Package intermine :: Module query :: Class Template

Class Template

object --+    
         |    
     Query --+
             |
            Template

A Class representing a predefined query

Templates are ways of saving queries and allowing others to run them simply. They are the main interface to querying in the webapp

SYNOPSIS

example:

 service = Service("http://www.flymine.org/query/service")
 template = service.get_template("Gene_Pathways")
 for row in template.results(A={"value":"eve"}):
   process_row(row)
   ...

A template is a subclass of query that comes predefined. They are typically retrieved from the webservice and run by specifying the values for their existing constraints. They are a concise and powerful way of running queries in the webapp.

Being subclasses of query, everything is true of them that is true of a query. They are just less work, as you don't have to design each one. Also, you can store your own templates in the web-app, and then access them as a private webservice method, from anywhere, making them a kind of query in the cloud - for this you will need to authenticate by providing log in details to the service.

The most significant difference is how constraint values are specified for each set of results.

See Also: Template.results

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
Instantiation is identical that of queries.

source code

dict

to_query_params(self)
Template.to_query_params() -> dict(string, string)

source code

string

get_results_path(self)
Template.get_results_path() → str

source code

Template

get_adjusted_template(self, con_values)
Template.get_adjusted_template(con_values) → Template

source code

intermine.webservice.ResultIterator

results(self, row='object', start=0, size=None, **con_values)
This method returns the same values with the same options as the method of the same name in Query (see intermine.query.Query). source code

list

get_results_list(self, row='object', start=0, size=None, **con_values)
This method performs the same as the method of the same name in Query, and it shares the semantics of Template.results(). source code

get_row_list(self, start=0, size=None, **con_values)
Return a list of the rows returned by this query

source code

iterable<intermine.webservice.ResultRow>

rows(self, start=0, size=None, **con_values)
Get an iterator over the rows returned by this query

source code

int

count(self, **con_values)
Obtain the number of rows a particular query will return, without having to fetch and parse all the actual data.

source code

Inherited from Query: __add__, __and__, __iter__, __len__, __or__, __str__, __sub__, __xor__, add_constraint, add_join, add_path_description, add_sort_order, add_view, children, clear_view, clone, column, first, get_constraint, get_default_sort_order, get_list_append_uri, get_list_upload_uri, get_logic, get_sort_order, get_subclass_dict, make_list_constraint, one, outerjoin, prefix_path, select, set_logic, summarise, to_Node, to_formatted_xml, to_query, to_xml, validate_logic, validate_sort_order, verify, verify_constraint_paths, verify_join_paths, verify_pd_paths, verify_views, where

Inherited from Query (private): _from_paths, _set_questionable_logic

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Methods

[hide private]

Inherited from Query: from_xml

Class Variables

[hide private]

Inherited from Query: LEADING_OP_PATTERN, LOGIC_OPS, LOGIC_PRODUCT, LOGIC_SPLIT_PATTERN, ORPHANED_OP_PATTERN, SO_SPLIT_PATTERN, TRAILING_OP_PATTERN, x, y

Properties

[hide private]

editable_constraints
Template.editable_constraints -> list(intermine.constraints.Constraint)

Inherited from Query: coded_constraints, constraints

Inherited from object: __class__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

source code

Constructor

Instantiation is identical that of queries. As with queries, these are best obtained from the intermine.webservice.Service factory methods.

Parameters:

model - an instance of intermine.model.Model. Required
service - an instance of l{intermine.service.Service}. Optional, but you will not be able to make requests without one.
validate - a boolean - defaults to True. If set to false, the query will not try and validate itself. You should not set this to false.

