mofdb-client 0.10.0

Simple client for fetching data from mofdb

mofdb-client

A typed, fast, lightweight, client wrapping the mofdb api. This client is the fastest way to access mofdb since it utilizes the streaming bulk API. Using the regular paginated API will be slow for large page numbers.

Installation

python3 -m pip install mofdb_client==0.9.0

Example

from mofdb_client import fetch
for mof in fetch(vf_min=0.5, vf_max=0.99):
    print(f"Mof {mof.name} has {len(mof.isotherms)} isotherms and elements {[str(e) for e in mof.elements]}")
    print(f"This mof's cif file starts with: '{mof.cif.splitlines()[1]}'")

Mof UTEWUM_clean has 2 isotherms and elements ['Cu', 'H', 'C', 'N']
This mof's cif file starts with: '_audit_creation_date              2014-07-02'
Mof ZECKID_clean has 1 isotherms and elements ['Cu', 'H', 'C', 'N', 'O']
This mof's cif file starts with: '_audit_creation_date              2014-07-02'
Mof AQOMAW_clean has 2 isotherms and elements ['N', 'C', 'H', 'Co', 'Cl', 'O']
This mof's cif file starts with: '_cell_length_a       18.8345'
Mof AQOLOJ_clean has 2 isotherms and elements ['N', 'C', 'H', 'Co', 'Cl']
This mof's cif file starts with: '_cell_length_a       18.794'
Mof SENWOZ_clean has 2 isotherms and elements ['Zn', 'H', 'C', 'O']
This mof's cif file starts with: '_audit_creation_date              2014-07-02'
Mof IYUCIQ_clean has 2 isotherms and elements ['Dy', 'O', 'N', 'C', 'H']
This mof's cif file starts with: '_cell_length_a       29.162'
Mof ORUKET_clean has 2 isotherms and elements ['P', 'O', 'N', 'C', 'H', 'Mg']
This mof's cif file starts with: '_cell_length_a       18.571'
...

Parameters

fetch supports a number of arguments

• name: str
• pressure_unit: str
• loading_unit: str
• mofid: str
• mofkey: str
• vf_min: float
• vf_max: float
• lcd_min: float
• lcd_max: float
• pld_min: float
• pld_max: float
• sa_m2g_min: float
• sa_m2g_max: float
• sa_m2cm3_min: float
• sa_m2cm3_max: float
• database: str
• limit: int
• telemetry: bool default true (see telemetry section)

For valid values of pressure_units go here mof.tech.northwestern.edu/classifications.json. The mofdb_client will reject invalid units/pressures and throw InvalidUnit exception.

Design Note

fetch is lazy because mofDB is large. Be sure to loop over it with for mof in fetch() and NOT for mof in list(fetch()) since building the list will download all the mofs before it starts processing and this will be very slow and may well run out of memory.

Compatibility

Tested on Python 3.7 to 3.11.

Future Enhancements:

• Retries for transient network failures with exponential backoff
• Support for unit conversions
• Only download some columns to save time/bandwidth?

Telemetry

This package may phone home crash reports that happen in library code when the telemetry arg is true. This is done using sentry. Nothing in addition to fetch params and data captured by default by sentry is ever captured.

For example this could include:

• a stack trace including your code
• operating system version
• time
• python runtime version
• hostname
• anything else sentry captures by default

Publishing a new version

Update pyproject.toml version

python3 -m build -n
python3 -m twine upload dist/*

Change log

0.9.0

Do not report mofdb exceptions like "InvalidUnit" to sentry error monitoring. These indicate user error.

0.8.0

Fix for crashes on queries returning no mofs. Required a change to mofdb repo as well. Add a 204.response file to zip stream to signal empty response.