From 1600992807a0b3edbe10e8c0baf80a41636a7650 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 21:58:20 +0300
Subject: init commit for wgcna script

---
 scripts/wgcna_analysis.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 scripts/wgcna_analysis.R

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
new file mode 100644
index 0000000..e69de29
-- 
cgit v1.2.3


From ea0e92d3f63a9f403aacd5ab1590f61f2752158a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:12:43 +0300
Subject: load the required data for analysis

---
 scripts/wgcna_analysis.R | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index e69de29..a8170b6 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -0,0 +1,21 @@
+# initial workspace setup
+
+library(WGCNA);
+stringsAsFactors = FALSE
+
+# load expression data **assumes csv format row(traits)(columns info+samples)
+
+
+wgcnaRawData <- read.csv(file = "wgcna_data.csv")
+
+# transform expressionData
+
+datExpr <- as.data.frame(t(wgcnaRawData));
+
+
+
+
+
+
+
+
-- 
cgit v1.2.3


From 49fdd614d4b18f7d28126e4ebbf3adca57f0416f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:31:18 +0300
Subject: Checking data for excessive missing values

---
 scripts/wgcna_analysis.R | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index a8170b6..8e90d7d 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -10,10 +10,28 @@ wgcnaRawData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
-datExpr <- as.data.frame(t(wgcnaRawData));
+dataExpr <- as.data.frame(t(wgcnaRawData));
 
 
 
+# data cleaning
+
+# adopted from docs
+gsg = goodSamplesGenes(dataExpr, verbose = 3);
+
+
+
+if (!gsg$allOK)
+{
+# Optionally, print the gene and sample names that were removed:
+if (sum(!gsg$goodGenes)>0)
+printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
+if (sum(!gsg$goodSamples)>0)
+printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
+# Remove the offending genes and samples from the data:
+dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
+}
+
 
 
 
-- 
cgit v1.2.3


From 42c120dff2b3cac8a6b6546ebab9daf021aac11a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:42:43 +0300
Subject: compute the softthreshhold

---
 scripts/wgcna_analysis.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 8e90d7d..cb93492 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -5,15 +5,12 @@ stringsAsFactors = FALSE
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
-
 wgcnaRawData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
 dataExpr <- as.data.frame(t(wgcnaRawData));
 
-
-
 # data cleaning
 
 # adopted from docs
@@ -32,6 +29,17 @@ printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples]
 dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 }
 
+# network constructions and modules
+
+# choose softthreshhold (Calculate soft threshold if the user specified the)
+
+powers = c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft = pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+
+
+
+
 
 
 
-- 
cgit v1.2.3


From 1c98a10bf5015a85b856f9e937417d51ec05d781 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:49:43 +0300
Subject: construct  gene co-expression  network & module detection

---
 scripts/wgcna_analysis.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index cb93492..29f0259 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -33,9 +33,26 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 # choose softthreshhold (Calculate soft threshold if the user specified the)
 
-powers = c(c(1:10), seq(from = 12, to=20, by=2)) 
-sft = pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
-
+powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+# pass user options
+network <- blockwiseModules(dataExpr,
+                  #similarity  matrix options
+                  corType = "pearson",
+                  #adjacency  matrix options
+
+                  power = sft$powerEstimate,
+                  networkType = "unsigned",
+                  #TOM options
+                  TOMtype =  "unsigned",
+
+                  #module indentification
+
+                  minmodulesSize = 30,
+                  deepSplit = 5,
+                  PamRespectsDendro = FALSE
+                )
 
 
 
-- 
cgit v1.2.3


From b32f4ee074d55d8ab78863d4c5acc652ec9cd839 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:18:18 +0300
Subject: plot plotDendroAndColors and generate png

---
 scripts/wgcna_analysis.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 29f0259..65ff36e 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -54,6 +54,24 @@ network <- blockwiseModules(dataExpr,
                   PamRespectsDendro = FALSE
                 )
 
+# plot dendro add color
+
+# Convert labels to colors for plotting
+mergedColors = labels2colors(net$colors)
+# Plot the dendrogram and the module colors underneath 
+
+
+# generate random name for png && save the image location
+
+
+
+png("WGCNAoutput.png",width=1000,height=600,type='cairo-png')
+
+plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
+"Module colors",
+dendroLabels = FALSE, hang = 0.03,
+addGuide = TRUE, guideHang = 0.05)
+
 
 
 
-- 
cgit v1.2.3


From 49b852baa46c0f06caa2f0621b18d521cf334483 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:40:17 +0300
Subject: function to generate rand str for image

