code stringlengths 52 7.75k | docs stringlengths 1 5.85k |
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def subscribe_notice(self, access_token):
url = 'https://openapi.youku.com/v2/users/subscribe/notice.json'
params = {
'client_id': self.client_id,
'access_token': access_token
}
r = requests.get(url, params=params)
check_error(r)
return r.... | doc: http://open.youku.com/docs/doc?id=31 |
def find_show_by_id(self, show_id):
url = 'https://openapi.youku.com/v2/shows/show.json'
params = {
'client_id': self.client_id,
'show_id': show_id
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=59 |
def find_shows_by_ids(self, show_ids):
url = 'https://openapi.youku.com/v2/shows/show_batch.json'
params = {
'client_id': self.client_id,
'show_ids': show_ids
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=60 |
def find_show_premium_by_ids(self, show_ids, page=1, count=20):
url = 'https://openapi.youku.com/v2/shows/show_premium.json'
params = {
'client_id': self.client_id,
'show_ids': show_ids,
'page': page,
'count': count
}
r = requests.... | doc: http://open.youku.com/docs/doc?id=61 |
def find_shows_by_category(self, category, genre=None, area=None,
release_year=None, paid=None,
orderby='view-today-count',
streamtypes=None, person=None,
page=1, count=20):
url =... | doc: http://open.youku.com/docs/doc?id=62 |
def find_shows_by_related(self, show_id,
count=20):
url = 'https://openapi.youku.com/v2/shows/by_related.json'
params = {
'client_id': self.client_id,
'show_id': show_id,
'count': count
}
r = requests.get(url, par... | doc: http://open.youku.com/docs/doc?id=63 |
def find_videos_by_show(self, show_id, show_videotype=None,
show_videostage=None, orderby='videoseq-asc',
page=1, count=20):
url = 'https://openapi.youku.com/v2/shows/videos.json'
params = {
'client_id': self.client_id,
... | doc: http://open.youku.com/docs/doc?id=64 |
def prepare_video_params(self, title=None, tags='Others', description='',
copyright_type='original', public_type='all',
category=None, watch_password=None,
latitude=None, longitude=None, shoot_time=None
)... | util method for create video params to upload.
Only need to provide a minimum of two essential parameters:
title and tags, other video params are optional. All params spec
see: http://cloud.youku.com/docs?id=110#create .
Args:
title: string, 2-50 characters.
tag... |
def _save_upload_state_to_file(self):
if os.access(self.file_dir, os.W_OK | os.R_OK | os.X_OK):
save_file = self.file + '.upload'
data = {
'upload_token': self.upload_token,
'upload_server_ip': self.upload_server_ip
}
with ... | if create and create_file has execute, save upload state
to file for next resume upload if current upload process is
interrupted. |
def upload(self, params={}):
if self.upload_token is not None:
# resume upload
status = self.check()
if status['status'] != 4:
return self.commit()
else:
self.new_slice()
while self.slice_task_id != 0:
... | start uploading the file until upload is complete or error.
This is the main method to used, If you do not care about
state of process.
Args:
params: a dict object describe video info, eg title,
tags, description, category.
