def list(self,
after_time=None,
before_time=None,
epsg_code=None,
limit=None,
meta_string=None,
offset=None,
shapegrid_id=None):
"""Gets a list of gridsets matching the provided criteria.
Args:
after_time (str): Count gridsets modified after this time.
before_time (str): Count gridsets modified before this time.
epsg_code (int): The integer representing the map projection EPSG code for
the gridsets to count.
limit (int): The maximum number of records to return in this request.
meta_string (str): Metadata string to use to count gridsets.
offset (int): Start returned records after this offset (used for paging).
shapegrid_id (int): Count gridsets built from the shapegrid with this
identifier.
Returns:
list of dict: A list of JSON dictionaries for matching gridset metadata.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
before_time=before_time,
epsg_code=epsg_code,
limit=limit,
meta_string=meta_string,
offset=offset,
shapegrid_id=shapegrid_id)
def count(self,
after_time=None,
before_time=None,
epsg_code=None,
squid=None):
"""Counts layers matching the specified criteria.
Args:
after_time (:obj:`str`, optional): Matching layers are modified
after this time specified in ISO-8601 format.
before_time (:obj:`str`, optional): Matching layers are modified
before this time specified in ISO-8601 format.
epsg_code (:obj:`int`, optional): Matching layers will have the map
projection specified by this EPSG code.
squid (:obj:`str`, optional): Matching layers will have this hash-
based species identifier.
Returns:
int: The number of matching layers.
"""
return RestService.count(self,
'{}/count'.format(self.end_point),
after_time=after_time,
before_time=before_time,
epsg_code=epsg_code,
squid=squid)
def count(self,
after_time=None,
before_time=None,
cell_sides=None,
cell_size=None,
epsg_code=None):
"""Counts shapegrids matching the provided criteria.
Args:
after_time (:obj:`str`, optional): Count shapegrids modified after
this time (in ISO-8601 format).
before_time (:obj:`str`, optional): Count shapegrids modified
before this time (in ISO-8601 format).
cell_sides (:obj:`int`, optional): Count shapegrids that have cells
with the specified number of sides
(4 - rectangles, 6 - hexagons).
cell_size (:obj:`float`, optional): Count shapegrids with the
specified cell size (resolution).
epsg_code (:obj:`int`, optional): Count shapegrids that were
created using the specified spatial projection represented by
the EPSG code.
Returns:
int: The number of shapegrids matching the provided criteria.
"""
return RestService.count(self,
'{}/count'.format(self.end_point),
after_time=after_time,
before_time=before_time,
cell_sides=cell_sides,
cell_size=cell_size,
epsg_code=epsg_code)
def count(self,
after_time=None,
alt_pred_code=None,
before_time=None,
date_code=None,
epsg_code=None,
gcm_code=None):
"""Counts scenarios matching the provided criteria.
Args:
after_time (str): Count scenarios modified after this time.
alt_pred_code (str): Count scenarios containing this alternate prediction
code.
before_time (str): Count scenarios modified before this time.
date_code (str): Count scenarios with this date code.
epsg_code (int): Count scenarios using this map projection EPSG code.
gcm_code (str): Count scenario using this GCM code.
Returns:
int: The number of scenarios matching the criteria.
"""
return RestService.count(self,
'{}/count'.format(self.end_point),
after_time=after_time,
alt_pred_code=alt_pred_code,
before_time=before_time,
date_code=date_code,
epsg_code=epsg_code,
gcm_code=gcm_code)
def count(self,
after_time=None,
before_time=None,
epsg_code=None,
meta_string=None,
shapegrid_id=None):
"""Counts gridsets matching the provided criteria.
Args:
after_time (str): Count gridsets modified after this time.
before_time (str): Count gridsets modified before this time.
epsg_code (int): The integer representing the map projection EPSG code for
the gridsets to count.
meta_string (str): Metadata string to use to count gridsets.
shapegrid_id (int): Count gridsets built from the shapegrid with this
identifier.
Returns:
int: The number of gridsets matching the provided criteria.
"""
return RestService.count(self,
'{}/count'.format(self.end_point),
after_time=after_time,
meta_string=meta_string,
shapegrid_id=shapegrid_id,
before_time=before_time,
epsg_code=epsg_code)
def get_facets(self):
"""Attempts to get Global PAM facets.