---
 scripts/wgcna_analysis.R | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 65ff36e..efe0336 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,7 +1,9 @@
 # initial workspace setup
 
 library(WGCNA);
-stringsAsFactors = FALSE
+library(stringi);
+
+options(stringsAsFactors = FALSE);
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
@@ -64,8 +66,18 @@ mergedColors = labels2colors(net$colors)
 # generate random name for png && save the image location
 
 
+genImageRandStr <- function(prefix){
+
+	randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
+
+	return(paste(randStr,".png",sep=""))
+}
+
+
+
+png(genImageRandStr,width=1000,height=600,type='cairo-png')
+
 
-png("WGCNAoutput.png",width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
 "Module colors",
-- 
cgit v1.2.3


From 56092341abe9579b995ff6105722154183b31d22 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:41:46 +0300
Subject: remove debug statements

---
 scripts/wgcna_analysis.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index efe0336..16a44fd 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -56,14 +56,6 @@ network <- blockwiseModules(dataExpr,
                   PamRespectsDendro = FALSE
                 )
 
-# plot dendro add color
-
-# Convert labels to colors for plotting
-mergedColors = labels2colors(net$colors)
-# Plot the dendrogram and the module colors underneath 
-
-
-# generate random name for png && save the image location
 
 
 genImageRandStr <- function(prefix){
@@ -74,6 +66,7 @@ genImageRandStr <- function(prefix){
 }
 
 
+mergedColors = labels2colors(net$colors)
 
 png(genImageRandStr,width=1000,height=600,type='cairo-png')
 
-- 
cgit v1.2.3


From e0f25dedea08842820424ced51af9af0c7eaab4b Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 02:13:03 +0300
Subject: Fetch IMAGE_DIR env and add img location

---
 scripts/wgcna_analysis.R | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 16a44fd..54650df 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,10 +1,14 @@
 # initial workspace setup
 
+
+# todo pass required input data here
 library(WGCNA);
 library(stringi);
 
 options(stringsAsFactors = FALSE);
 
+imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
+
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
 wgcnaRawData <- read.csv(file = "wgcna_data.csv")
@@ -33,7 +37,7 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 # network constructions and modules
 
-# choose softthreshhold (Calculate soft threshold if the user specified the)
+# choose softthreshhold (Calculate soft threshold)
 
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
@@ -65,12 +69,12 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
+mergedColors <- labels2colors(net$colors)
 
-mergedColors = labels2colors(net$colors)
-
-png(genImageRandStr,width=1000,height=600,type='cairo-png')
+imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
 
 
+png(imageLoc,width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
 "Module colors",
@@ -79,9 +83,3 @@ addGuide = TRUE, guideHang = 0.05)
 
 
 
-
-
-
-
-
-
-- 
cgit v1.2.3


From 94e2e79141cbddb48456fb5707eb0e4e36e97d3b Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 02:19:03 +0300
Subject: rename variables && delete debugs

---
 scripts/wgcna_analysis.R | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 54650df..390bee4 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,7 +1,3 @@
-# initial workspace setup
-
-
-# todo pass required input data here
 library(WGCNA);
 library(stringi);
 
@@ -11,15 +7,14 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
-wgcnaRawData <- read.csv(file = "wgcna_data.csv")
+inputData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
-dataExpr <- as.data.frame(t(wgcnaRawData));
+dataExpr <- as.data.frame(t(inputData));
 
 # data cleaning
 
-# adopted from docs
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
 
-- 
cgit v1.2.3


From cee10bacd4316eb807c36b8a11e84f9be5945f44 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 04:34:26 +0300
Subject: minor fixes

---
 scripts/wgcna_analysis.R | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 390bee4..267cd86 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,3 +1,5 @@
+
+
 library(WGCNA);
 library(stringi);
 
@@ -6,6 +8,7 @@ options(stringsAsFactors = FALSE);
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
+# pass the file_path as arg
 
 inputData <- read.csv(file = "wgcna_data.csv")
 
@@ -13,26 +16,29 @@ inputData <- read.csv(file = "wgcna_data.csv")
 
 dataExpr <- as.data.frame(t(inputData));
 
-# data cleaning
+## data cleaning
 
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
-
+# https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
 
 if (!gsg$allOK)
 {
-# Optionally, print the gene and sample names that were removed:
 if (sum(!gsg$goodGenes)>0)
-printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
+printFlush(paste("Removing genes:", paste(names(dataExpr)[!gsg$goodGenes], collapse = ", ")));
 if (sum(!gsg$goodSamples)>0)
-printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
+printFlush(paste("Removing samples:", paste(rownames(dataExpr)[!gsg$goodSamples], collapse = ", ")));
 # Remove the offending genes and samples from the data:
 dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 }
 
