Labcollector Web Service Application Programming Interface Software User Guide

Version 2.0 – November 2021
Web Service Application Programming Interface Software
User Guide

Web Service Application Programming Interface Software

INTRODUCTION

The LabCollector Web Service Application Programming Interface (API) allows third-party applications to interact with LabCollector’s database (modules) and add- ons (ELN and LSM).
The API is based on a Representational State Transfer (REST) architecture allowing access to resources through Uniform Resource Identifier (URI) and actions on them.
Note: Since June 2017 API v1 was discontinued and all new evolutions are in API v2.

LABCOLLECTOR API

2-1. API setup
First of all, you have to declare your application in your LabCollector software. To access the application declaration setup form, log in to LabCollector with super-administrator rights and go to Admin > Setup page. Then select the Web Service API link. You are now on the Web Service API applications management page. To declare a new application, simply complete this form:

• Name: name of your application.
• Modules connected to this application: select modules in which the application can access.
• Default operator: select the contact that will be the default operator if you don’t want to insert this information in each request.
• IP Restriction: security option allows you to declare a list of IP addresses, which will be allowed you to perform requests on the API.

The Application list shows all the applications for your LabCollector and you can, at any time, modify their scope.
You have also access to the Token which is necessary to identify your application during requests to the API.

Note: To use this feature, you need to activate Curl on your PHP preferences. In Linux, install the PHP-Curl package.
On windows and with our automatic installer, edit PHP.ini and uncomment extensions for Curl (extension=php_curl.dll).
2-2. Requests
The dialog between third-party applications and the LabCollector web service API is based on the HTTP 1.1 protocol.
2-2-1. API Method
You can send HTTP or HTTPS requests to the web service with a method to act on a resource.

• GET method for reading a resource
• POST method to create a new resource
• PUT method to modify a resource
• DELETE method to delete a resource

2-2-2. Headers
A request to the API requires some specific HTTP/HTTPS headers:

• The Accept header defines the desired response format of your request, text/XML, or application/JSON.
• The X-LC-APP-Auth header is where you put your application token which is necessary to authorize your request to the API.
• The X-LC-APP-Charset header defines the character encoding of your application. It allows the API to send back the response with the appropriate encoding and to correctly convert your POST and PUT requests to the LabCollector’s character encoding (ISO 8859-1).

2-2-3. Tool
You can try to retrieve data from or send data to the API with some software app as Postman (https://www.getpostman.com/).

Uniform Resource Identifier (URI)

2-3-1. GET method
General
Each LabCollector module data is identified by a unique URI (see annex for a complete list of the module’s URI):
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE] This request replies to the list of all data in a module.
You can do searching into module data by adding parameters to your URI. You can pass a parameter with a keyword matching a field value, like:[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?name=[KEYWORD]e.g.
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?name=First%20Record
This request returns the records where their name value contains the “First Record” keyword.
They are some custom parameters that the API uses to perform searching and filtering actions.
Custom parameters

• The record_id parameter to specify data by its ID:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?record_id=[RECORD_ID]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?record_id=1,19
This request returns records with ID 1 and ID 19. You can specify multiple IDs by separating them with a comma.

• The by_keywords parameter performs a keyword search:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?by_keywords=[KEYWORD]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?by_keywords=cell
This request performs a search into all fields of all records and returns matching cells. You can specify multiple keywords by separating them with a comma.

• The by_keywords parameter performs a keyword search:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?by_keywords=[KEYWORD]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?by_keywords=cell
This request performs a search into all fields of all records and returns a matching cell. You can specify multiple keywords by separating them with a comma.

• The fields parameters, If you want to retrieve only some fields values in the API response:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?fields=[FIELD1],[FIELD2]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?fields=count,name
This request returns all records from the module but with only count and name fields. You can specify multiple fields by separating them with a comma.
The request accepts now multiple values separated by a comma, for custom fields of type “select”

• The search_on parameter allows you to search for data. And you can use it to search by date range as follow:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]&
search_on=date_field&from=XXXXXX&to=ZZZZZZ
If you only use FROM, the result will give all dates bigger than the FROM date. If you only use too, it will return all the value until this date.

• The sort_by parameter allows you to sort your search:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?sort_by=[FIELD1]_DESC
e.g. [PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?sort_by=name_DESC
This request returns all records sorted in descending order on the name field. You can specify multiple sort_by separating them with a comma and specified order ascendant  _ASC” or descendant “_DESC” for each field.

• The limit_to parameter allows you to limit the number of results:

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]?limit_to=0,10
This request returns 10 records beginning at index 0. If you do not specify the index, only the number of results indicated is returned.
The API also returns two custom fields in the header response, “X-LC-QUERY-RESULT” containing the number of results returned in the body response and “X-LC-QUERY- TOTAL” containing the total of records matching your search.
Each record also has a unique URI:
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]/[DATA_ID]
This request replies a unique record. [DATA_ID] must match the unique ID of the record you want to retrieve.
Storage
You also have Tube Sorter filtering functions for every item linked to storage:
[PATH_TO_LABCOLLECTOR]/webservice/index.php?v=2&action=tube_sorter&box_i d=[BOX_ID]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.php?v=2&action=tube_sorter&box_i d=34
This request returns storage info on box ID 34 like tube sorter. You can specify multiple IDs by separating them with a comma.