Returns:
list of dict: A list of facets for the gridset.
"""
return RestService.get(self, '{}/gridset'.format(self.end_point))
def list(self,
after_time=None,
before_time=None,
epsg_code=None,
limit=None,
offset=None,
squid=None):
"""Gets a list of layers matching the specified criteria.
Args:
after_time (:obj:`str`, optional): Matching layers are modified
after this time specified in ISO-8601 format.
before_time (:obj:`str`, optional): Matching layers are modified
before this time specified in ISO-8601 format.
epsg_code (:obj:`int`, optional): Matching layers will have the map
projection specified by this EPSG code.
limit (:obj:`int`, optional): Return, at most, this many layers.
offset (:obj:`int`, optional): Offset the returned layers by this
amount. Useful for paging.
squid (:obj:`str`, optional): Matching layers will have this hash-
based species identifier.
Returns:
list of dicts - A list of layer dictionary objects with metadata
about each one. The response format is JSON.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
before_time=before_time,
epsg_code=epsg_code,
squid=squid,
limit=limit,
offset=offset)
def list(self,
after_time=None,
before_time=None,
limit=None,
offset=None,
scenario_id=None):
"""Gets a list of scenario package matching the provided criteria.
Args:
after_time (str): Return scenario packages modified after this time.
before_time (str): Return scenario packages modified before this time.
limit (int): The maximum number of scenario packages to return.
offset (int): Offset the returned scenario packages by this amount.
scenario_id (int): Return scenario packages containing this scenario.
Returns:
list of dict: A list of JSON dictionaries of scenario package metadata for
the matching scenario packages.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
scenario_id=scenario_id,
before_time=before_time,
limit=limit,
offset=offset)
def list(self,
after_time=None,
alt_pred_code=None,
before_time=None,
date_code=None,
epsg_code=None,
env_code=None,
env_type_id=None,
gcm_code=None,
scenario_id=None,
limit=None,
offset=None):
"""Gets a list of environmental layers matching the specified criteria.
Args:
after_time (:obj:`str`, optional): Matching environmental layers
are modified after this time specified in ISO-8601 format.
alt_pred_code (:obj:`str`, optional): Matching environmental layers
must have this alternate prediction code.
before_time (:obj:`str`, optional): Matching environmental layers
are modified before this time specified in ISO-8601 format.
date_code (:obj:`str`, optional): Matching environmental layers
will have this date code.
epsg_code (:obj:`int`, optional): Matching environmental layers
will have the map projection specified by this EPSG code.
env_code (:obj:`str`, optional): Matching environmental layers
will have this environment code.
env_type_id (:obj:`str`, optional): Matching environmental layers
will have this environmental layer type identifier.
gcm_code (:obj:`str`, optional): Matching environmental layers
will have this GCM code.
scenario_id (:obj:`int`, optional): Matching environmental layers
will belong to the Lifemapper scenario specified by this
identifier.
limit (:obj:`int`, optional): Return, at most, this many
environmental layers.
offset (:obj:`int`, optional): Offset the returned environmental
layers by this amount. Useful for paging.
Returns:
list of dicts - A list of environmental layer dictionary objects
with metadata about each one. The response format is JSON.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
alt_pred_code=alt_pred_code,
before_time=before_time,
date_code=date_code,
epsg_code=epsg_code,
env_code=env_code,
env_type_id=env_type_id,
gcm_code=gcm_code,
scenario_id=scenario_id,
limit=limit,
offset=offset)
def list(self,
after_status=None,
after_time=None,
algorithm_code=None,
before_status=None,
before_time=None,
display_name=None,
epsg_code=None,
limit=None,
model_scenario_code=None,
occurrence_set_id=None,
offset=None,
projection_scenario_code=None,
scenario_id=None,
status=None,
gridset_id=None):
"""Gets a list of projections matching the provided criteria.