-# network constructions and modules
+## network constructions and modules
+
+# Allow multi-threading within WGCNA
+enableWGCNAThreads()
 
 # choose softthreshhold (Calculate soft threshold)
+# xtodo allow users to pass args
 
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
-- 
cgit v1.2.3


From 488ad475ca7112d64f9f1f0d4934c3293388bf1a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 16:06:52 +0300
Subject: remove golang package causing build failure

---
 guix.scm | 2 --
 1 file changed, 2 deletions(-)

diff --git a/guix.scm b/guix.scm
index 729d089..75ed4a9 100644
--- a/guix.scm
+++ b/guix.scm
@@ -43,7 +43,6 @@
  (gnu packages databases)
  (gnu packages statistics)
  (gnu packages bioconductor)
- (gn packages golang)
  (gnu packages python)
  (gnu packages python-check)
  (gnu packages python-crypto)
@@ -83,7 +82,6 @@
                       #:recursive? #t
                       #:select? git-file?))
   (propagated-inputs `(("coreutils" ,coreutils)
-                       ("csvdiff" ,go-github-com-aswinkarthik-csvdiff)
                        ("gemma-wrapper" ,gemma-wrapper)
                        ("gunicorn" ,gunicorn)
                        ("python" ,python-wrapper)
-- 
cgit v1.2.3


From 6494a093e6d96015f65416a8c3fde88a9a3c8c71 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 16:17:02 +0300
Subject: init wgcna file to run  r script and preprocess data

---
 gn3/computations/wgcna.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 gn3/computations/wgcna.py

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
new file mode 100644
index 0000000..e69de29
-- 
cgit v1.2.3


From 129ecfe26a857c2c66a2402c9c7364b309e9f1c0 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 16:17:30 +0300
Subject: initial test file for wgcna

---
 tests/unit/computations/test_wgcna.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 tests/unit/computations/test_wgcna.py

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
new file mode 100644
index 0000000..1ce69a1
--- /dev/null
+++ b/tests/unit/computations/test_wgcna.py
@@ -0,0 +1,15 @@
+"""module contains python code for wgcna"""
+from unittest import TestCase
+
+
+def compute_sum(rhs_val, lhs_val):
+    """function to compute sum of two numbers"""
+    return rhs_val+lhs_val
+
+
+class TestWgcna(TestCase):
+    """test class for wgcna"""
+
+    def test_compute_sum(self):
+        """test for compute sum function"""
+        self.assertEqual(compute_sum(1, 2), 3)
-- 
cgit v1.2.3


From a3ef298678b32ee83cac7bd7462d3d92f8eaec26 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 08:23:35 +0300
Subject: function to parse form data and write to json file

---
 gn3/computations/wgcna.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index e69de29..3819b62 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -0,0 +1,18 @@
+"""module contains code to preprocess and call wgcna script"""
+
+import os
+import json
+import uuid
+from gn3.settings import TMPDIR
+
+
+def dump_wgcna_data(request_data):
+    """function to dump request data to json file"""
+    filename = f"{str(uuid.uuid4())}.json"
+
+    temp_file_path = os.path.join(TMPDIR, filename)
+
+    with open(temp_file_path, "w") as output_file:
+        json.dump(request_data, output_file)
+
+    return temp_file_path
-- 
cgit v1.2.3


From 38cbc95f216548d4a2f46b8e25cd328ff8c52d62 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 08:54:01 +0300
Subject: add  function to compose and run wgcna script

---
 gn3/computations/wgcna.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 3819b62..bcd3a0a 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -5,8 +5,10 @@ import json
 import uuid
 from gn3.settings import TMPDIR
 
+from gn3.commands import run_cmd
 
-def dump_wgcna_data(request_data):
+
+def dump_wgcna_data(request_data: dict):
     """function to dump request data to json file"""
     filename = f"{str(uuid.uuid4())}.json"
 
@@ -16,3 +18,16 @@ def dump_wgcna_data(request_data):
         json.dump(request_data, output_file)
 
     return temp_file_path
+
+
+def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
+    """function to componse wgcna cmd"""
+    cmd = f"Rscript {rscript_path}  {temp_file_path}"
+    return cmd
+
+
+def call_wgcna_script(rscript_path: str, request_data: dict):
+    """function to call wgcna script"""
+    generated_file = dump_wgcna_data(request_data)
+    cmd = compose_gemma_cmd(rscript_path, generated_file)
+    run_cmd(cmd=cmd)
-- 
cgit v1.2.3