Overrides: object.__init__

to_query_params(self)

source code

Returns the query parameters needed for the webservice

Template.to_query_params() -> dict(string, string)

Overrides the method of the same name in query to provide the parameters needed by the templates results service. These are slightly more complex:

name: The template's name
for each constraint: (where [i] is an integer incremented for each constraint)
- constraint[i]: the path
- op[i]: the operator
- value[i]: the value
- code[i]: the code
- extra[i]: the extra value for ternary constraints (optional)

Returns: dict
Overrides: Query.to_query_params

get_results_path(self)

source code

Returns the path section pointing to the REST resource

Template.get_results_path() → str

Internally, this just calls a constant property in intermine.service.Service

This overrides the method of the same name in Query

Returns: string: the path to the REST resource
Overrides: Query.get_results_path

get_adjusted_template(self, con_values)

source code

Gets a template to run

Template.get_adjusted_template(con_values) → Template

When templates are run, they are first cloned, and their values are changed to those desired. This leaves the original template unchanged so it can be run again with different values. This method does the cloning and changing of constraint values

Returns: Template

Raises:

ConstraintError - if the constraint values specify values for a non-editable constraint.

results(self, row=`'object'`, start=0, size=None, **con_values)

source code

Get an iterator over result rows

This method returns the same values with the same options as the method of the same name in Query (see intermine.query.Query). The main difference in in the arguments.

The template result methods also accept a key-word pair set of arguments that are used to supply values to the editable constraints. eg:

 template.results(
   A = {"value": "eve"},
   B = {"op": ">", "value": 5000}
 )

The keys should be codes for editable constraints (you can inspect these with Template.editable_constraints) and the values should be a dictionary of constraint properties to replace. You can replace the values for "op" (operator), "value", and "extra_value" and "values" in the case of ternary and multi constraints.

Parameters:

row - The format for each result. One of "object", "rr", "dict", "list", "tsv", "csv", "jsonrows", "jsonobjects"
start - the index of the first result to return (default = 0)
size - The maximum number of results to return (default = all)
summary_path - A column name to optionally summarise. Specifying a path will force "jsonrows" format, and return an iterator over a list of dictionaries. Use this when you are interested in processing a summary in order of greatest count to smallest.

Returns: intermine.webservice.ResultIterator

Raises:

WebserviceError - if the request is unsuccessful

Overrides: Query.results

get_results_list(self, row=`'object'`, start=0, size=None, **con_values)

source code

Get a list of result rows

This method performs the same as the method of the same name in Query, and it shares the semantics of Template.results().

Returns: list
Overrides: Query.get_results_list

See Also:: intermine.query.Query.get_results_list, intermine.query.Template.results

get_row_list(self, start=0, size=None, **con_values)

source code

Return a list of the rows returned by this query

Overrides: Query.get_row_list

rows(self, start=0, size=None, **con_values)

source code

Get an iterator over the rows returned by this query

Parameters:

start - the index of the first result to return (default = 0)
size - The maximum number of results to return (default = all)

Returns: iterable<intermine.webservice.ResultRow>

Overrides: Query.rows

count(self, **con_values)

source code

Return the total number of rows this template returns

Obtain the number of rows a particular query will return, without having to fetch and parse all the actual data. This method makes a request to the server to report the count for the query, and is sugar for a results call.

Returns: int

Raises:

WebserviceError - if the request is unsuccessful.

Overrides: Query.count

Property Details

[hide private]

editable_constraints

Return the list of constraints you can edit

Template.editable_constraints -> list(intermine.constraints.Constraint)

Templates have a concept of editable constraints, which is a way of hiding complexity from users. An underlying query may have five constraints, but only expose the one that is actually interesting. This property returns this subset of constraints that have the editable flag set to true.

Get Method:: unreachable.editable_constraints(self) - Template.editable_constraints -> list(intermine.constraints.Constraint)

Class Template

A Class representing a predefined query

SYNOPSIS

__init__(self, *args, **kwargs) (Constructor)

Constructor

to_query_params(self)

Returns the query parameters needed for the webservice

get_results_path(self)

Returns the path section pointing to the REST resource

get_adjusted_template(self, con_values)

Gets a template to run

results(self, row='object', start=0, size=None, **con_values)

Get an iterator over result rows

get_results_list(self, row='object', start=0, size=None, **con_values)

Get a list of result rows

get_row_list(self, start=0, size=None, **con_values)

rows(self, start=0, size=None, **con_values)

count(self, **con_values)

Return the total number of rows this template returns

editable_constraints

Return the list of constraints you can edit

init(self, *args, **kwargs)
(Constructor)

results(self, row=`'object'`, start=0, size=None, **con_values)

get_results_list(self, row=`'object'`, start=0, size=None, **con_values)