labarchive-integration

Name: labarchive-integration
Author: K-Dense-AI

31kstars3.1kforks

How to install labarchive-integration?

k-dense-ai/scientific-agent-skills/labarchive-integration

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill labarchive-integration

Installs into the current project.

Summary

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Files · 1

View on GitHub

SKILL.md

1	# LabArchives Integration
2
3	## Overview
4
5	LabArchives is an electronic lab notebook platform for research documentation and data management. Access notebooks, manage entries and attachments, generate reports, and integrate with third-party tools programmatically via REST API.
6
7	## When to Use This Skill
8
9	This skill should be used when:
10	- Working with LabArchives REST API for notebook automation
11	- Backing up notebooks programmatically
12	- Creating or managing notebook entries and attachments
13	- Generating site reports and analytics
14	- Integrating LabArchives with third-party tools (Protocols.io, Jupyter, REDCap)
15	- Automating data upload to electronic lab notebooks
16	- Managing user access and permissions programmatically
17
18	## Core Capabilities
19
20	### 1. Authentication and Configuration
21
22	Set up API access credentials and regional endpoints for LabArchives API integration.
23
24	Prerequisites:
25	- Enterprise LabArchives license with API access enabled
26	- API access key ID and password from LabArchives administrator
27	- User authentication credentials (email and external applications password)
28
29	Configuration setup:
30
31	Use the `scripts/setup_config.py` script to create a configuration file:
32
33	```bash
34	python3 scripts/setup_config.py
35	```
36
37	This creates a `config.yaml` file with the following structure:
38
39	```yaml
40	api_url: https://api.labarchives.com/api # or regional endpoint
41	access_key_id: YOUR_ACCESS_KEY_ID
42	access_password: YOUR_ACCESS_PASSWORD
43	```
44
45	Regional API endpoints:
46	- US/International: `https://api.labarchives.com/api`
47	- Australia: `https://auapi.labarchives.com/api`
48	- UK: `https://ukapi.labarchives.com/api`
49
50	For detailed authentication instructions and troubleshooting, refer to `references/authentication_guide.md`.
51
52	### 2. User Information Retrieval
53
54	Obtain user ID (UID) and access information required for subsequent API operations.
55
56	Workflow:
57
58	1. Call the `users/user_access_info` API method with login credentials
59	2. Parse the XML/JSON response to extract the user ID (UID)
60	3. Use the UID to retrieve detailed user information via `users/user_info_via_id`
61
62	Example using Python wrapper:
63
64	```python
65	from labarchivespy.client import Client
66
67	# Initialize client
68	client = Client(api_url, access_key_id, access_password)
69
70	# Get user access info
71	login_params = {'login_or_email': user_email, 'password': auth_token}
72	response = client.make_call('users', 'user_access_info', params=login_params)
73
74	# Extract UID from response
75	import xml.etree.ElementTree as ET
76	uid = ET.fromstring(response.content)[0].text
77
78	# Get detailed user info
79	params = {'uid': uid}
80	user_info = client.make_call('users', 'user_info_via_id', params=params)
81	```
82
83	### 3. Notebook Operations
84
85	Manage notebook access, backup, and metadata retrieval.
86
87	Key operations:
88
89	- List notebooks: Retrieve all notebooks accessible to a user
90	- Backup notebooks: Download complete notebook data with optional attachment inclusion
91	- Get notebook IDs: Retrieve institution-defined notebook identifiers for integration with grants/project management systems
92	- Get notebook members: List all users with access to a specific notebook
93	- Get notebook settings: Retrieve configuration and permissions for notebooks
94
95	Notebook backup example:
96
97	Use the `scripts/notebook_operations.py` script:
98
99	```bash
100	# Backup with attachments (default, creates 7z archive)
101	python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID
102
103	# Backup without attachments, JSON format
104	python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID --json --no-attachments
105	```
106
107	API endpoint format:
108	```
109	https://<api_url>/notebooks/notebook_backup?uid=<UID>&nbid=<NOTEBOOK_ID>&json=true&no_attachments=false
110	```
111
112	For comprehensive API method documentation, refer to `references/api_reference.md`.
113
114	### 4. Entry and Attachment Management
115
116	Create, modify, and manage notebook entries and file attachments.
117
118	Entry operations:
119	- Create new entries in notebooks
120	- Add comments to existing entries
121	- Create entry parts/components
122	- Upload file attachments to entries
123
124	Attachment workflow:
125
126	Use the `scripts/entry_operations.py` script:
127
128	```bash
129	# Upload attachment to an entry
130	python3 scripts/entry_operations.py upload --uid USER_ID --nbid NOTEBOOK_ID --entry-id ENTRY_ID --file /path/to/file.pdf
131
132	# Create a new entry with text content
133	python3 scripts/entry_operations.py create --uid USER_ID --nbid NOTEBOOK_ID --title "Experiment Results" --content "Results from today's experiment..."
134	```
135
136	Supported file types:
137	- Documents (PDF, DOCX, TXT)
138	- Images (PNG, JPG, TIFF)
139	- Data files (CSV, XLSX, HDF5)
140	- Scientific formats (CIF, MOL, PDB)
141	- Archives (ZIP, 7Z)
142
143	### 5. Site Repo

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labarchive-integration

31kstars3.1kforks

View on GitHub

How to install labarchive-integration?

k-dense-ai/scientific-agent-skills/labarchive-integration

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill labarchive-integration

Installs into the current project.

