# Test the low level fbget API, which defines a 1-1 mapping of the entire suite
# of FireBrowse RESTful api endpoints to a series of Python classes and members
# within them.  The low level interface is therefore more verbose (and somewhat
# less Pythonic than) the high level interface (which scientific end users may
# generally prefer, for its brevity and sensible choice of defaults, et cetera)

import firebrowse as fb
from testcommon import *

S = fb.Samples()
A = fb.Analyses()
M = fb.Metadata()

# Use long-winded syntax, with a pathologically ugly but still usable gene list
result = S.mRNASeq(gene="tp53, brca1      ,    ,    ,   egfr         ", cohort="brca",page=fb.PAGES_ALL,format="tsv")
baseline = "tests/baselines/BRCA-paged-mRNASeq-egfr-brca1-tp53.tsv"
baseline = open(baseline, "r").read()
compare(result, baseline, "mRNASeq(gene=BRCA-tp53-brca1-egfr)")

call="http://%s/api/v1/Analyses/Mutation/MAF?format=tsv&cohort=tHcA&tool=MutSig2CV&page_size=2&page=3" % fb.get_host()
baseline = fb.requests.get(call).text
result = A.MutationMAF(format="tsv", cohort="tHcA", tool="MutSig2CV", page_size=2, page=3)
compare(result, baseline, "MutationMAF()")

print "---- BEGIN MutationMAF help for zero-arg call"
print A.MutationMAF()
print "---- END   MutationMAF help for zero-arg call"

# Test importing all of firebrowse into current namespace, and using "as is"
from firebrowse import *
#   ... and while we're at it, exercise object-level defaults for page & format
samples_djson = Samples(page=fb.PAGES_ALL,format=fb.CODEC_DJSON)
#   ... showing how they are utilized by default for methods of that class
result = samples_djson.mRNASeq(gene="tp53,brca1,egfr", cohort="brca")
print type(result)
print result.keys()
# As of 2015_02_04 dataset this returned 3636 records
print len(result['mRNASeq'])
print result['mRNASeq'][0]
print result['mRNASeq'][1800]
print result['mRNASeq'][3600]

print M.Cohort()

# Cohort function ends with a path parameter, but multiple cohorts ARE accepted
print M.Cohort("acc         blca,       UcS")

# Barcode func ends with path param, too, but multiple cohorts ARE NOT accepted
# (only 1 barcode will be translated per call, as the next statement shows)
print M.SampleTypeBarcode("TCGA-GF-A4EO-06,TCGA-EL-A3D5-01A-22D-A202-08")

# Demonstrate that strings or sequences are accepted as parameter values
amp = A.CopyNumberGenesAmplified(gene="erbb2,  egfr                       bad",format="tsv")
print amp
amp2 = A.CopyNumberGenesAmplified(gene=["erbb2","egfr","bad"],format="tsv")
compare(amp, amp2, "CopyNumberGenesAmplified(string_vs_list)")

amp3 = A.CopyNumberGenesAmplified(gene=("erbb2","egfr","bad"),format="tsv")
compare(amp, amp3, "CopyNumberGenesAmplified(string_vs_tuple)")

amp4 = A.CopyNumberGenesAmplified(gene={"erbb2","egfr","bad"},format="tsv")
compare(amp, amp3, "CopyNumberGenesAmplified(string_vs_set)")