From 8854e3070f32bed95cb489eb36e7f258c02ec46e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 09:32:42 +0300
Subject: add initial endpoint for wgcna

---
 gn3/api/wgcna.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 gn3/api/wgcna.py

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
new file mode 100644
index 0000000..a3bacdd
--- /dev/null
+++ b/gn3/api/wgcna.py
@@ -0,0 +1,13 @@
+"""endpoint to run wgcna analysis"""
+from flask import Blueprint
+from flask import request
+
+wgcna = Blueprint("wgcna", __name__)
+
+
+@wgcna.route("/run_wgcna", methods=["POST"])
+def run_wgcna():
+
+    _wgcna_data = request.json
+
+    return "success", 200
-- 
cgit v1.2.3


From 6f9fd1a1866e292ec4b84c214efd61ccb9f5bb58 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 09:45:16 +0300
Subject: register wgcna blueprint

---
 gn3/app.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gn3/app.py b/gn3/app.py
index 046b5de..b2f77f9 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -9,6 +9,7 @@ from gn3.api.rqtl import rqtl
 from gn3.api.general import general
 from gn3.api.correlation import correlation
 from gn3.api.data_entry import data_entry
+from gn3.api.wgcna import wgcna
 
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
@@ -32,4 +33,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     app.register_blueprint(rqtl, url_prefix="/api/rqtl")
     app.register_blueprint(correlation, url_prefix="/api/correlation")
     app.register_blueprint(data_entry, url_prefix="/api/dataentry")
+    app.register_blueprint(wgcna, url_prefix="/api/wgcna")
     return app
-- 
cgit v1.2.3


From 3d8f7f069d76cd6ee35b5e9d72d37e38721188d2 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 10:13:10 +0300
Subject: run cmd and add exception handler

---
 gn3/computations/wgcna.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index bcd3a0a..f0f0fa2 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -29,5 +29,9 @@ def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
 def call_wgcna_script(rscript_path: str, request_data: dict):
     """function to call wgcna script"""
     generated_file = dump_wgcna_data(request_data)
-    cmd = compose_gemma_cmd(rscript_path, generated_file)
-    run_cmd(cmd=cmd)
+    cmd = compose_wgcna_cmd(rscript_path, generated_file)
+
+    try:
+        return run_cmd(cmd)
+    except Exception as error:
+        raise error
-- 
cgit v1.2.3


From f53a8a98206b4e8aedbf4b86e49f41ea140c9c6a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 14:02:13 +0300
Subject: pass user input to call script

---
 gn3/api/wgcna.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index a3bacdd..5d49493 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -1,13 +1,21 @@
 """endpoint to run wgcna analysis"""
 from flask import Blueprint
 from flask import request
+from flask import current_app
+
+from gn3.computations.wgcna import call_wgcna_script
 
 wgcna = Blueprint("wgcna", __name__)
 
 
 @wgcna.route("/run_wgcna", methods=["POST"])
 def run_wgcna():
+    """run wgcna:output should be a json with a the data"""
+
+    wgcna_data = request.json
+
+    wgcna_script = current_app.config["WGCNA_RSCRIPT"]
 
-    _wgcna_data = request.json
+    results = call_wgcna_script(wgcna_script, wgcna_data)
 
-    return "success", 200
+    return results, 200
-- 
cgit v1.2.3


From ce045ec96bf965eaba077fdba99847a483281aba Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 14:03:25 +0300
Subject: init tests for wgcna

---
 tests/unit/computations/test_wgcna.py | 36 +++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 1ce69a1..8a68985 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -1,15 +1,35 @@
 """module contains python code for wgcna"""
 from unittest import TestCase
-
-
-def compute_sum(rhs_val, lhs_val):
-    """function to compute sum of two numbers"""
-    return rhs_val+lhs_val
+from gn3.computations.wgcna import dump_wgcna_data
+from gn3.computations.wgcna import compose_wgcna_cmd
 
 
 class TestWgcna(TestCase):
     """test class for wgcna"""
 
