1 files changed, 132 insertions, 0 deletions
diff --git a/gn2/wqflask/ctl/gn3_ctl_analysis.py b/gn2/wqflask/ctl/gn3_ctl_analysis.py
new file mode 100644
index 00000000..64c2ff0d
--- /dev/null
+++ b/gn2/wqflask/ctl/gn3_ctl_analysis.py
@@ -0,0 +1,132 @@
+import requests
+import itertools
+
+from gn2.utility import genofile_parser
+from gn2.utility.tools import GN3_LOCAL_URL
+from gn2.utility.tools import locate
+
+from gn2.base.trait import create_trait
+from gn2.base.trait import retrieve_sample_data
+from gn2.base import data_set
+
+
+def process_significance_data(dataset):
+    col_names = ["trait", "marker", "trait_2", "LOD", "dcor"]
+    dataset_rows = [[] for _ in range(len(dataset["trait"]))]
+    for col in col_names:
+        for (index, col_data) in enumerate(dataset[col]):
+            if col in ["dcor", "LOD"]:
+                dataset_rows[index].append(round(float(col_data), 2))
+            else:
+                dataset_rows[index].append(col_data)
+
+    return {
+        "col_names": col_names,
+        "data_set_rows": dataset_rows
+    }
+
+
+def parse_geno_data(dataset_group_name) -> dict:
+    """
+    Args:
+        dataset_group_name: string name
+
+    @returns : dict with keys genotypes,markernames & individuals
+    """
+    genofile_location = locate(dataset_group_name + ".geno", "genotype")
+    parser = genofile_parser.ConvertGenoFile(genofile_location)
+    parser.process_csv()
+    markers = []
+    markernames = []
+    for marker in parser.markers:
+        markernames.append(marker["name"])
+        markers.append(marker["genotypes"])
+
+    return {
+
+        "genotypes": list(itertools.chain(*markers)),
+        "markernames": markernames,
+        "individuals": parser.individuals
+
+
+    }
+
+
+def parse_phenotype_data(trait_list, dataset, individuals):
+    """
+    Args:
+        trait_list:list contains the traits
+        dataset:  object
+        individuals:a list contains the individual vals
+    Returns:
+           traits_db_List:parsed list of traits 
+           traits: list contains trait names
+           individuals
+
+    """
+
+    traits = []
+    for trait in trait_list:
+        if trait != "":
+            ts = trait.split(':')
+            gt = create_trait(name=ts[0], dataset_name=ts[1])
+            gt = retrieve_sample_data(gt, dataset, individuals)
+            for ind in individuals:
+                if ind in list(gt.data.keys()):
+                    traits.append(gt.data[ind].value)
+                else:
+                    traits.append("-999")
+
+    return {
+        "trait_db_list": trait_list,
+        "traits": traits,
+        "individuals": individuals
+    }
+
+
+def parse_form_data(form_data: dict):
+
+    trait_db_list = [trait.strip()
+                     for trait in form_data['trait_list'].split(',')]
+
+    form_data["trait_db_list"] = [x for x in trait_db_list if x]
+    form_data["nperm"] = int(form_data["nperm"])
+    form_data["significance"] = float(form_data["significance"])
+    form_data["strategy"] = form_data["strategy"].capitalize()
+
+    return form_data
+
+
+def run_ctl(requestform):
+    """function to make an api call
+    to gn3 and run ctl"""
+    ctl_api = f"{GN3_LOCAL_URL}/api/ctl/run_ctl"
+
+    form_data = parse_form_data(requestform.to_dict())
+    trait_db_list = form_data["trait_db_list"]
+    dataset = data_set.create_dataset(trait_db_list[0].split(":")[1])
+    geno_data = parse_geno_data(dataset.group.name)
+    pheno_data = parse_phenotype_data(
+        trait_db_list, dataset, geno_data["individuals"])
+
+    try:
+
+        response = requests.post(ctl_api, json={
+
+            "genoData": geno_data,
+            "phenoData": pheno_data,
+            **form_data,
+
+        })
+        if response.status_code != 200:
+            return {"error": response.json()}
+        response = response.json()["results"]
+        response["significance_data"] = process_significance_data(
+            response["significance_data"])
+
+        return response
+
+    except requests.exceptions.ConnectionError:
+        return {
+            "error": "A connection error to perform computation occurred"
+        }