Args:
after_status (int): Return projections with a status greater than this.
after_time (str): Return projections modified after this time.
algorithm_code (str): Return projections built with this algorithm.
before_status (int): Return projections with a status less than this.
before_time (str): Return projections modified before this time.
display_name (str): Return projections with this display name.
epsg_code (int): Return projections using this map projection.
limit (int): The maximum number of projections to return.
model_scenario_code (str): Return projections built from this model.
occurrence_set_id (int): Return projections built from this occurrence set.
offset (int): Start returned projections after this offset.
projection_scenario_code (str): Return projections using this scenario.
scenario_id (int): Return projections using this scenario identifier.
status (int): Return projections with this exact status.
gridset_id (int): Return projections in this gridset.
Returns:
list of dict: A list of JSON dictionary metadata for matching scenarios.
"""
return RestService.list(
self,
self.end_point,
after_time=after_time,
scenario_id=scenario_id,
before_time=before_time,
limit=limit,
offset=offset,
after_status=after_status,
algorithm_code=algorithm_code,
before_status=before_status,
display_name=display_name,
epsg_code=epsg_code,
model_scenario_code=model_scenario_code,
status=status,
occurrence_set_id=occurrence_set_id,
projection_scenario_code=projection_scenario_code,
gridset_id=gridset_id)
def list(self,
after_time=None,
agent=None,
before_time=None,
catalog_number=None,
collection=None,
ident1=None,
ident2=None,
operation=None,
provider=None,
url=None,
who=None,
why=None):
"""Lists snippets matching the provided criteria.
Args:
after_time (:obj:`str`, optional): Only return snippets modified
after this time (in ISO-8601 format).
agent (:obj:`str`, optional): Return snippets initiated by this
agent.
before_time (:obj:`str`, optional): Only return snippets modified
before this time (in ISO-8601 format).
catalog_number (:obj:`str`, optional): List snippets for occurrence
records with this catalog number.
collection (:obj:`str`, optional): List snippets for this
collection.
ident1 (:obj:`str`, optional): List snippets with this primary
object identifier.
ident2 (:obj:`str`, optional): List snippets with this secondary
object identifier.
operation (:obj:`str`, optional): List snippets for this operation.
provider (:obj:`str`, optional): List snippets for this occurrence
point provider.
url (:obj:`str`, optional): List snippets related to this URL.
who (:obj:`str`, optional): List snippets created by this entity.
why (:obj:`str`, optional): List snippets that were created for
this reason.
Returns:
list of dict: A list of JSON dictionaries for matching snippets.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
agent=agent,
before_time=before_time,
catalog_number=catalog_number,
collection=collection,
ident1=ident1,
ident2=ident2,
operation=operation,
provider=provider,
url=url,
who=who,
why=why)
def delete_tree(self, gridset_id):
"""Attempts to delete a gridset's tree.
Args:
gridset_id (int): The identifier of the tree to delete.
Returns:
HTTP Response: An indication from the server if the delete was successful.
"""
return RestService.delete(
self, '{}/{}/tree'.format(self.end_point, gridset_id))
def delete(self, tree_id):
"""Attempts to delete the tree specified by tree_id.
Args:
tree_id (int): The identifier of the tree to delete.
Returns:
HTTP Response: Indication of deletion success.
"""
return RestService.delete(self, '{}/{}'.format(self.end_point,
tree_id))
def delete(self, shapegrid_id):
"""Attempts to delete a shapegrid.
Args:
shapegrid_id (int): The database identifier of the shapegrid to delete.
Returns:
HTTP Response: HTTP status indicating success.
"""
return RestService.delete(self, '{}/{}'.format(self.end_point,
shapegrid_id))
def delete(self, sdmproject_id):
"""Attempts to delete a projection.
Args:
sdmproject_id (int): The identifier of the projection to delete.
Returns:
HTTP Response: An HTTP response indicating success.
"""
return RestService.delete(
self, '{}/{}'.format(self.end_point, sdmproject_id))
def delete(self, scenario_id):
"""Attempts to delete a scenario.
Args:
scenario_id (int): The identifier of the scenario to delete.
Returns:
HTTP Response: An HTTP status message indicating success.
"""
return RestService.delete(self, '{}/{}'.format(self.end_point,
scenario_id))
def delete(self, gridset_id):
"""Attempts to delete a gridset.
Args:
gridset_id (int): The identifier for the gridset to delete.
Returns:
HTTP Response: Confirmation or failure response associated with the delete
request.
