senaite.api 1.1.0

SENAITE API

SENAITE API

The API provides a unified interface for developers to work with SENAITE CORE.

SENAITE API DOCTEST

The SENAITE LIMS API provides single functions for single purposes. This Test builds completely on the API without any further imports needed.

Running this test from the buildout directory:

bin/test test_doctests -t API

Introduction

The purpose of this API is to help coders to follow the DRY principle (Don’t Repeat Yourself). It also ensures that the most effective and efficient method is used to achieve a task.

Import it first:

>>> from senaite import api

Getting the Portal

The Portal is the SENAITE LIMS root object:

>>> portal = api.get_portal()
>>> portal
<PloneSite at /plone>

Getting the Bika Setup object

The Bika Setup object gives access to all of the Bika configuration settings:

>>> bika_setup = api.get_bika_setup()
>>> bika_setup
<BikaSetup at /plone/bika_setup>

Creating new Content

Creating new contents in Bika LIMS requires some special knowledge. This function helps to do it right and creates a content for you.

Here we create a new Client in the plone/clients folder:

>>> client = api.create(portal.clients, "Client", title="Test Client")
>>> client
<Client at /plone/clients/client-1>

 >>> client.Title()
 'Test Client'

Getting a Tool

There are many ways to get a tool in Bika LIMS / Plone. This function centralizes this functionality and makes it painless:

>>> api.get_tool("bika_setup_catalog")
<BikaSetupCatalog at /plone/bika_setup_catalog>

Trying to fetch an non-existing tool raises a custom SenaiteAPIError.

>>> api.get_tool("NotExistingTool")
Traceback (most recent call last):
[...]
SenaiteAPIError: No tool named 'NotExistingTool' found.

This error can also be used for custom methods with the fail function:

>>> api.fail("This failed badly")
Traceback (most recent call last):
[...]
SenaiteAPIError: This failed badly

Getting an Object

Getting a tool from a catalog brain is a common task in Bika LIMS. This function provides an unified interface to portal objects and brains. Furthermore it is idempotent, so it can be called multiple times in a row.

We will demonstrate the usage on the client object we created above:

>>> api.get_object(client)
<Client at /plone/clients/client-1>

>>> api.get_object(api.get_object(client))
<Client at /plone/clients/client-1>

Now we show it with catalog results:

>>> portal_catalog = api.get_tool("portal_catalog")
>>> brains = portal_catalog(portal_type="Client")
>>> brains
[<Products.ZCatalog.Catalog.mybrains object at 0x...>]

>>> brain = brains[0]

>>> api.get_object(brain)
<Client at /plone/clients/client-1>

>>> api.get_object(api.get_object(brain))
<Client at /plone/clients/client-1>

No supported objects raise an error:

>>> api.get_object(object())
Traceback (most recent call last):
[...]
SenaiteAPIError: <object object at 0x...> is not supported.

To check if an object is supported, e.g. is an ATCT, Dexterity, ZCatalog or Portal object, we can use the is_object function:

  >>> api.is_object(client)
  True

  >>> api.is_object(brain)
  True

  >>> api.is_object(api.get_portal())
  True

  >>> api.is_object(None)
  False

>>> api.is_object(object())
  False

Checking if an Object is the Portal

Sometimes it can be handy to check if the current object is the portal:

>>> api.is_portal(portal)
True

>>> api.is_portal(client)
False

>>> api.is_portal(object())
False

Checking if an Object is a Catalog Brain

Knowing if we have an object or a brain can be handy. This function checks this for you:

>>> api.is_brain(brain)
True

>>> api.is_brain(api.get_object(brain))
False

>>> api.is_brain(object())
False

Checking if an Object is a Dexterity Content

This function checks if an object is a Dexterity content type:

>>> api.is_dexterity_content(client)
False

>>> api.is_dexterity_content(portal)
False

We currently have no Dexterity contents, so testing this comes later…

Checking if an Object is an AT Content

This function checks if an object is an Archetypes content type:

>>> api.is_at_content(client)
True

>>> api.is_at_content(portal)
False

>>> api.is_at_content(object())
False

Getting the Schema of a Content

The schema contains the fields of a content object. Getting the schema is a common task, but differs between ATContentType based objects and Dexterity based objects. This function brings it under one umbrella:

>>> schema = api.get_schema(client)
>>> schema
<Products.Archetypes.Schema.Schema object at 0x...>

Catalog brains are also supported:

>>> api.get_schema(brain)
<Products.Archetypes.Schema.Schema object at 0x...>

Getting the Fields of a Content

The fields contain all the values that an object holds and are therefore responsible for getting and setting the information.

