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Feature/add mapping endpoints #529

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Feature/add mapping endpoints #529

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5046192
add endpoint for each mapping
Alexanderlacuna Dec 10, 2020
060ae33
delete run_mapping endpoint
Alexanderlacuna Dec 10, 2020
5371f9a
add loading for each mapping
Alexanderlacuna Dec 18, 2020
1e40b58
delete loading enpoint
Alexanderlacuna Dec 18, 2020
82198ed
add start vars container to render template
Alexanderlacuna Dec 18, 2020
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376 changes: 200 additions & 176 deletions wqflask/wqflask/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -611,182 +611,6 @@ def comp_bar_chart_page():
def mapping_results_container_page():
return render_template("mapping_results_container.html")

@app.route("/loading", methods=('POST',))
def loading_page():
logger.info(request.url)
initial_start_vars = request.form
start_vars_container = {}
n_samples = 0 #ZS: So it can be displayed on loading page
if 'wanted_inputs' in initial_start_vars:
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
for key, value in list(initial_start_vars.items()):
if key in wanted or key.startswith(('value:')):
start_vars[key] = value

if 'n_samples' in start_vars:
n_samples = int(start_vars['n_samples'])
else:
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
else:
dataset = create_dataset(start_vars['dataset'])
genofile_samplelist = []
samples = start_vars['primary_samples'].split(",")
if 'genofile' in start_vars:
if start_vars['genofile'] != "":
genofile_string = start_vars['genofile']
dataset.group.genofile = genofile_string.split(":")[0]
genofile_samples = run_mapping.get_genofile_samplelist(dataset)
if len(genofile_samples) > 1:
samples = genofile_samples

for sample in samples:
value = start_vars.get('value:' + sample)
if value != "x":
n_samples += 1

start_vars['n_samples'] = n_samples
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']

start_vars_container['start_vars'] = start_vars
else:
start_vars_container['start_vars'] = initial_start_vars

rendered_template = render_template("loading.html", **start_vars_container)

return rendered_template

@app.route("/run_mapping", methods=('POST',))
def mapping_results_page():
initial_start_vars = request.form
#logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
logger.info(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
'trait_id',
'dataset',
'group',
'species',
'samples',
'vals',
'first_run',
'output_files',
'geno_db_exists',
'method',
'mapping_results_path',
'trimmed_markers',
'selected_chr',
'chromosomes',
'mapping_scale',
'plotScale',
'score_type',
'suggestive',
'significant',
'num_perm',
'permCheck',
'perm_strata',
'strat_var',
'categorical_vars',
'perm_output',
'num_bootstrap',
'bootCheck',
'bootstrap_results',
'LRSCheck',
'covariates',
'maf',
'use_loco',
'manhattan_plot',
'color_scheme',
'manhattan_single_color',
'control_marker',
'control_marker_db',
'do_control',
'genofile',
'genofile_string',
'pair_scan',
'startMb',
'endMb',
'graphWidth',
'lrsMax',
'additiveCheck',
'showSNP',
'showGenes',
'viewLegend',
'haplotypeAnalystCheck',
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno',
'temp_trait',
'reaper_version',
'n_samples',
'transform'
)
start_vars = {}
for key, value in list(initial_start_vars.items()):
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
#logger.debug("Mapping called with start_vars:", start_vars)

version = "v3"
key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
#logger.info("key is:", pf(key))
with Bench("Loading cache"):
result = None # Just for testing
#result = Redis.get(key)

#logger.info("************************ Starting result *****************")
#logger.info("result is [{}]: {}".format(type(result), result))
#logger.info("************************ Ending result ********************")

if result:
logger.info("Cache hit!!!")
with Bench("Loading results"):
result = pickle.loads(result)
else:
logger.info("Cache miss!!!")
with Bench("Total time in RunMapping"):
try:
template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
if template_vars.no_results:
rendered_template = render_template("mapping_error.html")
return rendered_template
except:
rendered_template = render_template("mapping_error.html")
return rendered_template

#if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")

result = template_vars.__dict__

if result['pair_scan']:
with Bench("Rendering template"):
img_path = result['pair_scan_filename']
logger.info("img_path:", img_path)
initial_start_vars = request.form
logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(TEMPDIR + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = base64.b64encode(imgdata)
bytesarray = array.array('B', imgB64)
result['pair_scan_array'] = bytesarray
rendered_template = render_template("pair_scan_results.html", **result)
else:
gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
#pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
#logger.info("pickled result length:", len(pickled_result))
#Redis.set(key, pickled_result)
#Redis.expire(key, 1*60)

with Bench("Rendering template"):
#if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
#gn1_template_vars.pop('qtlresults', None)
rendered_template = render_template("mapping_results.html", **gn1_template_vars)

return rendered_template

@app.route("/export_mapping_results", methods = ('POST',))
def export_mapping_results():
logger.info("request.form:", request.form)
Expand Down Expand Up @@ -940,3 +764,203 @@ def json_default_handler(obj):
else:
raise TypeError('Object of type %s with value of %s is not JSON serializable' % (
type(obj), repr(obj)))