-    def test_compute_sum(self):
-        """test for compute sum function"""
-        self.assertEqual(compute_sum(1, 2), 3)
+    def test_compose_wgcna_cmd(self):
+        """test for composing wgcna cmd"""
+        wgcna_cmd = compose_wgcna_cmd("/wgcna.r", "/tmp/wgcna.json")
+        self.assertEqual(wgcna_cmd, f"Rscript /wgcna.r  /tmp/wgcna.json")
+
+    def test_create_json_data(self):
+        """test for writing the data to a csv file"""
+        # # All the traits we have data for (should not contain duplicates)
+        # All the strains we have data for (contains duplicates)
+
+        trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142, "A/J": 7.31, "AKR/J": 7.49,
+                                            "B6D2F1": 6.899, "BALB/cByJ": 7.172, "BALB/cJ": 7.396},
+                             "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05, "AKR/J": 7.313,
+                                            "B6D2F1": 6.999, "BALB/cByJ": 7.293, "BALB/cJ": 7.117},
+                             "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246, "AKR/J": 7.754,
+                                            "B6D2F1": 6.866, "BALB/cByJ": 6.752, "BALB/cJ": 7.269}
+
+                             }
+
+        expected_input = {
+            "trait_sample_data": trait_sample_data,
+            "TOMtype": "unsigned",
+            "minModuleSize": 30
+        }
+
+        _results = dump_wgcna_data(expected_input)
-- 
cgit v1.2.3


From e8f3a7131e8f1fcaf803dedab3177374f46e3709 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 14:04:23 +0300
Subject: Add WGCNA_SCRIT env to settings

---
 gn3/settings.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gn3/settings.py b/gn3/settings.py
index f4866d5..d3d7ea0 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -24,3 +24,6 @@ GN2_BASE_URL = "http://www.genenetwork.org/"
 
 # biweight script
 BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
+
+# wgcna script
+WGCNA_RSCRIPT = "wgcna_analysis.R"
-- 
cgit v1.2.3


From ab8b53a50a601cb95dc0b54279246431c791dd70 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 22:56:21 +0300
Subject: pylint fixes

---
 tests/unit/computations/test_wgcna.py | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 8a68985..9a88515 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -9,20 +9,28 @@ class TestWgcna(TestCase):
 
     def test_compose_wgcna_cmd(self):
         """test for composing wgcna cmd"""
-        wgcna_cmd = compose_wgcna_cmd("/wgcna.r", "/tmp/wgcna.json")
-        self.assertEqual(wgcna_cmd, f"Rscript /wgcna.r  /tmp/wgcna.json")
+        wgcna_cmd = compose_wgcna_cmd(
+            "/wgcna.r", "/tmp/wgcna.json")
+        self.assertEqual(
+            wgcna_cmd, "Rscript /wgcna.r  /tmp/wgcna.json")
 
-    def test_create_json_data(self):
+    def test_create_json_file(self):
         """test for writing the data to a csv file"""
         # # All the traits we have data for (should not contain duplicates)
         # All the strains we have data for (contains duplicates)
 
-        trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142, "A/J": 7.31, "AKR/J": 7.49,
-                                            "B6D2F1": 6.899, "BALB/cByJ": 7.172, "BALB/cJ": 7.396},
-                             "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05, "AKR/J": 7.313,
-                                            "B6D2F1": 6.999, "BALB/cByJ": 7.293, "BALB/cJ": 7.117},
-                             "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246, "AKR/J": 7.754,
-                                            "B6D2F1": 6.866, "BALB/cByJ": 6.752, "BALB/cJ": 7.269}
+        trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142,
+                                            "A/J": 7.31, "AKR/J": 7.49,
+                                            "B6D2F1": 6.899, "BALB/cByJ": 7.172,
+                                            "BALB/cJ": 7.396},
+                             "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05,
+                                            "AKR/J": 7.313,
+                                            "B6D2F1": 6.999, "BALB/cByJ": 7.293,
+                                            "BALB/cJ": 7.117},
+                             "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246,
+                                            "AKR/J": 7.754,
+                                            "B6D2F1": 6.866, "BALB/cByJ": 6.752,
+                                            "BALB/cJ": 7.269}
 
                              }
 
@@ -32,4 +40,7 @@ class TestWgcna(TestCase):
             "minModuleSize": 30
         }
 
-        _results = dump_wgcna_data(expected_input)
+        results = dump_wgcna_data(
+            expected_input)
+
+        self.assertEqual(results, {})
-- 
cgit v1.2.3


From 580778386f054706086d7ab3d49f2c4f91f110e0 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Sep 2021 00:48:37 +0300
Subject: init endpoint tests for wgcna