all video para... |
def sync_groups(self):
if self.settings.GROUP_FILTER:
ldap_groups = self.ldap.search(self.settings.GROUP_FILTER, self.settings.GROUP_ATTRIBUTES.keys())
self._sync_ldap_groups(ldap_groups)
logger.info("Groups are synchronized") | Synchronize LDAP groups with local group model. |
def sync_users(self):
if self.settings.USER_FILTER:
user_attributes = self.settings.USER_ATTRIBUTES.keys() + self.settings.USER_EXTRA_ATTRIBUTES
ldap_users = self.ldap.search(self.settings.USER_FILTER, user_attributes)
self._sync_ldap_users(ldap_users)
lo... | Synchronize LDAP users with local user model. |
def search_videos_by_tag(self, tag, category=None,
period='today',
orderby='relevance',
page=1, count=20):
url = 'https://openapi.youku.com/v2/searches/video/by_tag.json'
params = {
'client_id': s... | doc: http://open.youku.com/docs/doc?id=80 |
def search_videos_by_keyword(self, keyword, category=None,
period='week', orderby='relevance',
public_type='all', paid=None,
timeless=None, timemore=None,
streamtypes=None,
... | doc: http://open.youku.com/docs/doc?id=81 |
def search_shows_by_keyword(self, keyword, unite=0, source_site=None,
category=None, release_year=None,
area=None, orderby='view-count',
paid=None, hasvideotype=None,
page=1, count=20):
... | doc: http://open.youku.com/docs/doc?id=82 |
def search_keyword_complete(self, keyword):
url = 'https://openapi.youku.com/v2/searches/keyword/complete.json'
params = {
'client_id': self.client_id,
'keyword': keyword
}
r = requests.get(url, params=params)
check_error(r)
return r.json(... | doc: http://open.youku.com/docs/doc?id=83 |
def search_keyword_top(self, category=None, count=20, period='today'):
url = 'https://openapi.youku.com/v2/searches/keyword/top.json'
params = {
'client_id': self.client_id,
'count': count,
'period': period
}
if category:
params['c... | doc: http://open.youku.com/docs/doc?id=84 |
def search_show_address_unite(self, progammeId,
source_site=None, type=None):
url = 'https://openapi.youku.com/v2/searches/show/address_unite.json'
params = {
'client_id': self.client_id,
'progammeId': progammeId,
'source_sit... | doc: http://open.youku.com/docs/doc?id=85 |
def search_show_top_unite(self, category, genre=None, area=None,
year=None, orderby=None, headnum=1,
tailnum=1, onesiteflag=None,
page=1, count=20):
url = 'https://openapi.youku.com/v2/searches/show/top_unite.json... | doc: http://open.youku.com/docs/doc?id=86 |
def find_playlist_by_id(self, playlist_id):
url = 'https://openapi.youku.com/v2/playlists/show.json'
params = {
'client_id': self.client_id,
'playlist_id': playlist_id
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=66 |
def find_playlists_by_ids(self, playlist_ids):
url = 'https://openapi.youku.com/v2/playlists/show_batch.json'
params = {
'client_id': self.client_id,
'playlist_ids': playlist_ids
}
r = requests.get(url, params=params)
check_error(r)
return... | doc: http://open.youku.com/docs/doc?id=67 |
def find_videos_by_playlist(self, playlist_id, page=1, count=20):
url = 'https://openapi.youku.com/v2/playlists/videos.json'
params = {
'client_id': self.client_id,
'playlist_id': playlist_id,
'page': page,
'count': count
}
r = req... | doc: http://open.youku.com/docs/doc?id=71 |
def update_playlist(self, access_token, playlist_id, title,
tags=None, category=None, description=None):
url = 'https://openapi.youku.com/v2/playlists/update.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'pl... | doc: http://open.youku.com/docs/doc?id=73 |
def destroy_playlist(self, access_token, playlist_id):
url = 'https://openapi.youku.com/v2/playlists/destroy.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'playlist_id': playlist_id
}
r = requests.post(url, data=dat... | doc: http://open.youku.com/docs/doc?id=74 |
def add_videos_to_playlist(self, access_token, playlist_id, video_ids):
url = 'https://openapi.youku.com/v2/playlists/video/add.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'playlist_id': playlist_id,
'video_ids': vide... | doc: http://open.youku.com/docs/doc?id=75 |
def set_cover_video_for_playlist(self, access_token, playlist_id,
video_id):
url = 'https://openapi.youku.com/v2/playlists/video/setcover.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'playlist_... | doc: http://open.youku.com/docs/doc?id=77 |
def find_next_video_in_playlist(self, playlist_id, cur_video_id):
url = 'https://openapi.youku.com/v2/playlists/video/next.json'
