plugins/calendars.py | def field_dict(self, model):
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Helper function that returns a dictionary of all DateFields or
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if self.field_names is None:
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Helper function that returns a dictionary of all DateFields or
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train | kmer_dag | Optionally launches a Spark cluster and then runs ADAM to count k-mers on an
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:param job: Toil job
:param input_file: URL/path to input file to count k-mers on
:param output_path: URL/path to save k-mer counts at
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:param spa... | src/toil_scripts/adam_kmers/count_kmers.py | def kmer_dag(job,
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workers,
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memory,
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'''
Optionally launches a Spark cluster and then runs ADAM to count k-mers on an
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:param ... | def kmer_dag(job,
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'''
Optionally launches a Spark cluster and then runs ADAM to count k-mers on an
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train | download_count_upload | Runs k-mer counting.
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3. The k-mers are counted and saved as text.
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:param job: T... | src/toil_scripts/adam_kmers/count_kmers.py | def download_count_upload(job,
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'''
Runs k-mer counting... | def download_count_upload(job,
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'''
Sets up command line parser for Toil/ADAM based k-mer counter, and launches
k-mer counter with optional Spark cluster.
'''
parser = argparse.ArgumentParser()
# add parser arguments
parser.add_argument('--input_path',
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'''
Sets up command line parser for Toil/ADAM based k-mer counter, and launches
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train | joint_genotype_and_filter | Checks for enough disk space for joint genotyping, then calls the genotype and filter pipeline function.
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train | genotype_and_filter | Genotypes one or more GVCF files and runs either the VQSR or hard filtering pipeline. Uploads the genotyped VCF file
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train | annotate_vcfs | Runs Oncotator for a group of VCF files. Each sample is annotated individually.
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train | parse_manifest | Parses manifest file for Toil Germline Pipeline
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Parses manifest file for Toil Germline Pipeline
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train | download_shared_files | Downloads shared reference files for Toil Germline pipeline
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:param Namespace config: Pipeline configuration options
:return: Updated config with shared fileStoreIDS
:rtype: Namespace | src/toil_scripts/gatk_germline/germline.py | def download_shared_files(job, config):
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Downloads shared reference files for Toil Germline pipeline
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Pipeline configuration options
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Downloads shared reference files for Toil Germline pipeline
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:param Namespace config: Pipeline configuration options and shared files.
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Creates a genome fasta index and sequence dictionary file if not already present in the pipeline config.
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train | prepare_bam | Prepares BAM file for Toil germline pipeline.
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- Uploads preprocessed BAM to output directory
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Prepares BAM file for Toil germline pipeline.
Steps in pipeline
0: Download and align BAM or FASTQ sample
1: Sort BAM
2: Index BAM
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- Uploads preprocessed BAM to ... | def prepare_bam(job, uuid, url, config, paired_url=None, rg_line=None):
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train | setup_and_run_bwakit | Downloads and runs bwakit for BAM or FASTQ files
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:param str uuid: Unique sample identifier
:param str url: FASTQ or BAM file URL. BAM alignment URL must have .bam extension.
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train | gatk_haplotype_caller | Uses GATK HaplotypeCaller to identify SNPs and INDELs. Outputs variants in a Genomic VCF file.
:param JobFunctionWrappingJob job: passed automatically by Toil
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:param str bai: FileStoreID for BAM index file
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train | main | GATK germline pipeline with variant filtering and annotation. | src/toil_scripts/gatk_germline/germline.py | def main():
"""
GATK germline pipeline with variant filtering and annotation.
"""
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"""
GATK germline pipeline with variant filtering and annotation.
