acarapetis / libDAL-Python3

Python 3 interface to DAL

Python 3 DALClient library!

Very similar to the Java DALClient library.

How to Install

clone this repo:

git clone https://github.com/kddart/libDAL-Python3.git

Then:

cd libDAL-python3
sudo python3 setup.py install

Example usage:

(Remember to replace 'YOUR_URL' with a valid KDDart instance DAL URL) (DAL REST documentation, along with all commands can be found at: http://www.kddart.org/reference.html)

from diversityarrays.dalclient.DefaultDALClient import DefaultDALClient
from diversityarrays.dalclient.ResponseType import ResponseType
from diversityarrays.dalclient.DALResponseVisitor import DALResponseVisitor
from diversityarrays.dalclient.DALResponseException import DALResponseException
from diversityarrays.dalclient.DALEntityBuilder import DALEntityBuilder
import getpass

"""
Below is the example login for DALClient along with some basic commands
and response handling
"""

# URL of the KddartInstance
url = "YOUR_URL"

# Username for User
user = input("Please enter username: ")

# Password (entered)
password = getpass.getpass()

# Initialising client and setting the URL
client = DefaultDALClient(debug=1)
client.URL = url

# Setting response content type to .json
client.reponse_type = ResponseType(xmlTrue=False)

# Logging In
client.login(user, password)

# Queries the dal for a response to list Genus's
dalResponse = client.perform_query("list/genus")

# Building a visitor function and passing it in to visit the response records (Genus's)
# If the visitor function returns True, it means continue, this way a visitor loop can be
# Broken once a specific entity is found.
def visitorFunction(responseRecord):
    print("Row data for object ->" + str(responseRecord.rowdata))
dalResponse.visit_response(DALResponseVisitor(visitorFunction))

# List to be populated
genuses = []

# Building a visitor function and passing it in to visit the response records (Genus's)
# Here though Class objects reflecting the entity e.g. Genus, are created dynamically for use.
# Also, the visitor function always returns ture, meaning we want to visit every entity returned.
def visitorFunction(genus):
    genuses.append(genus)
    print("Genus name for found entity: " + str(genus.GenusName))
    return True

dalResponse.visit_entities(DALResponseVisitor(visitorFunction))

# Queries the dal to get Specimen with id: 424856 (May not be applicable to your Kddart)
dalResponse = client.perform_query("get/specimen/%s" % "424856")

# Building a visitor function and passing it in to visit the response records (Specimen's)
def visitorFunction(specimen):
    print("Specimen name " + str(specimen.SpecimenName))
    print("Pedigree: " + str(specimen.Pedigree))
    print("Filial generation: " + str(specimen.FilialGeneration))
    return True

    # DAL provides entities with nested data sometimes.
    # This can be useful. In the example of Specimen, its
    # Genotype is returned as nested data (This is also dynamically turned into an object):
    specimenGenotype = specimen.Genotype[0]

    print("Genotype name: " + str(specimenGenotype.GenotypeName))
    print("Genotype Id: " + str(specimenGenotype.GenotypeId))

dalResponse.visit_entities(DALResponseVisitor(visitorFunction))

# using Site Id (This may not be applicable to your Kddart)
siteId = 1

# Listing Trials for Site 1
dalResponse = client.perform_query("site/%s/list/trial" % siteId)

# Printing Id and Name of Trials for site 1
def visitorFunction(trial):
    print("Found Trial Id: " + trial.TrialId)
    print("Found Trial Name: " + trial.TrialName)
    return True

dalResponse.visit_entities(DALResponseVisitor(visitorFunction))

# Uploading a new Genus (For other entities check the APIDoc at www.Kddart.org)
newGenusData = {"GenusName":"Dartian"}
response = client.perform_update("add/genus", newGenusData)

# Lets set the Id's for the new Genus (returned by dal)
print(str(response.returned_ids))
returnedIds = response.returned_ids
for idObject in returnedIds:
    # Setting a new Id field
    idFieldName = idObject[DefaultDALClient.ATTR_PARA_NAME]
    id = idObject[DefaultDALClient.ATTR_VALUE]

    # Adding to the map of to-be attributes for the new object
    newGenusData[idFieldName] = id

# We can use this to build a new Genus object from the entity data
entityBuilder = DALEntityBuilder()
genusObject = entityBuilder.build_entity("Genus", newGenusData)

# Lets look at the new entity!
print("New genus Id in Kddart -> " + genusObject.GenusId)

# If we attempt to add the a Genus of the same name again, we get an error:
try:
 response = client.perform_update("add/genus", newGenusData)
except DALResponseException as e:
    pass

# Exporting samples for all Trial's available (This may not be applicable to your Kddart - if you have no Trial data)
response = client.perform_query("export/samplemeasurement/csv")

# Output files to collect for download (DAL creates the file on the fly following the export query)
outputFiles = response.output_files

# Download the content. It is returned, or you can specify a file to write the data to
content = client.download_file(outputFiles[0]["csv"], localFile="./TrialData.csv")

See Direcotory: 'Examples' for some more simple examples.