---
 tests/integration/test_wgcna.py | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 tests/integration/test_wgcna.py

diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
new file mode 100644
index 0000000..65763c1
--- /dev/null
+++ b/tests/integration/test_wgcna.py
@@ -0,0 +1,37 @@
+"""integration tests for wgcna"""
+
+from unittest import TestCase
+from unittest import mock
+
+from gn3.app import create_app
+
+
+class WgcnaIntegrationTest(TestCase):
+    """class contains wgcna integration tests"""
+
+    def setUp(self):
+        self.app = create_app().test_client()
+
+    @mock.patch("gn3.api.wgcna.call_wgcna_script")
+    def test_wgcna_endpoint(self, mock_wgcna_api):
+        """test /api/wgcna/run_wgcna endpoint"""
+
+        wgcna_api_data = {
+            "eigengenes": ["1224_at", "121412_at", "32342342-at"],
+            "dendrogram_file_location": "/tmp/dend1.png"
+
+        }
+        mock_wgcna_api.return_value = wgcna_api_data
+
+        request_data = {
+
+            "trait_sample_data": [],
+
+
+        }
+
+        response = self.app.post("/api/wgcna/run_wgcna",
+                                 json=request_data, follow_redirects=True)
+
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.get_json(), wgcna_api_data)
-- 
cgit v1.2.3


From 6f7c60e6c438ada9a3b9032c8e4509351384e04f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Sep 2021 00:49:22 +0300
Subject: jsonify results

---
 gn3/api/wgcna.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index 5d49493..89784c4 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -2,6 +2,7 @@
 from flask import Blueprint
 from flask import request
 from flask import current_app
+from flask import jsonify
 
 from gn3.computations.wgcna import call_wgcna_script
 
@@ -18,4 +19,4 @@ def run_wgcna():
 
     results = call_wgcna_script(wgcna_script, wgcna_data)
 
-    return results, 200
+    return jsonify(results), 200
-- 
cgit v1.2.3


From f4242f9743c7f236a00917fd187fbd603831dda1 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Sep 2021 01:51:44 +0300
Subject: add required wgcna dependencies to guix.scm

---
 guix.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/guix.scm b/guix.scm
index 75ed4a9..509c9ff 100644
--- a/guix.scm
+++ b/guix.scm
@@ -101,6 +101,7 @@
                        ("r-optparse" ,r-optparse)
                        ("r-qtl" ,r-qtl)
                        ("r-stringi" ,r-stringi)
+                       ("r-wgcna" ,r-wgcna)
                        ("python-plotly" ,python-plotly)
                        ("python-pandas" ,python-pandas)))
   (build-system python-build-system)
-- 
cgit v1.2.3


From 0f871f49e749eb625f58326adf8f80b3d3b5b932 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Sep 2021 01:53:45 +0300
Subject: add init tests for call to script

---
 tests/unit/computations/test_wgcna.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 9a88515..fd90732 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -1,12 +1,27 @@
 """module contains python code for wgcna"""
+from unittest import skip
 from unittest import TestCase
+from unittest import mock
+
 from gn3.computations.wgcna import dump_wgcna_data
 from gn3.computations.wgcna import compose_wgcna_cmd
+from gn3.computations.wgcna import call_wgcna_script
 
 
 class TestWgcna(TestCase):
     """test class for wgcna"""
 
+    @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+    def test_call_wgcna_script(self, mock_dump):
+        """call wgcna script"""
+
+        mock_dump.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        results = call_wgcna_script(
+            "/home/kabui/project/genenetwork3/scripts/wgcna_analysis.R", {})
+
+        self.assertEqual(results, "dsedf")
+
     def test_compose_wgcna_cmd(self):
         """test for composing wgcna cmd"""
         wgcna_cmd = compose_wgcna_cmd(
@@ -14,6 +29,7 @@ class TestWgcna(TestCase):
         self.assertEqual(
             wgcna_cmd, "Rscript /wgcna.r  /tmp/wgcna.json")
 
+    @skip("to  update tests")
     def test_create_json_file(self):
         """test for writing the data to a csv file"""
         # # All the traits we have data for (should not contain duplicates)
-- 
cgit v1.2.3


From 3d36fe96c94cebb6e7ea93b735148b25c4b95f6d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:22:10 +0300
Subject: load data  from json file and and convert to dt

---
 scripts/wgcna_analysis.R | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 267cd86..d0ba91a 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -2,26 +2,29 @@
 
 library(WGCNA);
 library(stringi);
+library(rjson)
 
 options(stringsAsFactors = FALSE);
 
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
-# load expression data **assumes csv format row(traits)(columns info+samples)
+# load expression data **assumes from json files row(traits)(columns info+samples)
 # pass the file_path as arg
 
-inputData <- read.csv(file = "wgcna_data.csv")
+results <- fromJSON(file = "file_path.json")
 
-# transform expressionData
+# trait_sample_data <- results$trait_sample_data
+trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
-dataExpr <- as.data.frame(t(inputData));
 
