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1.3.2
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@mbaudis
mbaudis committed Oct 24, 2023
1 parent 138353e commit 7d35aa1
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Showing 12 changed files with 156 additions and 1,458 deletions.
1 change: 0 additions & 1 deletion bycon/__init__.py
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Expand Up @@ -14,7 +14,6 @@
from args_parsing import *
from beacon_response_generation import *
from bycon_helpers import *
from bycon_plot import *
from cgi_parsing import *
from clustering_utils import *
from dataset_parsing import *
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2 changes: 1 addition & 1 deletion bycon/beaconServer/tests/GET-examples.md
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Expand Up @@ -18,5 +18,5 @@ http://progenetix.org/beacon/biosamples/onekgbs-HG00142/g_variants

http://progenetix.org/beacon/biosamples/pgxbs-kftvhyvb/phenopackets

http://progenetix.org/beacon/biosamples/pgxbs-kftvkafc/?datasetIds=progenetix&output=samplesplot&plot_chros=3,5,6,14&debug=
http://progenetix.org/services/sampleplots/pgxbs-kftvkafc/?datasetIds=progenetix&plotType=samplesplot&plot_chros=3,5,6,14

8 changes: 4 additions & 4 deletions bycon/config/handover_definitions.yaml
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Expand Up @@ -17,8 +17,8 @@ h->o_types:
- biosample
- analysis
h->o_key: 'biosamples.id'
script_path_web: '/beacon/biosamples'
output: histoplot
script_path_web: '/services/sampleplots'
plotType: histoplot

samplesplot:
handoverType:
Expand All @@ -29,8 +29,8 @@ h->o_types:
- biosample
- analysis
h->o_key: 'biosamples.id'
script_path_web: '/beacon/biosamples'
output: samplesplot
script_path_web: '/services/sampleplots'
plotType: samplesplot

biosamples:
handoverType:
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171 changes: 2 additions & 169 deletions bycon/lib/beacon_response_generation.py
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Expand Up @@ -2,7 +2,6 @@
from deepmerge import always_merger
from os import environ

from bycon_plot import ByconPlot
from bycon_helpers import mongo_result_list, mongo_test_mode_query, return_paginated_list
from cgi_parsing import prdbug
from datatable_utils import export_datatable_download
Expand Down Expand Up @@ -595,8 +594,8 @@ def populatedResultSets(self):
self.__retrieve_variants_data()
# tables before reshaping ...
self.__check_datasets_data_table_export()
self.__check_datasets_results_histoplot_delivery()
self.__check_datasets_results_samplesplot_delivery()
# self.__check_datasets_results_histoplot_delivery()
# self.__check_datasets_results_samplesplot_delivery()
self.__check_biosamples_map_delivery()
# finally populating the standard Beacon response
self.__populate_result_sets()
Expand All @@ -618,41 +617,6 @@ def datasetsResults(self):
return self.datasets_results


# -------------------------------------------------------------------------#

def samplesPlot(self):
self.output = "samplesplot"
self.__datasets_results_samplesplot_generation()
return self.svg


# -------------------------------------------------------------------------#

def samplesPlotWeb(self):
self.output = "samplesplot"
self.__datasets_results_samplesplot_generation()
print_svg_response(self.svg, self.env)


# -------------------------------------------------------------------------#

def histoPlot(self):
self.output = "histoplot"
self.__datasets_results_histoplot_generation()
return self.svg

# -------------------------------------------------------------------------#

def plotSVGtoWeb(self, plot_type="histoplot"):
self.output = plot_type
self.svg = '<svg>___empty___</svg>'
prdbug(self.byc, self.output)
self.__datasets_results_histoplot_generation()
self.__datasets_results_samplesplot_generation()
print_svg_response(self.svg, self.env)



# -------------------------------------------------------------------------#
# ----------------------------- private -----------------------------------#
# -------------------------------------------------------------------------#
Expand Down Expand Up @@ -756,137 +720,6 @@ def __check_datasets_results_histoplot_delivery(self):
print_svg_response(self.svg, self.env)