Summary

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Files · 1

View on GitHub

SKILL.md

1	# LabArchives Integration
2
3	## Overview
4
5	LabArchives is an electronic lab notebook platform for research documentation and data management. Access notebooks, manage entries and attachments, generate reports, and integrate with third-party tools programmatically via REST API.
6
7	## When to Use This Skill
8
9	This skill should be used when:
10	- Working with LabArchives REST API for notebook automation
11	- Backing up notebooks programmatically
12	- Creating or managing notebook entries and attachments
13	- Generating site reports and analytics
14	- Integrating LabArchives with third-party tools (Protocols.io, Jupyter, REDCap)
15	- Automating data upload to electronic lab notebooks
16	- Managing user access and permissions programmatically
17
18	## Core Capabilities
19
20	### 1. Authentication and Configuration
21
22	Set up API access credentials and regional endpoints for LabArchives API integration.
23
24	Prerequisites:
25	- Enterprise LabArchives license with API access enabled
26	- API access key ID and password from LabArchives administrator
27	- User authentication credentials (email and external applications password)
28
29	Configuration setup:
30
31	Use the `scripts/setup_config.py` script to create a configuration file:
32
33	```bash
34	python3 scripts/setup_config.py
35	```
36
37	This creates a `config.yaml` file with the following structure:
38
39	```yaml
40	api_url: https://api.labarchives.com/api # or regional endpoint
41	access_key_id: YOUR_ACCESS_KEY_ID
42	access_password: YOUR_ACCESS_PASSWORD
43	```
44
45	Regional API endpoints:
46	- US/International: `https://api.labarchives.com/api`
47	- Australia: `https://auapi.labarchives.com/api`
48	- UK: `https://ukapi.labarchives.com/api`
49
50	For detailed authentication instructions and troubleshooting, refer to `references/authentication_guide.md`.
51
52	### 2. User Information Retrieval
53
54	Obtain user ID (UID) and access information required for subsequent API operations.
55
56	Workflow:
57
58	1. Call the `users/user_access_info` API method with login credentials
59	2. Parse the XML/JSON response to extract the user ID (UID)
60	3. Use the UID to retrieve detailed user information via `users/user_info_via_id`
61
62	Example using Python wrapper:
63
64	```python
65	from labarchivespy.client import Client
66
67	# Initialize client
68	client = Client(api_url, access_key_id, access_password)
69
70	# Get user access info
71	login_params = {'login_or_email': user_email, 'password': auth_token}
72	response = client.make_call('users', 'user_access_info', params=login_params)
73
74	# Extract UID from response
75	import xml.etree.ElementTree as ET
76	uid = ET.fromstring(response.content)[0].text
77
78	# Get detailed user info
79	params = {'uid': uid}
80	user_info = client.make_call('users', 'user_info_via_id', params=params)
81	```
82
83	### 3. Notebook Operations
84
85	Manage notebook access, backup, and metadata retrieval.
86
87	Key operations:
88
89	- List notebooks: Retrieve all notebooks accessible to a user
90	- Backup notebooks: Download complete notebook data with optional attachment inclusion
91	- Get notebook IDs: Retrieve institution-defined notebook identifiers for integration with grants/project management systems
92	- Get notebook members: List all users with access to a specific notebook
93	- Get notebook settings: Retrieve configuration and permissions for notebooks
94
95	Notebook backup example:
96
97	Use the `scripts/notebook_operations.py` script:
98
99	```bash
100	# Backup with attachments (default, creates 7z archive)
101	python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID
102
103	# Backup without attachments, JSON format
104	python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID --json --no-attachments
105	```
106
107	API endpoint format:
108	```
109	https://<api_url>/notebooks/notebook_backup?uid=<UID>&nbid=<NOTEBOOK_ID>&json=true&no_attachments=false
110	```
111
112	For comprehensive API method documentation, refer to `references/api_reference.md`.
113
114	### 4. Entry and Attachment Management
115
116	Create, modify, and manage notebook entries and file attachments.
117
118	Entry operations:
119	- Create new entries in notebooks
120	- Add comments to existing entries
121	- Create entry parts/components
122	- Upload file attachments to entries
123
124	Attachment workflow:
125
126	Use the `scripts/entry_operations.py` script:
127
128	```bash
129	# Upload attachment to an entry
130	python3 scripts/entry_operations.py upload --uid USER_ID --nbid NOTEBOOK_ID --entry-id ENTRY_ID --file /path/to/file.pdf
131
132	# Create a new entry with text content
133	python3 scripts/entry_operations.py create --uid USER_ID --nbid NOTEBOOK_ID --title "Experiment Results" --content "Results from today's experiment..."
134	```
135
136	Supported file types:
137	- Documents (PDF, DOCX, TXT)
138	- Images (PNG, JPG, TIFF)
139	- Data files (CSV, XLSX, HDF5)
140	- Scientific formats (CIF, MOL, PDB)
141	- Archives (ZIP, 7Z)
142
143	### 5. Site Repo

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Type