This function returns the fields as a dictionary mapping of {“key”: value}:

>>> fields = api.get_fields(client)
>>> fields.get("ClientID")
<Field ClientID(string:rw)>

Catalog brains are also supported:

>>> api.get_fields(brain).get("ClientID")
<Field ClientID(string:rw)>

Getting the ID of a Content

Getting the ID is a common task in Bika LIMS. This function takes care that catalog brains are not waked up for this task:

>>> api.get_id(portal)
'plone'

>>> api.get_id(client)
'client-1'

>>> api.get_id(brain)
'client-1'

Getting the Title of a Content

Getting the Title is a common task in Bika LIMS. This function takes care that catalog brains are not waked up for this task:

>>> api.get_title(portal)
u'Plone site'

>>> api.get_title(client)
'Test Client'

>>> api.get_title(brain)
'Test Client'

Getting the Description of a Content

Getting the Description is a common task in Bika LIMS. This function takes care that catalog brains are not waked up for this task:

>>> api.get_description(portal)
''

>>> api.get_description(client)
''

>>> api.get_description(brain)
''

Getting the UID of a Content

Getting the UID is a common task in Bika LIMS. This function takes care that catalog brains are not waked up for this task.

The portal object actually has no UID. This funciton defines it therfore to be 0:

>>> api.get_uid(portal)
'0'

>>> uid_client = api.get_uid(client)
>>> uid_client_brain = api.get_uid(brain)
>>> uid_client is uid_client_brain
True

Getting the URL of a Content

Getting the URL is a common task in Bika LIMS. This function takes care that catalog brains are not waked up for this task:

>>> api.get_url(portal)
'http://nohost/plone'

>>> api.get_url(client)
'http://nohost/plone/clients/client-1'

>>> api.get_url(brain)
'http://nohost/plone/clients/client-1'

Getting the Icon of a Content

>>> api.get_icon(client)
'<img width="16" height="16" src="http://nohost/plone/++resource++bika.lims.images/client.png" title="Test Client" />'

>>> api.get_icon(brain)
'<img width="16" height="16" src="http://nohost/plone/++resource++bika.lims.images/client.png" title="Test Client" />'

>>> api.get_icon(client, html_tag=False)
'http://nohost/plone/++resource++bika.lims.images/client.png'

>>> api.get_icon(client, html_tag=False)
'http://nohost/plone/++resource++bika.lims.images/client.png'

Getting an object by UID

This function finds an object by its uinique ID (UID). The portal object with the defined UId of ‘0’ is also supported:

>>> api.get_object_by_uid('0')
<PloneSite at /plone>

>>> api.get_object_by_uid(uid_client)
<Client at /plone/clients/client-1>

>>> api.get_object_by_uid(uid_client_brain)
<Client at /plone/clients/client-1>

If a default value is provided, the function will never fail. Any exception or error will result in the default value being returned:

>>> api.get_object_by_uid('invalid uid', 'default')
'default'

>>> api.get_object_by_uid(None, 'default')
'default'

Getting an object by Path

This function finds an object by its physical path:

>>> api.get_object_by_path('/plone')
<PloneSite at /plone>

>>> api.get_object_by_path('/plone/clients/client-1')
<Client at /plone/clients/client-1>

Paths outside the portal raise an error:

>>> api.get_object_by_path('/root')
Traceback (most recent call last):
[...]
SenaiteAPIError: Not a physical path inside the portal.

Any exception returns default value:

>>> api.get_object_by_path('/invaid/path', 'default')
'default'

>>> api.get_object_by_path(None, 'default')
'default'

Getting the Physical Path of an Object

The physical path describes exactly where an object is located inside the portal. This function unifies the different approaches to get the physical path and does so in the most efficient way:

>>> api.get_path(portal)
'/plone'

>>> api.get_path(client)
'/plone/clients/client-1'

>>> api.get_path(brain)
'/plone/clients/client-1'

>>> api.get_path(object())
Traceback (most recent call last):
[...]
SenaiteAPIError: <object object at 0x...> is not supported.

Getting the Physical Parent Path of an Object

This function returns the physical path of the parent object:

>>> api.get_parent_path(client)
'/plone/clients'

>>> api.get_parent_path(brain)
'/plone/clients'

However, this function goes only up to the portal object:

>>> api.get_parent_path(portal)
'/plone'

Like with the other functions, only portal objects are supported:

>>> api.get_parent_path(object())
Traceback (most recent call last):
[...]
SenaiteAPIError: <object object at 0x...> is not supported.