params = {
'client_id': self.client_id,
'playlist_id': playlist_id,
'video_id': cur_video_id
}
r = requests.get(ur... | doc: http://open.youku.com/docs/doc?id=78 |
def from_geo(geo, level):
pixel = TileSystem.geo_to_pixel(geo, level)
tile = TileSystem.pixel_to_tile(pixel)
key = TileSystem.tile_to_quadkey(tile, level)
return QuadKey(key) | Constucts a quadkey representation from geo and level
geo => (lat, lon)
If lat or lon are outside of bounds, they will be clipped
If level is outside of bounds, an AssertionError is raised |
def is_ancestor(self, node):
if self.level <= node.level or self.key[:len(node.key)] != node.key:
return None
return self.level - node.level | If node is ancestor of self
Get the difference in level
If not, None |
def xdifference(self, to):
x,y = 0,1
assert self.level == to.level
self_tile = list(self.to_tile()[0])
to_tile = list(to.to_tile()[0])
if self_tile[x] >= to_tile[x] and self_tile[y] <= self_tile[y]:
ne_tile, sw_tile = self_tile, to_tile
else:
... | Generator
Gives the difference of quadkeys between self and to
Generator in case done on a low level
Only works with quadkeys of same level |
def unwind(self):
return [ QuadKey(self.key[:l+1]) for l in reversed(range(len(self.key))) ] | Get a list of all ancestors in descending order of level, including a new instance of self |
def find_comment_by_id(self, comment_id):
url = 'https://openapi.youku.com/v2/comments/show.json'
params = {
'client_id': self.client_id,
'comment_id': comment_id
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=32 |
def find_comments_by_ids(self, comment_ids):
url = 'https://openapi.youku.com/v2/comments/show_batch.json'
params = {
'client_id': self.client_id,
'comment_ids': comment_ids
}
r = requests.get(url, params=params)
check_error(r)
return r.js... | doc: http://open.youku.com/docs/doc?id=34 |
def find_comments_by_video(self, video_id, page=1, count=20):
url = 'https://openapi.youku.com/v2/comments/by_video.json'
params = {
'client_id': self.client_id,
'video_id': video_id,
'page': page,
'count': count
}
r = requests.get... | doc: http://open.youku.com/docs/doc?id=35 |
def find_comments_by_me(self, access_token, page=1, count=20):
url = 'https://openapi.youku.com/v2/comments/by_me.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'page': page,
'count': count
}
r = requests... | doc: http://open.youku.com/docs/doc?id=37 |
def create_comment(self, access_token, video_id, content,
reply_id=None, captcha_key=None, captcha_text=None):
url = 'https://openapi.youku.com/v2/comments/create.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
... | doc: http://open.youku.com/docs/doc?id=41 |
def destroy_comment(self, access_token, comment_id):
url = 'https://openapi.youku.com/v2/comments/destroy.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'comment_id': comment_id
}
r = requests.post(url, data=data)
... | doc: http://open.youku.com/docs/doc?id=42 |
def validate(self):
if self.GROUP_ATTRIBUTES and self.GROUPNAME_FIELD not in self.GROUP_ATTRIBUTES.values():
raise ImproperlyConfigured("LDAP_SYNC_GROUP_ATTRIBUTES must contain '%s'" % self.GROUPNAME_FIELD)
if not self.model._meta.get_field(self.USERNAME_FIELD).unique:
... | Apply validation rules for loaded settings. |
def user_active_directory_enabled(user, attributes, created, updated):
try:
user_account_control = int(attributes['userAccountControl'][0])
if user_account_control & 2:
user.is_active = False
else:
user.is_active = True
except KeyError:
pass | Activate/deactivate user accounts based on Active Directory's
userAccountControl flags. Requires 'userAccountControl'
to be included in LDAP_SYNC_USER_EXTRA_ATTRIBUTES. |
def find_video_by_id(self, video_id):
url = 'https://openapi.youku.com/v2/videos/show_basic.json'
params = {
'client_id': self.client_id,
'video_id': video_id
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=44 |
def find_video_by_url(self, video_url):
url = 'https://openapi.youku.com/v2/videos/show_basic.json'
params = {
'client_id': self.client_id,
'video_url': video_url
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=44 |
def find_videos_by_ids(self, video_ids):
url = 'https://openapi.youku.com/v2/videos/show_basic_batch.json'
params = {
'client_id': self.client_id,
'video_ids': video_ids
}
r = requests.get(url, params=params)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=45 |