[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&box_i d=[BOX_ID]&record_name=[RECORD_NAME]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&box_i d=206&record_name=ST-260
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&recor d_name=[RECORD_NAME]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&recor d_name=ST-260
These requests perform filtering on a record named ST-260. You can specify multiple record names by separating them with a comma. You can also specify box ID, here 206.[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&box_n ame=[BOX_NAME]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=tube_sorter&box_n ame=test-rack_06
This request performs filtering on box test-rack_06. You can specify multiple box names by separating them with a comma.
Other search parameters to action=tube_sorter can be:

• location_id
• location_name
• facility_id
• facility_name
  It will return empty boxes as well.
• The storage_sec parameter allows retrieving information about secondary storage.

[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]&data_id=[DATA_ID]& fields=storage_sec

Product lot

• The action get lot allows retrieving lot and reagent info

[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getLot
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getLot&lo t_id=1/LT
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getLot&ch em_id=2
Optional parameters are lot_id (in format 1 or 1/LT) and chem_id. If it doesn’t receive parameters, then it retrieves all active lots.
Recipe
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe s
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe &recipe_id=[record_id]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe &recipe_id=509
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe Logs
[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe Report&log_id=[record_id]
e.g. [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action=getRecipe Report&log_id=1218
IDs are examples but are mandatory in these calls.
get recipes prints the following info: id, name, description, category

get recipes prints the following info for that recipe_id: id, name, description, category, and then the components getRecipeLogs prints the following info: id, name, description, category getRecipeReport prints the report PDF for that log_id under the format base64 that can be decoded into PDF.

2-3-2. POST method
To create a new resource, simply send a request with the POST method to the desired module URI:
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]
Your parameter keys have to match the field’s name.
Check for uniqueness fields that have been added, when creating new records (POST) or update (PUT)
If exists a different record with the same value for a field Uniqueness, API will not complete the action and will return code 409 (Conflict), and the text: Value for field ‘XXX’ must be unique. Value ‘YYY’ already exists in table ‘ZZZ’. (see screenshot) 

Note: project_code field can be used in POST and PUT and it expects text (not id). You can now create a new project code if it does not exist and if the operator has permissions enough (administrator or super-administrator).

• The action addBox allows you to create a box

[PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2&action= addBox

• Required parameters:
  o name
  o type (must be a valid type: box, box_nogrid, plate, microplate, visit be, bag, shelf part)
  o equipment (supports id or name and must exist in LabCollector storage).
  o size (depends on the type of box: should be numeric for a visit be, and the format (A:1.H:8) for a box, a plate, and a microplate)
• Optional parameters:
  o description
  o rack
  o keeper

2-3-3. PUT method
To modify a resource, simply send a request with the PUT method to the desired record URI:
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]/[DATA_ID]
Your parameter keys have to match the field’s name you want to modify.
For the following actions, note that for PUT requests, parameters must be on the body (not in the URL).
The URL is [PATH_TO_LABCOLLECTOR]/webservice/index.PHP?v=2
The headers are: X-LC-APP-Auth, Accept.

• Remove Volume
  – Parameters:
  o removeVolume (mandatory)
  o barcode, unique_code, or aliquot_barcode (one of them must be present)
  o quantity (mandatory)
  – Response: OK
  
• Remove Storage
  – Parameters:
  o remote storage (mandatory)
  o barcode, unique_code, or aliquot_barcode (one of them must be present)
  – Response: OK
  
• Add Registry Book
  – URL:
  [PATH_TO_LABCOLLECTOR]/webservice/index.php?v=2&module=[m odule]
  – Parameters:
  o addRegistryBook (mandatory)
  o record_id (mandatory)
  o date (mandatory, format yy yy/mm/dd or yyyy-mm-dd)
  o comments (mandatory)
  o operator (optional, if it does not send the API default operator will be used)
  o action (optional, must be a valid ‘Storage Action Type’ defined in LC
  >Admin >Preferences > Process & Actions Type)
  – Response: OK
  
• Add Secondary storage
  – Parameters:
  o add secondary storage (mandatory)
  o barcode (mandatory)
  o box_id (mandatory)
  o box_details (mandatory only for the box with grid divider, tube tray, and microplate. If the box is without a grid, a bag, a visit be or a shelf part, it is not required)
  o unique_code (optional)
  o volume (optional)
  o comments (optional)
  o cap_color (optional)

Note: An error message is returned if mandatory parameters are not present; if the barcode does not exist; if the unique_code is present, but it isn’t unique; and, if the color is present but it doesn’t exist.
If the parameter box_details is not received and the type of box needs position (box with grid, tube tray, or microplate), an error message is returned. Note: project_code field can be used in POST and PUT and it expects text (not id). You can now create a new project code if it does not exist and if the operator has permissions enough (administrator or super-administrator).
2-3-4. DELETE method
To delete a resource, simply send a request with the DELETE method to the desired record URI:
[PATH_TO_LABCOLLECTOR]/webservice/v2/[MODULE]/[DATA_ID]

API ERROR MESSAGES

LABCOLLECTOR WEB SERVICE API – ANNEX

The URI system of the API uses a simple and clean URL. Be sure to enable the rewrite engine from Apache to use the URI referenced in the following table. If the LabCollector server does not support the rewrite engine please use the full URL pattern for your request (secondary URL of each line).

http://[email protected]
AgileBio USA
5473 Kearny Villa Road Suite 255
San Diego, CA 92123
USA
Tel: 347 368 1315
Fax: (800) 453 9128
http://www.agilebio.com
AgileBio Headquarters
75 rue de Lourmel
75015 Paris
FRANCE
Tel: 01 41 79 15 85
Fax: 01 72 70 40 22

References

• IT solutions for laboratories - AgileBio
• IT solutions for laboratories - AgileBio
• All-in-One Lab Management & Notebook | LabCollector LIMS
• All-in-One Lab Management & Notebook | LabCollector LIMS
• Postman