def test_simple_equals(self):
expected = {
"fieldName": "cntn_id",
"operator": "equals",
"value": "test"
}
self.assertEqual(expected, equals("cntn_id", "test").to_dict())
def test_fetch_advanced(self):
def request_callback(request):
body = json.loads(request.body)
self.assertEqual(body["startRow"], 0)
self.assertEqual(body["endRow"], 1)
self.assertEqual(body["sortBy"], ["cntn_createdOn"])
self.assertEqual(body["criteria"]["operator"], "equals")
self.assertEqual(body["criteria"]["fieldName"], "cntn_id")
self.assertEqual(body["criteria"]["value"], "test")
return (200, {}, json.dumps({"entities": []}))
responses.add_callback(
responses.GET,
'http://localhost:9999/rest/Content/advanced',
callback=request_callback,
content_type='application/json',
)
slims = Slims("testSlims", "http://localhost:9999", "admin", "admin")
entities = slims.fetch("Content",
equals("cntn_id", "test"),
sort=["cntn_createdOn"],
start=0,
end=1)
self.assertEquals(entities, [])
def test_not(self):
expected = {
"operator":
"not",
"criteria": [
{
"fieldName": "cntn_id",
"operator": "equals",
"value": "test"
},
]
}
criteria = is_not(equals("cntn_id", "test"))
self.assertEqual(expected, criteria.to_dict())
def test_conjunction(self):
expected = {
"operator":
"and",
"criteria": [
{
"fieldName": "cntn_id",
"operator": "equals",
"value": "test"
},
{
"fieldName": "cntn_barCode",
"operator": "iStartsWith",
"value": "blah"
},
]
}
criteria = conjunction().add(equals("cntn_id", "test")).add(
starts_with("cntn_barCode", "blah"))
self.assertEqual(expected, criteria.to_dict())
# Example N_1:
# We fetch Content records without criteria
# This means that the fetch includes all the contents in the database
# By giving start and end parameters the output is limited to the 10th to the
# 30th record to be returned
print("Example 1")
records = slims.fetch("Content", None, start=10, end=30)
# The fields cntn_id and cntn_barCode of the content records will be displayed
display_results(records, ["cntn_id", "cntn_barCode"])
# Example N_2:
# Fetching content records with the equals criteria;
# The parameters are the field on which to filter and the value. This way the
# filter only returns contents whose cntn_id is equal to "fish"
print("\n\nExample 2")
records = slims.fetch("Content", equals("cntn_id", "fish"))
display_results(records, ["cntn_id", "cntn_createdOn"])
# Example N_3:
# Fetching content records with a conjunction (and). This filters
# on content records for which the cntn_id is not null and the cntn_id starts
# with fish
print("\n\nExample 3")
records = slims.fetch(
"Content",
conjunction().add(is_not_null("cntn_id")).add(
starts_with("cntn_id", "fish")))
# display_results has three arguments, the list of records, the list of fields
# to display and finally the number of results to display
display_results(records, ["cntn_id"], 10)
from __future__ import print_function
import web
from web import form
from slims.slims import Slims
from slims.criteria import is_not
from slims.criteria import equals
from slims.content import Status
render = web.template.render('templates/')
slims = Slims("slims", "http://localhost:9999", "admin", "admin")
# Populate the comboboxes
# Searching for data by fetching
order_types = slims.fetch("OrderType", None)
content_types = slims.fetch("ContentType", equals("cntp_useBarcodeAsId", True))
locations = slims.fetch("Location", None)
requestables = slims.fetch("Requestable", is_not(equals("rqbl_type", "WORKFLOW")))
dic_order_type = {}
for order_type in order_types:
dic_order_type.update({order_type.rdtp_name.value: order_type})
dic_content_type = {}
for content_type in content_types:
dic_content_type.update({content_type.cntp_name.value: content_type})
dic_location = {}
for location in locations:
dic_location.update({location.lctn_name.value: location})
A BMI Calculation is done based on both.
The plotting requires matplotlib (pip install matplotlib)
run this script using the underneath command in the folder plotting
python main.py
"""
from __future__ import division
from slims.slims import Slims
from slims.criteria import equals, is_one_of
import matplotlib.pyplot as plt
slims = Slims("slims", "http://localhost:9999", "admin", "admin")
# Data fetch -> selection of patients and their results
patients = slims.fetch("Content", equals("cntp_name", "Patient"))
patient_pks = map(lambda patient: patient.pk(), patients)
results = slims.fetch("Result", is_one_of("rslt_fk_content", patient_pks))
lengths = []
weights = []
BMI = []
x_axis_values = []
# Identification of the result per test
print("Fetching necessary data...")
for result in results:
# first identification the length Test results
if result.rslt_fk_test.displayValue in "length Test":
lengths.append(result.rslt_value.value)
from __future__ import print_function
from slims.slims import Slims
from slims.criteria import equals
from slims.content import Status
import sys
slims = Slims("slims", "http://localhost:9999", "admin", "admin")
# Example N_1: Creating a content record; here a Content of content type DNA
# in the location Building Test. Requires a location called
# "Building test" (of location type Building) and a content type
# "DNA" (with use barcode as id)
print("Example 1")
# Fetch DNA content type
dna_type = slims.fetch("ContentType", equals("cntp_name", "DNA"))
if not dna_type:
sys.exit("No DNA Content type found, can not continue")
# Fetch Building Test location (ideally with location type Building,
# but this is not mandatory)
locations = slims.fetch("Location", equals("lctn_name", "Building Test"))
if not locations:
sys.exit("No location called Building Test found, can not continue")
print("Creating DNA Record...")
created_dna = slims.add(
"Content", {
'cntn_fk_contentType': dna_type[0].pk(),