"""
return RestService.delete(self, '{}/{}'.format(self.end_point,
gridset_id))
def delete(self, occurrence_id):
"""Attempts to delete the occurrence set specified by occurrence_id.
Args:
occurrence_id (int): The identifier of the occurrence set to delete.
Returns:
HTTP Response: A response from the server with the HTTP status indicating
success of the delete request.
"""
return RestService.delete(
self, '{}/{}'.format(self.end_point, occurrence_id))
def post(self, scenario_json):
"""Post a new scenario to the server.
Args:
scenario_json (dict): A JSON dictionary of scenario metadata.
Returns:
dict: A JSON dictionary of scenario metadata.
"""
return RestService.post(self,
self.end_point,
body=scenario_json,
headers={'Content-Type': 'application/json'})
def post(self, taxon_ids):
"""Get points for the provided taxon identifiers.
Args:
taxon_ids (list): A list of taxonomic identifiers to get points for.
Returns:
dict: A dictionary (JSON) of metadata about the points request.
"""
return RestService.post(self,
self.end_point,
body=json.dumps(taxon_ids),
headers={'Content-Type': 'application/json'})
def post(self, taxon_ids):
"""Submit a POST request to the Open Tree endpoint to get a tree from ids.
Args:
taxon_ids (list): A list of taxonomic identifiers established by GBIF.
Returns:
dict: A JSON dictionary of Open Tree response data.
"""
return RestService.post(self,
self.end_point,
body=json.dumps(taxon_ids),
headers={'Content-Type': 'application/json'})
def post(self, boom_post_json):
"""POST a new gridset creation request.
Args:
boom_post_json (dict): A JSON dictionary of gridset parameters.
Returns:
HTTP Response: A success indication as an HTTP response status.
"""
return RestService.post(self,
self.end_point,
body=json.dumps(boom_post_json),
headers={'Content-Type': 'application/json'})
def get(self, gridset_id, interface=None):
"""Attempts to get a gridset.
Args:
gridset_id (int): The identifier of the gridset to retrieve.
interface (str): The format interface the gridset should be returned as.
Returns:
xml string: Returned if the interface is 'xml'
dict: A JSON dictionary of gridset metadata.
"""
return RestService.get(self,
'{}/{}'.format(self.end_point, gridset_id),
interface=interface)
def count(self,
after_status=None,
after_time=None,
algorithm_code=None,
before_status=None,
before_time=None,
display_name=None,
epsg_code=None,
model_scenario_code=None,
occurrence_set_id=None,
projection_scenario_code=None,
scenario_id=None,
status=None,
gridset_id=None):
"""Counts projections matching the provided criteria.
Args:
after_status (int): Count projections with a status greater than this.
after_time (str): Count projections modified after this time.
algorithm_code (str): Count projections built with this algorithm.
before_status (int): Count projections with a status less than this.
before_time (str): Count projections modified before this time.
display_name (str): Count projections with this display name.
epsg_code (int): Count projections using this map projection.
model_scenario_code (str): Count projections built from this model.
occurrence_set_id (int): Count projections built from this occurrence set.
projection_scenario_code (str): Count projections using this scenario.
scenario_id (int): Count projections using this scenario identifier.
status (int): Count projections with this exact status.
gridset_id (int): Count projections in this gridset.
Returns:
int: The number of projections matching the criteria.
"""
return RestService.count(
self,
'{}/count'.format(self.end_point),
after_status=after_status,
after_time=after_time,
algorithm_code=algorithm_code,
before_status=before_status,
before_time=before_time,
display_name=display_name,
epsg_code=epsg_code,
model_scenario_code=model_scenario_code,
occurrence_set_id=occurrence_set_id,
projection_scenario_code=projection_scenario_code,
scenario_id=scenario_id,
status=status,
gridset_id=gridset_id)
def post(self, boom_post_json):
"""Post a new experiment.
Args:
boom_post_json (dict): A dictionary of BOOM parameters for submitting an
experiment.
Returns:
HTTP Response: An indication of success of the experiment post.
"""
return RestService.post(self,
self.end_point,
body=boom_post_json,
headers={'Content-Type': 'application/json'})
def post(self, names_list):
"""Submit a request to get accepted names from a provided list of names.
Args:
names_list (list of str): A list of names to get the GBIF accepted names
for, if they are available.