def find_video_detail_by_id(self, video_id, ext=None):
url = 'https://api.youku.com/videos/show.json'
params = {
'client_id': self.client_id,
'video_id': video_id
}
if ext:
params['ext'] = ext
r = requests.get(url, params=params)
... | doc: http://cloud.youku.com/docs?id=46 |
def find_video_details_by_ids(self, video_ids, ext=None):
url = 'https://openapi.youku.com/v2/videos/show_batch.json'
params = {
'client_id': self.client_id,
'video_ids': video_ids
}
if ext:
params['ext'] = ext
r = requests.get(url, pa... | doc: http://open.youku.com/docs/doc?id=47 |
def update_video(self, access_token, video_id, title=None,
tags=None, category=None, copyright_type=None,
public_type=None, watch_password=None,
description=None, thumbnail_seq=None):
url = 'https://openapi.youku.com/v2/videos/update.json'
... | doc: http://open.youku.com/docs/doc?id=50 |
def find_videos_by_related(self, video_id, count=20):
url = 'https://openapi.youku.com/v2/videos/by_related.json'
params = {
'client_id': self.client_id,
'video_id': video_id,
'count': count
}
r = requests.get(url, params=params)
check... | doc: http://open.youku.com/docs/doc?id=52 |
def find_favorite_videos_by_userid(self, user_id,
orderby='favorite-time',
page=1, count=20):
url = 'https://openapi.youku.com/v2/videos/favorite/by_user.json'
params = {
'client_id': self.client_id,
... | doc: http://open.youku.com/docs/doc?id=54 |
def find_favorite_videos_by_username(self, user_name,
orderby='favorite-time',
page=1, count=20):
url = 'https://openapi.youku.com/v2/videos/favorite/by_user.json'
params = {
'client_id': self.client_i... | doc: http://open.youku.com/docs/doc?id=54 |
def create_favorite_video(self, access_token, video_id):
url = 'https://openapi.youku.com/v2/videos/favorite/create.json'
data = {
'client_id': self.client_id,
'access_token': access_token,
'video_id': video_id
}
r = requests.post(url, data=da... | doc: http://open.youku.com/docs/doc?id=55 |
def search(self, filterstr, attrlist):
return self._paged_search_ext_s(self.settings.BASE, ldap.SCOPE_SUBTREE, filterstr=filterstr,
attrlist=attrlist, page_size=self.settings.PAGE_SIZE) | Query the configured LDAP server. |
def _paged_search_ext_s(self, base, scope, filterstr='(objectClass=*)', attrlist=None, attrsonly=0,
serverctrls=None, clientctrls=None, timeout=-1, sizelimit=0, page_size=10):
request_ctrl = SimplePagedResultsControl(True, size=page_size, cookie='')
results = []
... | Behaves similarly to LDAPObject.search_ext_s() but internally uses the
simple paged results control to retrieve search results in chunks.
Taken from the python-ldap paged_search_ext_s.py demo, showing how to use
the paged results control: https://bitbucket.org/jaraco/python-ldap/ |
def video_category(self):
url = 'https://openapi.youku.com/v2/schemas/video/category.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=90 |
def upload_spec(self):
url = 'https://openapi.youku.com/v2/schemas/upload/spec.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=91 |
def comment_expression(self):
url = 'https://openapi.youku.com/v2/schemas/comment/expression.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=92 |
def show_category(self):
url = 'https://openapi.youku.com/v2/schemas/show/category.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=93 |
def playlist_category(self):
url = 'https://openapi.youku.com/v2/schemas/playlist/category.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=94 |
def searche_top_category(self):
url = 'https://openapi.youku.com/v2/schemas/searche/top/category.json'
r = requests.get(url)
check_error(r)
return r.json() | doc: http://open.youku.com/docs/doc?id=95 |
def cli(ctx, feature_id, name, organism="", sequence=""):
return ctx.gi.annotations.set_name(feature_id, name, organism=organism, sequence=sequence) | Set a feature's name
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, feature_id, organism="", sequence=""):
return ctx.gi.annotations.delete_sequence_alteration(feature_id, organism=organism, sequence=sequence) | [UNTESTED] Delete a specific feature alteration
Output:
A list of sequence alterations(?) |
def fetch_lid(self, woeid):
rss = self._fetch_xml(LID_LOOKUP_URL.format(woeid, "f"))
# We are pulling the LID from the permalink tag in the XML file
# returned by Yahoo.
try:
link = rss.find("channel/link").text
except AttributeError:
return Non... | Fetch a location's corresponding LID.