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train | sample_loop | Loops over the sample_ids (uuids) in the manifest, creating child jobs to process each | src/toil_scripts/adam_gatk_pipeline/align_and_call.py | def sample_loop(job, uuid_list, inputs):
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train | static_dag | Prefer this here as it allows us to pull the job functions from other jobs
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train | main | This is a Toil pipeline used to perform alignment of fastqs. | src/toil_scripts/adam_gatk_pipeline/align_and_call.py | def main():
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train | generate_unique_key | Input1: Path to the BD2K Master Key (for S3 Encryption)
Input2: S3 URL (e.g. https://s3-us-west-2.amazonaws.com/cgl-driver-projects-encrypted/wcdt/exome_bams/DTB-111-N.bam)
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Returns: 32-byte unique key generated for that URL
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train | download_encrypted_file | Downloads encrypted file from S3
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train | return_input_paths | Returns the paths of files from the FileStore
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Input3: jobstore id dictionary
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train | move_to_output_dir | Moves files from work_dir to output_dir
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train | batch_start | Downloads shared files that are used by all samples for alignment and places them in the jobstore. | src/toil_scripts/bwa_alignment/old_alignment_script/batch_align.py | def batch_start(job, input_args):
"""
Downloads shared files that are used by all samples for alignment and places them in the jobstore.
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train | spawn_batch_jobs | Spawns an alignment job for every sample in the input configuration file | src/toil_scripts/bwa_alignment/old_alignment_script/batch_align.py | def spawn_batch_jobs(job, shared_ids, input_args):
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train | alignment | Runs BWA and then Bamsort on the supplied fastqs for this sample
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train | upload_bam_to_s3 | Uploads output BAM from sample to S3
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Input3: Input arguments dictionary
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Input3: Input arguments dictionary
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train | vqsr_pipeline | Runs GATK Variant Quality Score Recalibration.
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"""
Runs GATK Variant Quality Score Recalibration.
0: Start 0 --> 1 --> 3 --> 4 --> 5
1: Recalibrate SNPs | |
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4: Apply INDEL ... | def vqsr_pipeline(job, uuid, vcf_id, config):
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... | f878d863defcdccaabb7fe06f991451b7a198fb7 |
train | parse_sra | Parses genetorrent config file. Returns list of samples: [ [id1, id1 ], [id2, id2], ... ]
Returns duplicate of ids to follow UUID/URL standard. | src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py | def parse_sra(path_to_config):
"""
Parses genetorrent config file. Returns list of samples: [ [id1, id1 ], [id2, id2], ... ]
Returns duplicate of ids to follow UUID/URL standard.
"""
samples = []
with open(path_to_config, 'r') as f:
for line in f.readlines():
if not line.iss... | def parse_sra(path_to_config):
"""
Parses genetorrent config file. Returns list of samples: [ [id1, id1 ], [id2, id2], ... ]
Returns duplicate of ids to follow UUID/URL standard.
"""
samples = []
with open(path_to_config, 'r') as f:
for line in f.readlines():
if not line.iss... | [
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"... | f878d863defcdccaabb7fe06f991451b7a198fb7 |
train | tarball_files | Tars a group of files together into a tarball
work_dir: str Current Working Directory
tar_name: str Name of tarball
uuid: str UUID to stamp files with
files: str(s) List of filenames to place in the tarball from working directory | src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py | def tarball_files(work_dir, tar_name, uuid=None, files=None):
"""
Tars a group of files together into a tarball
work_dir: str Current Working Directory
tar_name: str Name of tarball
uuid: str UUID to stamp files with
files: str(s) List of filenames to place in the ta... | def tarball_files(work_dir, tar_name, uuid=None, files=None):
"""
Tars a group of files together into a tarball
work_dir: str Current Working Directory
tar_name: str Name of tarball
uuid: str UUID to stamp files with
files: str(s) List of filenames to place in the ta... | [
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] | BD2KGenomics/toil-scripts | python | https://github.com/BD2KGenomics/toil-scripts/blob/f878d863defcdccaabb7fe06f991451b7a198fb7/src/toil_scripts/transfer_gtex_to_s3/transfer_gtex_to_s3.py#L95-L109 | [
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... | f878d863defcdccaabb7fe06f991451b7a198fb7 |
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