Getting the Parent Object

This function returns the parent object:

>>> api.get_parent(client)
<ClientFolder at /plone/clients>

Brains are also supported:

>>> api.get_parent(brain)
<ClientFolder at /plone/clients>

The function can also use a catalog query on the portal_catalog and return a brain, if the passed parameter catalog_search was set to true.

>>> api.get_parent(client, catalog_search=True)
<Products.ZCatalog.Catalog.mybrains object at 0x...>

>>> api.get_parent(brain, catalog_search=True)
<Products.ZCatalog.Catalog.mybrains object at 0x...>

However, this function goes only up to the portal object:

>>> api.get_parent(portal)
<PloneSite at /plone>

Like with the other functions, only portal objects are supported:

>>> api.get_parent(object())
Traceback (most recent call last):
[...]
SenaiteAPIError: <object object at 0x...> is not supported.

Searching Objects

Searching in Bika LIMS requires knowledge in which catalog the object is indexed. This function unifies all Bika LIMS catalog to a single search interface:

>>> results = api.search({'portal_type': 'Client'})
>>> results
[<Products.ZCatalog.Catalog.mybrains object at 0x...>]

Multiple content types are also supported:

>>> results = api.search({'portal_type': ['Client', 'ClientFolder'], 'sort_on': 'getId'})
>>> map(api.get_id, results)
['client-1', 'clients']

Now we create some objects which are located in the bika_setup_catalog:

>>> instruments = bika_setup.bika_instruments
>>> instrument1 = api.create(instruments, "Instrument", title="Instrument-1")
>>> instrument2 = api.create(instruments, "Instrument", title="Instrument-2")
>>> instrument3 = api.create(instruments, "Instrument", title="Instrument-3")

>>> results = api.search({'portal_type': 'Instrument', 'sort_on': 'getId'})
>>> len(results)
3

>>> map(api.get_id, results)
['instrument-1', 'instrument-2', 'instrument-3']

Queries which result in multiple catalogs will be refused, as it would require manual merging and sorting of the results afterwards. Thus, we fail here:

>>> results = api.search({'portal_type': ['Client', 'ClientFolder', 'Instrument'], 'sort_on': 'getId'})
Traceback (most recent call last):
[...]
SenaiteAPIError: Multi Catalog Queries are not supported, please specify a catalog.

Catalog queries w/o any portal_type, default to the portal_catalog, which will not find the following items:

>>> analysiscategories = bika_setup.bika_analysiscategories
>>> analysiscategory1 = api.create(analysiscategories, "AnalysisCategory", title="AC-1")
>>> analysiscategory2 = api.create(analysiscategories, "AnalysisCategory", title="AC-2")
>>> analysiscategory3 = api.create(analysiscategories, "AnalysisCategory", title="AC-3")

>>> results = api.search({"id": "analysiscategory-1"})
>>> len(results)
0

Would we add the portal_type, the search function would ask the archetype_tool for the right catalog, and it would return a result:

>>> results = api.search({"portal_type": "AnalysisCategory", "id": "analysiscategory-1"})
>>> len(results)
1

We could also explicitly define a catalog to achieve the same:

>>> results = api.search({"id": "analysiscategory-1"}, catalog="bika_setup_catalog")
>>> len(results)
1

To see inactive or dormant items, we must explicitly query them of filter them afterwars manually:

>>> results = api.search({"portal_type": "AnalysisCategory", "id": "analysiscategory-1"})
>>> len(results)
1

Now we deactivate the item:

>>> analysiscategory1 = api.do_transition_for(analysiscategory1, 'deactivate')
>>> api.is_active(analysiscategory1)
False

The search will still find the item:

>>> results = api.search({"portal_type": "AnalysisCategory", "id": "analysiscategory-1"})
>>> len(results)
1

Unless we filter it out manually:

>>> len(filter(api.is_active, results))
0

Or provide a correct query:

>>> results = api.search({"portal_type": "AnalysisCategory", "id": "analysiscategory-1", "inactive_status": "active"})
>>> len(results)
1

Getting the registered Catalogs

Bika LIMS uses multiple catalogs registered via the Archetype Tool. This function returns a list of registered catalogs for a brain or object:

>>> api.get_catalogs_for(client)
[<CatalogTool at /plone/portal_catalog>]

