Source code for nexusLIMS.instruments
# This file has been co-edited by both Euclid Techlabs and NIST.
# For LICENSING information, please refer to the LICENSE file in the root directory of NexusLIMS
"""
**Attributes**
Attributes
----------
instrument_db : dict
A dictionary of :py:class:`~nexusLIMS.instruments.Instrument` objects.
Each object in this dictionary represents an instrument detected in the
NexusLIMS remote database.
"""
from nexusLIMS.utils import is_subpath as _is_subpath
from nexusLIMS.utils import get_from_db
import os as _os
import nexusLIMS
CONFIG = nexusLIMS.get_config()
[docs]def get_instrument_db():
"""
Connect to the NexusLIMS database and get a list of all the instruments
contained within.
Returns
-------
instrument_db : dict
A dictionary of `Instrument` instances that describe all the
instruments that were found in the ``instruments`` table of the
NexusLIMS database
"""
results, col_names = get_from_db("SELECT * from instruments")
instr_db = {}
for line in results:
this_dict = {}
for key, val in zip(col_names, line):
this_dict[key] = val
key = this_dict.pop('instrument_pid')
this_dict['name'] = key
instr_db[key] = Instrument(**this_dict)
return instr_db
[docs]class Instrument:
"""
A simple object to hold information about an instrument in the Microscopy
Nexus facility, fetched from the external NexusLIMS database
Parameters
----------
api_url : str or None
The calendar API url for this instrument
calendar_name : str or None
The "user-friendly" name of the calendar for this instrument as
displayed on the sharepoint resource (e.g. "FEI Titan TEM")
calendar_url : str or None
The URL to this instrument's web-accessible calendar on the
sharepoint resource
location : str or None
The physical location of this instrument (building and room number)
name : str or None
The unique identifier for an instrument in the Nexus Microscopy facility
schema_name : str or None
The name of instrument as defined in the Nexus Microscopy schema and
displayed in the records
property_tag : str or None
The NIST property tag for this instrument
filestore_path : str or None
The path (relative to the Nexus facility root) on the central file
storage where this instrument stores its data
computer_name : str or None
The name of the 'support PC' connected to this instrument
computer_ip : str or None
The REN IP address of the 'support PC' connected to this instrument
computer_mount : str or None
The full path where the files are saved on the 'support PC' for the
instrument (e.g. 'M:/')
"""
def __init__(self,
api_url=None,
calendar_name=None,
calendar_url=None,
location=None,
name=None,
schema_name=None,
property_tag=None,
filestore_path=None,
computer_ip=None,
computer_name=None,
computer_mount=None):
"""
Create a new Instrument
"""
self.api_url = api_url
self.calendar_name = calendar_name
self.calendar_url = calendar_url
self.location = location
self.name = name
self.schema_name = schema_name
self.property_tag = property_tag
self.filestore_path = filestore_path
self.computer_ip = computer_ip
self.computer_name = computer_name
self.computer_mount = computer_mount
def __repr__(self):
return f'Nexus Instrument: {self.name}\n' \
f'API url: {self.api_url}\n' \
f'Calendar name: {self.calendar_name}\n' \
f'Calendar url: {self.calendar_url}\n' \
f'Schema name: {self.schema_name}\n' \
f'Location: {self.location}\n' \
f'Property tag: {self.property_tag}\n' \
f'Filestore path: {self.filestore_path}\n' \
f'Computer IP: {self.computer_ip}\n' \
f'Computer name: {self.computer_name}\n' \
f'Computer mount: {self.computer_mount}\n'
def __str__(self):
return f'{self.name}' + f' in {self.location}' if self.location else ''
[docs]def get_instr_from_filepath(path):
"""
Using the NexusLIMS database, get an instrument object by a given path.
Parameters
----------
path : str
A path (relative or absolute) to a file saved in the central
filestore that will be used to search for a matching instrument
Returns
-------
instrument : Instrument or None
An `_Instrument` instance matching the path, or None if no match was
found
Examples
--------
>>> inst = get_instr_from_filepath('/mnt/**REMOVED**_mmfnexus/Titan/**REMOVED**/' +
... '190628 - **REMOVED** Training/' +
... '6_28_2019 Box6 4S/4_330mm.dm3')
>>> str(inst)
'**REMOVED** in **REMOVED**'
"""
for k, v in get_instrument_db().items():
if _is_subpath(path, _os.path.join(CONFIG["mmfnexus_path"],
v.filestore_path)):
return v
return None
[docs]def get_instr_from_calendar_name(cal_name):
"""
Using the NexusLIMS database, get an instrument object by a calendar name.
Parameters
----------
cal_name : str
A calendar name (e.g. "**REMOVED**") that will be used to search
for a matching instrument in the ``api_url`` values
Returns
-------
instrument : Instrument or None
An `_Instrument` instance matching the path, or None if no match was found.
Examples
--------
>>> inst = get_instr_from_calendar_name('JEOL_TEM_01')
>>> str(inst)
'JEOL_TEM_01 in Location_01'
"""
# To-do: calendar_name in Instrument class and the database is currently set to be the same as
# instrument_pid. This was inherited from the original NexusLIMS, but can be changed.
# In the SQLite, instrument_pid and api_url have to be unique, but calendar_name does not.
# If ones needs this function to do its job, then calendar_name needs to be unique,
# but it can be different from instrument_pid
for k, v in get_instrument_db().items():
if cal_name == v.calendar_name:
return v
return None
[docs]def get_instr_from_api_url(url):
"""
Using the NexusLIMS database, get an instrument object by a calendar API url.
Parameters
----------
url : str
The **unique** API url for the instrument calendar.
Returns
-------
instrument : Instrument or None
An `_Instrument` instance matching the API url, or None if no match was found.
Examples
--------
>>> inst = get_instr_from_api_url('URL_FOR_YOUR_INSTRUMENT_CALENDAR')
>>> str(inst)
'JEOL_TEM_01 in Location_01'
"""
for k, v in get_instrument_db().items():
if url == v.api_url:
return v
return None