-## data cleaning
+dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
+# trait_sample_data <- as.data.frame(t(results$trait_sample_data))
+# transform expressionData
 
+dataExpr <- data.frame(t(dataExpr))
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
 # https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
-
 if (!gsg$allOK)
 {
 if (sum(!gsg$goodGenes)>0)
@@ -49,7 +52,7 @@ network <- blockwiseModules(dataExpr,
                   corType = "pearson",
                   #adjacency  matrix options
 
-                  power = sft$powerEstimate,
+                  power = 5,
                   networkType = "unsigned",
                   #TOM options
                   TOMtype =  "unsigned",
@@ -70,14 +73,13 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
-mergedColors <- labels2colors(net$colors)
+mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
 
-
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
-plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
+plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
 "Module colors",
 dendroLabels = FALSE, hang = 0.03,
 addGuide = TRUE, guideHang = 0.05)
-- 
cgit v1.2.3


From e5a50e6becabb9ebe4884714f7a182fad4490490 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:22:51 +0300
Subject: add rjson dependency

---
 guix.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/guix.scm b/guix.scm
index 509c9ff..3e7dcea 100644
--- a/guix.scm
+++ b/guix.scm
@@ -102,6 +102,7 @@
                        ("r-qtl" ,r-qtl)
                        ("r-stringi" ,r-stringi)
                        ("r-wgcna" ,r-wgcna)
+                       ("r-rjson" ,r-rjson)
                        ("python-plotly" ,python-plotly)
                        ("python-pandas" ,python-pandas)))
   (build-system python-build-system)
-- 
cgit v1.2.3


From 95620e1aef5a9c56875845769d58d2aab20dacca Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:37:51 +0300
Subject: pass other variables from user input for network constr

---
 scripts/wgcna_analysis.R | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index d0ba91a..73d0e3f 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -13,12 +13,19 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 results <- fromJSON(file = "file_path.json")
 
-# trait_sample_data <- results$trait_sample_data
-trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
+# parse the json data input
+
+minModuleSize <-results$minModuleSize
+
+TOMtype <-results$TOMtype
+
+corType <-results$corType
+# 
+
+trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
 dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
-# trait_sample_data <- as.data.frame(t(results$trait_sample_data))
 # transform expressionData
 
 dataExpr <- data.frame(t(dataExpr))
@@ -49,18 +56,18 @@ sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
-                  corType = "pearson",
+                  corType = corType,
                   #adjacency  matrix options
 
                   power = 5,
                   networkType = "unsigned",
                   #TOM options
-                  TOMtype =  "unsigned",
+                  TOMtype =  TOMtype,
 
                   #module indentification
 
-                  minmodulesSize = 30,
-                  deepSplit = 5,
+                  minmodulesSize = minModuleSize,
+                  deepSplit = 3,
                   PamRespectsDendro = FALSE
                 )
 
@@ -76,7 +83,7 @@ genImageRandStr <- function(prefix){
 mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
-
+imageLoc
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
-- 
cgit v1.2.3


From 4a8e40f7331f61ba8b7038e8ad48f86018ac7dc6 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:47:27 +0300
Subject: pass json file path as an arg

---
 scripts/wgcna_analysis.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 73d0e3f..53b59d5 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -7,11 +7,20 @@ library(rjson)
 options(stringsAsFactors = FALSE);
 
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
-
 # load expression data **assumes from json files row(traits)(columns info+samples)
 # pass the file_path as arg
+# pass the file path to read json data
+
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args)==0) {
+  stop("Argument for the file location is requires", call.=FALSE)
+} else {
+  # default output file
+  json_file_path  = args[1]
+}
 
-results <- fromJSON(file = "file_path.json")
+results <- fromJSON(file = json_file_path)
 
 
 # parse the json data input
-- 
cgit v1.2.3


From 655343aded3ece533f267bd9fd16aadf0cefff02 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:49:40 +0300
Subject: add mock test data for script