Returns:
dict: A dictionary (JSON) of name translation information.
"""
return RestService.post(self,
self.end_point,
body=json.dumps(names_list),
headers={'Content-Type': 'application/json'})
def get(self, scenario_id, interface=None):
"""Attempts to get a scenario.
Args:
scenario_id (int): The identifier of the scenario to retrieve.
interface (str): The format to return the scenario in.
Returns:
str: XML metadata for the scenario.
dict: JSON dictionary of scenario metadata.
"""
return RestService.get(self,
'{}/{}'.format(self.end_point, scenario_id),
interface=interface)
def list(self,
after_time=None,
before_time=None,
has_branch_lengths=None,
is_binary=None,
is_ultrametric=None,
limit=None,
meta_string=None,
name=None,
offset=None,
user=None):
"""Lists occurrence sets matching the provided criteria.
Args:
after_time (:obj:`str`, optional): Only trees modified after this
time (in ISO-8601 format).
before_time (:obj:`str`, optional): Only return trees modified
before this time (in ISO-8601 format).
has_branch_lengths (:obj:`bool`, optional): Return trees that have
or do not have branch lengths.
is_binary (:obj:`bool`, optional): Return trees that are or are not
binary.
is_ultrametric (:obj:`bool`, optional): Return trees that are or
are not ultrametric.
limit (:obj:`int`, optional): Return up to this number of trees.
meta_string (:obj:`str`, optional): Return trees with this metadata
string attached to them.
name (:obj:`str`, optional): Return trees that have this name.
offset (:obj:`int`, optional): Offset the list of returned trees by
this number.
user (:obj:`str`, optional): If 'public', return public trees. If
'anon', return anonymous trees. If None, return the user's
trees.
Returns:
list of dict: A list of tree metadata JSON dictionaries.
"""
return RestService.list(self,
self.end_point,
after_time=after_time,
before_time=before_time,
has_branch_lengths=has_branch_lengths,
is_binary=is_binary,
is_ultrametric=is_ultrametric,
limit=limit,
meta_string=meta_string,
name=name,
offset=offset,
user=user)
def count(self, after_status=None, after_time=None, before_status=None,
before_time=None, display_name=None, epsg_code=None,
gridset_id=None, minimum_number_of_points=None, squid=None,
status=None, user=None):
"""Counts the number of occurrence sets matching the provided criteria.
Args:
after_status (:obj:`int`, optional): Only return occurrence sets
that have a status value greater than this number.
after_time (:obj:`str`, optional): Only return occurrence sets
modified after this time (in ISO-8601 format).
before_status (:obj:`int`, optional): Only return occurrence sets
that have a status value less than this number.
before_time (:obj:`str`, optional): Only return occurrence sets
modified before this time (in ISO-8601 format).
display_name (:obj:`str`, optional): Only return occurrence sets
that have this display name.
epsg_code (:obj:`int`, optional): Only return occurrence sets that
have this EPSG code.
gridset_id (:obj:`int`, optional): Only return occurrence sets that
are part of the gridset with this ID.
minimum_number_of_points (:obj:`int`, optional): Only return
occurrence sets that have at least this many points.
squid (:obj:`str`, optional): Only return occurrence sets that have
this squid (hash value for species identifier).
status (:obj:`int`, optional): Only return occurrence sets that
have this status.
user (:obj:`str`, optional): If 'public', return public occurrence
sets. If 'anon', return anonymous occurrence sets. If None,
return the user's occurrence sets.
Returns:
int: The number of matching occurrence set records.
"""
return RestService.count(
self,
'{}/count'.format(self.end_point),
after_status=after_status,
after_time=after_time,
before_status=before_status,
before_time=before_time,
display_name=display_name,
epsg_code=epsg_code,
gridset_id=gridset_id,
minimum_number_of_points=minimum_number_of_points,
squid=squid,
status=status,
user=user
)
def list(self, search_string, limit=None):
"""Gets a list of specie hint matches.
Args:
search_string (str): A partial string to match species names against.
limit (int): The maximum number of results to return.
Returns:
list of strings: List of matching species.
"""
return RestService.list(
self,
'{}/{}'.format(self.end_point, search_string),
limit=limit
)