>>> api.get_catalogs_for(instrument1)
[<BikaSetupCatalog at /plone/bika_setup_catalog>, <CatalogTool at /plone/portal_catalog>]

>>> api.get_catalogs_for(analysiscategory1)
[<BikaSetupCatalog at /plone/bika_setup_catalog>]

Getting an Attribute of an Object

This function handles attributes and methods the same and returns their value. It also handles security and is able to return a default value instead of raising an Unauthorized error:

>>> uid_brain = api.safe_getattr(brain, "UID")
>>> uid_obj = api.safe_getattr(client, "UID")

>>> uid_brain == uid_obj
True

>>> api.safe_getattr(brain, "review_state")
'active'

>>> api.safe_getattr(brain, "NONEXISTING")
Traceback (most recent call last):
[...]
SenaiteAPIError: Attribute 'NONEXISTING' not found.

>>> api.safe_getattr(brain, "NONEXISTING", "")
''

Getting the Portal Catalog

This tool is needed so often, that this function just returns it:

>>> api.get_portal_catalog()
<CatalogTool at /plone/portal_catalog>

Getting the Review History of an Object

The review history gives information about the objects’ workflow changes:

>>> review_history = api.get_review_history(client)
>>> sorted(review_history[0].items())
[('action', None), ('actor', 'test_user_1_'), ('comments', ''), ('review_state', 'active'), ('time', DateTime('...'))]

Getting the Revision History of an Object

The review history gives information about the objects’ workflow changes:

>>> revision_history = api.get_revision_history(client)
>>> sorted(revision_history[0])
['action', 'actor', 'actor_home', 'actorid', 'comments', 'review_state', 'state_title', 'time', 'transition_title', 'type']
>>> revision_history[0]["transition_title"]
u'Create'

Getting the assigned Workflows of an Object

This function returns all assigned workflows for a given object:

>>> api.get_workflows_for(bika_setup)
('bika_one_state_workflow',)

>>> api.get_workflows_for(client)
('bika_client_workflow', 'bika_inactive_workflow')

This function also supports the portal_type as parameter:

>>> api.get_workflows_for(api.get_portal_type(client))
('bika_client_workflow', 'bika_inactive_workflow')

Getting the Workflow Status of an Object

This function returns the state of a given object:

>>> api.get_workflow_status_of(client)
'active'

It is also capable to get the state of another state variable:

>>> api.get_workflow_status_of(client, "inactive_state")
'active'

Deactivate the client:

>>> api.do_transition_for(client, "deactivate")
<Client at /plone/clients/client-1>

>>> api.get_workflow_status_of(client, "inactive_state")
'inactive'

>>> api.get_workflow_status_of(client)
'active'

Reactivate the client:

>>> api.do_transition_for(client, "activate")
<Client at /plone/clients/client-1>

>>> api.get_workflow_status_of(client, "inactive_state")
'active'

Getting the registered Catalogs of an Object

This function returns a list of all registered catalogs within the archetype_tool for a given portal_type or object:

>>> api.get_catalogs_for(client)
[<CatalogTool at /plone/portal_catalog>]

It also supports the portal_type as a parameter:

>>> api.get_catalogs_for("Analysis")
[<BikaAnalysisCatalog at /plone/bika_analysis_catalog>]

Transitioning an Object

This function performs a workflow transition and returns the object:

>>> client = api.do_transition_for(client, "deactivate")
>>> api.is_active(client)
False

>>> client = api.do_transition_for(client, "activate")
>>> api.is_active(client)
True

Getting inactive/cancellation state of different workflows

There are two workflows allowing an object to be set inactive. We provide the is_active function to return False if an item is set inactive with either of these workflows.

In the search() test above, the is_active function’s handling of brain states is tested. Here, I just want to test if object states are handled correctly.

For setup types, we use bika_inctive_workflow:

>>> method1 = api.create(portal.methods, "Method", title="Test Method")
>>> api.is_active(method1)
True
>>> method1 = api.do_transition_for(method1, 'deactivate')
>>> api.is_active(method1)
False

For transactional types, bika_cancellation_workflow is used:

>>> batch1 = api.create(portal.batches, "Batch", title="Test Batch")
>>> api.is_active(batch1)
True
>>> batch1 = api.do_transition_for(batch1, 'cancel')
>>> api.is_active(batch1)
False

Getting the granted Roles for a certain Permission on an Object

This function returns a list of Roles, which are granted the given Permission for the passed in object:

>>> api.get_roles_for_permission("Modify portal content", bika_setup)
['LabManager', 'Manager']

Checking if an Object is Versionable

Some contents in Bika LIMS support versioning. This function checks this for you.