@app.route("/run_gemma",methods=["POST"])
def gemma_results_page():
gemma_results=get_mapping_results(initial_start_vars=request.form)
return gemma_results
@app.route("/run_qtl",methods=["POST"])
def qtl_results_page():
qtl_mapping_results=get_mapping_results(initial_start_vars=request.form)
return qtl_mapping_results

@app.route("/run_reaper",methods=["POST"])
def reaper_results_page():
reaper_mapping_results=get_mapping_results(initial_start_vars=request.form)
return reaper_mapping_results

@app.route("/run_plink",methods=["POST"])
def plink_results_page():
plink_mapping_results = get_mapping_results(initial_start_vars=request.form)
return plink_mapping_results

@app.route("/gemma_loading", methods=["POST"])
def gemma_loading_page():
start_vars_container = get_loading_page_data(initial_start_vars=request.form)
return render_template("loading.html", **start_vars_container)


@app.route("/qtl_loading", methods=["POST"])
def qtl_loading_page():
start_vars_container = get_loading_page_data(initial_start_vars=request.form)
return render_template("loading.html", **start_vars_container)


@app.route("/reaper_loading", methods=["POST"])
def reaper_loading_page():
start_vars_container = get_loading_page_data(
initial_start_vars=request.form)
return render_template("loading.html", **start_vars_container)


@app.route("/plink_loading", methods=["POST"])
def plink_loading_page():
start_vars_container = get_loading_page_data(initial_start_vars=request.form)
return render_template("loading.html", **start_vars_container)

def get_wanted_mapping_keys():
wanted = (
'trait_id',
'dataset',
'group',
'species',
'samples',
'vals',
'first_run',
'output_files',
'geno_db_exists',
'method',
'mapping_results_path',
'trimmed_markers',
'selected_chr',
'chromosomes',
'mapping_scale',
'plotScale',
'score_type',
'suggestive',
'significant',
'num_perm',
'permCheck',
'perm_strata',
'strat_var',
'categorical_vars',
'perm_output',
'num_bootstrap',
'bootCheck',
'bootstrap_results',
'LRSCheck',
'covariates',
'maf',
'use_loco',
'manhattan_plot',
'color_scheme',
'manhattan_single_color',
'control_marker',
'control_marker_db',
'do_control',
'genofile',
'genofile_string',
'pair_scan',
'startMb',
'endMb',
'graphWidth',
'lrsMax',
'additiveCheck',
'showSNP',
'showGenes',
'viewLegend',
'haplotypeAnalystCheck',
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno',
'temp_trait',
'reaper_version',
'n_samples',
'transform'
)

return wanted
def get_mapping_results(initial_start_vars):
temp_uuid=initial_start_vars['temp_uuid']
wanted=get_wanted_mapping_values()
start_vars={}
for key, value in list(initial_start_vars.items()):
if key in wanted or key.startswith(('value:')):
start_vars[key] = value

version = "v3"
key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
with Bench("Loading cache"):
result = None
if result:
logger.info("Cache hit!!!")
with Bench("Loading results"):
result = pickle.loads(result)
else:
logger.info("Cache miss!!!")
with Bench("Total time in RunMapping"):
try:
template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
if template_vars.no_results:
rendered_template = render_template("mapping_error.html")
return rendered_template
except:
rendered_template = render_template("mapping_error.html")
return rendered_template
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")

result = template_vars.__dict__

if result['pair_scan']:
with Bench("Rendering template"):
img_path = result['pair_scan_filename']
logger.info("img_path:", img_path)
initial_start_vars = request.form
logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(TEMPDIR + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = base64.b64encode(imgdata)
bytesarray = array.array('B', imgB64)
result['pair_scan_array'] = bytesarray
rendered_template = render_template("pair_scan_results.html", **result)
else:
gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__

with Bench("Rendering template"):
rendered_template = render_template("mapping_results.html", **gn1_template_vars)

return rendered_template

def get_loading_page_data(initial_start_vars):
initial_start_vars = request.form
start_vars_container = {}
n_samples = 0 #ZS: So it can be displayed on loading page
if 'wanted_inputs' in initial_start_vars:
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
for key, value in list(initial_start_vars.items()):
if key in wanted or key.startswith(('value:')):
start_vars[key] = value

if 'n_samples' in start_vars:
n_samples = int(start_vars['n_samples'])
else:
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
else:
dataset = create_dataset(start_vars['dataset'])
genofile_samplelist = []
samples = start_vars['primary_samples'].split(",")
if 'genofile' in start_vars:
if start_vars['genofile'] != "":
genofile_string = start_vars['genofile']
dataset.group.genofile = genofile_string.split(":")[0]
genofile_samples = run_mapping.get_genofile_samplelist(dataset)
if len(genofile_samples) > 1:
samples = genofile_samples

for sample in samples:
value = start_vars.get('value:' + sample)
if value != "x":
n_samples += 1

start_vars['n_samples'] = n_samples
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']

start_vars_container['start_vars'] = start_vars
else:
start_vars_container['start_vars'] = initial_start_vars

return start_vars_container