Args:
woeid: (string) the location's WOEID.
Returns:
a string containing the requested LID or None if the LID could
not be found.
Raises:
urllib.error.URLError: urllib.request could not open the URL
... |
def fetch_woeid(self, location):
rss = self._fetch_xml(
WOEID_LOOKUP_URL.format(quote(location)))
try:
woeid = rss.find("results/Result/woeid").text
except AttributeError:
return None
return woeid | Fetch a location's corresponding WOEID.
Args:
location: (string) a location (e.g. 23454 or Berlin, Germany).
Returns:
a string containing the location's corresponding WOEID or None if
the WOEID could not be found.
Raises:
urllib.error.URLErr... |
def _degrees_to_direction(self, degrees):
try:
degrees = float(degrees)
except ValueError:
return None
if degrees < 0 or degrees > 360:
return None
if degrees <= 11.25 or degrees >= 348.76:
return "N"
elif degrees <= 33.75:... | Convert wind direction from degrees to compass direction. |
def _fetch_xml(self, url):
with contextlib.closing(urlopen(url)) as f:
return xml.etree.ElementTree.parse(f).getroot() | Fetch a url and parse the document's XML. |
def cli(ctx, feature_id, symbol, organism="", sequence=""):
return ctx.gi.annotations.set_symbol(feature_id, symbol, organism=organism, sequence=sequence) | Set a feature's description
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, feature={}, organism="", sequence=""):
return ctx.gi.annotations.add_feature(feature=feature, organism=organism, sequence=sequence) | Add a feature
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, common_name, directory, blatdb="", genus="", species="", public=False):
return ctx.gi.organisms.add_organism(common_name, directory, blatdb=blatdb, genus=genus, species=species, public=public) | Add an organism
Output:
a dictionary with information about the new organism |
def cli(ctx, url=None, api_key=None, admin=False, **kwds):
# TODO: prompt for values someday.
click.echo("""Welcome to Apollo's Arrow!""")
if os.path.exists(config.global_config_path()):
info("Your arrow configuration already exists. Please edit it instead: %s" % config.global_config_path())
... | Help initialize global configuration (in home directory) |
def cli(ctx, id_number, new_key, metadata=""):
return ctx.gi.cannedkeys.update_key(id_number, new_key, metadata=metadata) | Update a canned key
Output:
an empty dictionary |
def cli(ctx, organism, export_type="FASTA", seq_type="peptide", export_format="text", export_gff3_fasta=False, sequences=None, region=""):
return ctx.gi.io.write_downloadable(organism, export_type=export_type, seq_type=seq_type, export_format=export_format, export_gff3_fasta=export_gff3_fasta, sequences=sequen... | Prepare a download for an organism
Output:
a dictionary containing download information |
def cli(ctx, transcript={}, suppress_history=False, suppress_events=False, organism="", sequence=""):
return ctx.gi.annotations.add_transcript(transcript=transcript, suppress_history=suppress_history, suppress_events=suppress_events, organism=organism, sequence=sequence) | [UNTESTED] Add a transcript to a feature
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def add_value(self, value, metadata=""):
data = {
'value': value,
'metadata': metadata
}
return self.post('createValue', data) | Add a canned value
:type value: str
:param value: New canned value
:type metadata: str
:param metadata: Optional metadata
:rtype: dict
:return: A dictionnary containing canned value description |
def show_value(self, value):
values = self.get_values()
values = [x for x in values if x['label'] == value]
if len(values) == 0:
raise Exception("Unknown value")
else:
return values[0] | Get a specific canned value
:type value: str
:param value: Canned value to show
:rtype: dict
:return: A dictionnary containing canned value description |
def update_value(self, id_number, new_value, metadata=None):
data = {
'id': id_number,
'new_value': new_value
}
if metadata is not None:
data['metadata'] = metadata
return self.post('updateValue', data) | Update a canned value
:type id_number: int
:param id_number: canned value ID number
:type new_value: str
:param new_value: New canned value value
:type metadata: str
:param metadata: Optional metadata
:rtype: dict
:return: an empty dictionary |
def add_key(self, key, metadata=""):
data = {
'key': key,
'metadata': metadata
}
return self.post('createKey', data) | Add a canned key
:type key: str
:param key: New canned key
:type metadata: str
:param metadata: Optional metadata
:rtype: dict
:return: A dictionnary containing canned key description |
def show_key(self, value):
keys = self.get_keys()
keys = [x for x in keys if x['label'] == value]
if len(keys) == 0:
raise Exception("Unknown key")
else:
return keys[0] | Get a specific canned key
:type value: str
:param value: Canned key to show
:rtype: dict
:return: A dictionnary containing canned key description |
def update_key(self, id_number, new_key, metadata=None):
data = {
'id': id_number,
'new_key': new_key
}
if metadata is not None:
data['metadata'] = metadata
return self.post('updateKey', data) | Update a canned key
:type id_number: int
:param id_number: canned key ID number
:type new_key: str
:param new_key: New canned key value
:type metadata: str
:param metadata: Optional metadata
:rtype: dict
:return: an empty dictionary |
def cli(ctx, id_number, new_value, metadata=""):
return ctx.gi.cannedvalues.update_value(id_number, new_value, metadata=metadata) | Update a canned value
Output:
an empty dictionary |
def download(self, dest_pattern="{originalFilename}", override=True, parent=False):
if self.id is None:
raise ValueError("Cannot download image with no ID.")
pattern = re.compile("{(.*?)}")
dest_pattern = re.sub(pattern, lambda m: str(getattr(self, str(m.group(0))[1:-1], "_... | Download the original image.
Parameters
----------
dest_pattern : str, optional
Destination path for the downloaded image. "{X}" patterns are replaced by the value of X attribute
if it exists.
override : bool, optional
True if a file with same name ca... |
def filtered_elements(self, model):
if isinstance(model, self.element_type):
yield model
yield from (e for e in model.eAllContents() if isinstance(e, self.element_type)) | Return iterator based on `element_type`. |
def folder_path_for_package(cls, package: ecore.EPackage):
parent = package.eContainer()
if parent:
return os.path.join(cls.folder_path_for_package(parent), package.name)
return package.name | Returns path to folder holding generated artifact for given element. |
def imported_classifiers_package(p: ecore.EPackage):
classes = {c for c in p.eClassifiers if isinstance(c, ecore.EClass)}
references = itertools.chain(*(c.eAllReferences() for c in classes))
references_types = (r.eType for r in references)
imported = {c for c in references_type... | Determines which classifiers have to be imported into given package. |
def imported_classifiers(p: ecore.EPackage):
classes = {c for c in p.eClassifiers if isinstance(c, ecore.EClass)}
supertypes = itertools.chain(*(c.eAllSuperTypes() for c in classes))
imported = {c for c in supertypes if c.ePackage is not p}
attributes = itertools.chain(*(c.eAt... | Determines which classifiers have to be imported into given module. |
def classes(p: ecore.EPackage):
classes = (c for c in p.eClassifiers if isinstance(c, ecore.EClass))
return sorted(classes, key=lambda c: len(set(c.eAllSuperTypes()))) | Returns classes in package in ordered by number of bases. |
def filter_all_contents(value: ecore.EPackage, type_):
return (c for c in value.eAllContents() if isinstance(c, type_)) | Returns `eAllContents(type_)`. |
def filter_pyfqn(cls, value, relative_to=0):
def collect_packages(element, packages):
parent = element.eContainer()
if parent:
collect_packages(parent, packages)
packages.append(element.name)
packages = []
collect_packages(value, pac... | Returns Python form of fully qualified name.