Instruments are not versionable:

>>> api.is_versionable(instrument1)
False

Analysisservices are versionable:

>>> analysisservices = bika_setup.bika_analysisservices
>>> analysisservice1 = api.create(analysisservices, "AnalysisService", title="AnalysisService-1")
>>> analysisservice2 = api.create(analysisservices, "AnalysisService", title="AnalysisService-2")
>>> analysisservice3 = api.create(analysisservices, "AnalysisService", title="AnalysisService-3")

>>> api.is_versionable(analysisservice1)
True

Getting the Version of an Object

This function returns the version as an integer:

>>> api.get_version(analysisservice1)
0

Calling processForm bumps the version:

>>> analysisservice1.processForm()
>>> api.get_version(analysisservice1)
1

Getting a Browser View

Getting a browser view is a common task in Bika LIMS:

>>> api.get_view("plone")
<Products.Five.metaclass.Plone object at 0x...>

>>> api.get_view("workflow_action")
<Products.Five.metaclass.WorkflowAction object at 0x...>

Getting the Request

This function will return the global request object:

>>> api.get_request()
<HTTPRequest, URL=http://nohost>

Getting a Group

Users in Bika LIMS are managed in groups. A common group is the Clients group, where all users of client contacts are grouped. This function gives easy access and is also idempotent:

>>> clients_group = api.get_group("Clients")
>>> clients_group
<GroupData at /plone/portal_groupdata/Clients used for /plone/acl_users/source_groups>

>>> api.get_group(clients_group)
<GroupData at /plone/portal_groupdata/Clients used for /plone/acl_users/source_groups>

Non-existing groups are not found:

>>> api.get_group("NonExistingGroup")

Getting a User

Users can be fetched by their user id. The function is idempotent and handles user objects as well:

>>> from plone.app.testing import TEST_USER_ID
>>> user = api.get_user(TEST_USER_ID)
>>> user
<MemberData at /plone/portal_memberdata/test_user_1_ used for /plone/acl_users>

>>> api.get_user(api.get_user(TEST_USER_ID))
<MemberData at /plone/portal_memberdata/test_user_1_ used for /plone/acl_users>

Non-existing users are not found:

>>> api.get_user("NonExistingUser")

Getting User Properties

User properties, like the email or full name, are stored as user properties. This means that they are not on the user object. This function retrieves these properties for you:

>>> properties = api.get_user_properties(TEST_USER_ID)
>>> sorted(properties.items())
[('description', ''), ('email', ''), ('error_log_update', 0.0), ('ext_editor', False), ...]

>>> sorted(api.get_user_properties(user).items())
[('description', ''), ('email', ''), ('error_log_update', 0.0), ('ext_editor', False), ...]

An empty property dict is returned if no user could be found:

>>> api.get_user_properties("NonExistingUser")
{}

>>> api.get_user_properties(None)
{}

Getting Users by their Roles

>>> from operator import methodcaller

Roles in Bika LIMS are basically a name for one or more permissions. For example, a LabManager describes a role which is granted the most permissions.

To see which users are granted a certain role, you can use this function:

>>> labmanagers = api.get_users_by_roles(["LabManager"])
>>> sorted(labmanagers, key=methodcaller('getId'))
[<PloneUser 'test_labmanager'>, <PloneUser 'test_labmanager1'>, <PloneUser 'test-user'>]

A single value can also be passed into this function:

>>> sorted(api.get_users_by_roles("LabManager"), key=methodcaller('getId'))
[<PloneUser 'test_labmanager'>, <PloneUser 'test_labmanager1'>, <PloneUser 'test-user'>]

Getting the Current User

Getting the current logged in user:

>>> api.get_current_user()
<MemberData at /plone/portal_memberdata/test_user_1_ used for /plone/acl_users>

Changelog

1.1.0 (2018-01-03)

Added

Removed

Changed

• License changed to GPLv2

• Integration to SENAITE CORE

Fixed

• Fixed Tests

Security

1.0.2 (2017-11-24)

• #397(bika.lims) Fix Issue-396: AttributeError: uid_catalog on AR publication

1.0.1 (2017-09-30)

• Fixed broken release (missing MANIFEST.in)

1.0.0 (2017-09-30)

• First release