# -------------------------------------------------------------------------#

def __datasets_results_samplesplot_generation(self):
prdbug(self.byc, self.output)
if not "samplesplot" in self.output:
return
results = []

for ds_id, ds_res in self.datasets_results.items():
if not "callsets._id" in ds_res:
continue

mongo_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
cs_coll = mongo_client[ds_id]["callsets"]
var_coll = mongo_client[ds_id]["variants"]

cs_r = ds_res["callsets._id"]
cs__ids = cs_r["target_values"]
r_no = len(cs__ids)
if r_no < 1:
continue
cs__ids = return_paginated_list(cs__ids, self.skip, self.limit)

for cs__id in cs__ids:
cs = cs_coll.find_one({"_id": cs__id })
cs_id = cs.get("id", "NA")

cnv_chro_stats = cs.get("cnv_chro_stats", False)
cnv_statusmaps = cs.get("cnv_statusmaps", False)

if cnv_chro_stats is False or cnv_statusmaps is False:
continue

p_o = {
"dataset_id": ds_id,
"callset_id": cs_id,
"biosample_id": cs.get("biosample_id", "NA"),
"cnv_chro_stats": cs.get("cnv_chro_stats", {}),
"cnv_statusmaps": cs.get("cnv_statusmaps", {}),
"probefile": callset_guess_probefile_path(cs, self.byc),
"variants": []
}
if r_no == 1 and p_o["probefile"] is not False:
p_o.update({"cn_probes": ByconBundler(self.byc).read_probedata_file(p_o["probefile"]) })

v_q = {"callset_id": cs_id}

for v in var_coll.find(v_q):
p_o["variants"].append(ByconVariant(self.byc).byconVariant(v))

results.append(p_o)

plot_data_bundle = {"callsets_variants_bundles": results}
self.svg = ByconPlot(self.byc, plot_data_bundle).get_svg()


# -------------------------------------------------------------------------#

def __datasets_results_histoplot_generation(self):
if not "histoplot" in self.output:
return
f_d = self.filter_definitions
f_s_t = self.form_data.get("plot_group_by", "___none___")

interval_sets = []

for ds_id, ds_res in self.datasets_results.items():
if not "callsets._id" in ds_res:
continue
mongo_client = MongoClient(host=environ.get("BYCON_MONGO_HOST", "localhost"))
bios_coll = mongo_client[ds_id]["biosamples"]
cs_coll = mongo_client[ds_id]["callsets"]

f_s_dists = []
f_s_k = ""

if f_s_t in f_d.keys():
if not "biosamples._id" in ds_res:
continue
bios_q_v = ds_res["biosamples._id"].get("target_values", [])
if len(bios_q_v) < 1:
continue

f_s_k = f_d[f_s_t].get("db_key", "___none___")
f_s_p = f_d[f_s_t].get("pattern", False)
f_s_q = {"_id": {"$in": bios_q_v}}
f_s_dists = bios_coll.distinct(f_s_k, f_s_q)
if f_s_p is not False:
r = re.compile(f_s_p)
f_s_dists = list(filter(lambda d: r.match(d), f_s_dists))

for f_s_id in f_s_dists:

bios_id_q = {"$and": [
{f_s_k: f_s_id},
{"_id": {"$in": bios_q_v}}
]}

bios_ids = bios_coll.distinct("id", bios_id_q)
cs__ids = cs_coll.distinct("_id", {"biosample_id": {"$in": bios_ids}})
r_no = len(cs__ids)
if r_no > self.limit:
cs__ids = return_paginated_list(cs__ids, self.skip, self.limit)

label = f"Search Results (subset {f_s_id})"

iset = callset__ids_create_iset(ds_id, label, cs__ids, self.byc)
interval_sets.append(iset)

else:
cs_r = ds_res["callsets._id"]
cs__ids = cs_r["target_values"]
r_no = len(cs__ids)
# filter for CNV cs before evaluating number
if r_no > self.limit:
cs_cnv_ids = []
for _id in cs__ids:
cs = cs_coll.find_one({"_id":_id})
if "cnv_statusmaps" in cs:
cs_cnv_ids.append(_id)
cs__ids = cs_cnv_ids
cs__ids = return_paginated_list(cs__ids, self.skip, self.limit)

iset = callset__ids_create_iset(ds_id, "Search Results", cs__ids, self.byc)
interval_sets.append(iset)

plot_data_bundle = {"interval_frequencies_bundles": interval_sets}

self.svg = ByconPlot(self.byc, plot_data_bundle).get_svg()


# -------------------------------------------------------------------------#

def __result_sets_save_handovers(self):
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