Args:
relative_to: If greater 0, the returned path is relative to the first n directories. |
def create_environment(self, **kwargs):
environment = super().create_environment(**kwargs)
environment.tests.update({
'type': self.test_type,
'kind': self.test_kind,
'opposite_before_self': self.test_opposite_before_self,
})
environment.filter... | Return a new Jinja environment.
Derived classes may override method to pass additional parameters or to change the template
loader type. |
def generate(self, model, outfolder, *, exclude=None):
with pythonic_names():
super().generate(model, outfolder)
check_dependency = self.with_dependencies and model.eResource
if check_dependency:
if exclude is None:
exclude = set(... | Generate model code.
Args:
model: The meta-model to generate code for.
outfolder: Path to the directoty that will contain the generated code.
exclude: List of referenced resources for which code was already generated
(to prevent regeneration). |
def cli(ctx, feature_id, db, accession, organism="", sequence=""):
return ctx.gi.annotations.delete_dbxref(feature_id, db, accession, organism=organism, sequence=sequence) | Delete a dbxref from a feature
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def add_organism(self, common_name, directory, blatdb=None, genus=None,
species=None, public=False):
data = {
'commonName': common_name,
'directory': directory,
'publicMode': public,
}
if blatdb is not None:
data['bla... | Add an organism
:type common_name: str
:param common_name: Organism common name
:type directory: str
:param directory: Server-side directory
:type blatdb: str
:param blatdb: Server-side Blat directory for the organism
:type genus: str
:param genus: Gen... |
def update_organism(self, organism_id, common_name, directory, blatdb=None, species=None, genus=None, public=False):
data = {
'id': organism_id,
'name': common_name,
'directory': directory,
'publicMode': public,
}
if blatdb is not None:
... | Update an organism
:type organism_id: str
:param organism_id: Organism ID Number
:type common_name: str
:param common_name: Organism common name
:type directory: str
:param directory: Server-side directory
:type blatdb: str
:param blatdb: Server-side B... |
def cli(ctx, feature_id, organism="", sequence=""):
return ctx.gi.annotations.set_readthrough_stop_codon(feature_id, organism=organism, sequence=sequence) | Set the feature to read through the first encountered stop codon
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, exon_a, exon_b, organism="", sequence=""):
return ctx.gi.annotations.merge_exons(exon_a, exon_b, organism=organism, sequence=sequence) | Merge two exons
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, id_number, new_value):
return ctx.gi.status.update_status(id_number, new_value) | Update a status name
Output:
an empty dictionary |
def cli(ctx, feature_id, description, organism="", sequence=""):
return ctx.gi.annotations.set_description(feature_id, description, organism=organism, sequence=sequence) | Set a feature's description
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, group, user):
return ctx.gi.users.remove_from_group(group, user) | Remove a user from a group
Output:
an empty dictionary |
def cli(ctx, feature_id, end, organism="", sequence=""):
return ctx.gi.annotations.set_translation_end(feature_id, end, organism=organism, sequence=sequence) | Set a feature's end
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, transcript_id, organism="", sequence=""):
return ctx.gi.annotations.duplicate_transcript(transcript_id, organism=organism, sequence=sequence) | Duplicate a transcripte
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def cli(ctx, feature_id, organism="", sequence=""):
return ctx.gi.annotations.get_feature_sequence(feature_id, organism=organism, sequence=sequence) | [CURRENTLY BROKEN] Get the sequence of a feature
Output:
A standard apollo feature dictionary ({"features": [{...}]}) |
def show_group(self, group_id):
res = self.post('loadGroups', {'groupId': group_id})
if isinstance(res, list):
return _fix_group(res[0])
else:
return _fix_group(res) | Get information about a group
:type group_id: int
:param group_id: Group ID Number
:rtype: dict
:return: a dictionary containing group information |
def update_group(self, group_id, new_name):
data = {
'id': group_id,
'name': new_name,
}
try:
response = self.post('updateGroup', data)
except Exception:
pass
# Apollo returns a 404 here for some unholy reason, despite act... | Update the name of a group
:type group_id: int
:param group_id: group ID number
:type new_name: str
:param new_name: New name for the group
:rtype: dict
:return: a dictionary containing group information |
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