---
 scripts/wgcna_test_data.csv  |  9 +++++++
 scripts/wgcna_test_data.json | 64 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 scripts/wgcna_test_data.csv
 create mode 100644 scripts/wgcna_test_data.json

diff --git a/scripts/wgcna_test_data.csv b/scripts/wgcna_test_data.csv
new file mode 100644
index 0000000..8db9598
--- /dev/null
+++ b/scripts/wgcna_test_data.csv
@@ -0,0 +1,9 @@
+129S1/SvImJ,A/J,AKR/J,B6D2F1,BALB/cByJ,BALB/cJ
+7.142,7.31,7.49,6.899,7.172,7.396
+7.071,7.05,7.313,6.999,7.293,7.117
+7.221,7.246,7.754,6.866,6.752,7.269
+9.221,9.246,9.954,6.866,6.952,9.269
+7.221,7.246,7.754,6.866,6.752,7.269
+7.221,7.246,7.754,6.866,6.752,7.269
+11.221,11.246,11.1154,6.866,6.1152,11.269
+
diff --git a/scripts/wgcna_test_data.json b/scripts/wgcna_test_data.json
new file mode 100644
index 0000000..7348b4e
--- /dev/null
+++ b/scripts/wgcna_test_data.json
@@ -0,0 +1,64 @@
+{
+   "trait_sample_data":[
+  {
+    "129S1/SvImJ": 7.142,
+    "A/J": 7.31,
+    "AKR/J": 7.49,
+    "B6D2F1": 6.899,
+    "BALB/cByJ": 7.172,
+    "BALB/cJ": 7.396
+  },
+  {
+    "129S1/SvImJ": 7.071,
+    "A/J": 7.05,
+    "AKR/J": 7.313,
+    "B6D2F1": 6.999,
+    "BALB/cByJ": 7.293,
+    "BALB/cJ": 7.117
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 9.221,
+    "A/J": 9.246,
+    "AKR/J": 9.954,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.952,
+    "BALB/cJ": 9.269
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 11.221,
+    "A/J": 11.246,
+    "AKR/J": 11.1154,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.1152,
+    "BALB/cJ": 11.269
+  }
+   ],
+   "TOMtype": "unsigned",
+   "minModuleSize": 30,
+   "corType": "pearson"
+
+}
\ No newline at end of file
-- 
cgit v1.2.3


From 9216b6ae956b5c78a9b6d21dbd40b6df1e111264 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:22:14 +0300
Subject: validate required output

---
 scripts/wgcna_analysis.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 53b59d5..86ddffb 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -14,7 +14,7 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 args = commandArgs(trailingOnly=TRUE)
 
 if (length(args)==0) {
-  stop("Argument for the file location is requires", call.=FALSE)
+  stop("Argument for the file location is required", call.=FALSE)
 } else {
   # default output file
   json_file_path  = args[1]
@@ -92,7 +92,6 @@ genImageRandStr <- function(prefix){
 mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
-imageLoc
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
@@ -102,3 +101,13 @@ addGuide = TRUE, guideHang = 0.05)
 
 
 
+
+json_data <- list(ModEigens=network$MEs,soft_threshold=sft$fitIndices,
+  blockGenes =network$blockGenes[[1]],
+  net_colors =network$colors,
+  net_unmerged=network$unmergedColors,
+  imageLoc=imageLoc)
+
+json_data <- toJSON(json_data)
+
+write(json_data,"./output.json")
\ No newline at end of file
-- 
cgit v1.2.3


From eb2277a5fc96795bf6432e392e62601a3cf94058 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:22:31 +0300
Subject: sample output data

---
 scripts/output.json | 161 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 161 insertions(+)
 create mode 100644 scripts/output.json

diff --git a/scripts/output.json b/scripts/output.json
new file mode 100644
index 0000000..9caf837
--- /dev/null
+++ b/scripts/output.json
@@ -0,0 +1,161 @@
+{
+   "ModEigens":{
+      "MEturquoise":[
+         0.0646677768085351,
+         0.137200224277058,
+         0.63451113720732,
+         -0.544002665501479,
+         -0.489487590361863,
+         0.197111117570427
+      ]
+   },
+   "soft_threshold":{
+      "Power":[
+         1,
+         2,
+         3,
+         4,
+         5,
+         6,
+         7,
+         8,
+         9,
+         10,
+         12,
+         14,
+         16,
+         18,
+         20
+      ],
+      "SFT.R.sq":[
+         0.0181093215847335,
+         0.00011984142485113,
+         0.000171967046945159,
+         0.0105462010616537,
+         0.0341444584348834,
+         0.0687163726151286,
+         0.0306423506274298,
+         0.0492567394226327,
+         0.0789539269997996,
+         0.0944880158122527,
+         0.122195040270446,
+         0.0340768567186139,
+         0.0625860126119281,
+         0.100082257137014,
+         0.128277841930818
+      ],
+      "slope":[
+         3.81011386139005,
+         -0.170826531149538,
+         0.159161787390082,
+         -1.01047981107833,
+         -1.55943531024794,
+         -1.93420125756514,
+         -1.16799247295814,
+         -1.33414063070555,
+         -1.54984944650438,
+         -1.54715757057087,
+         -1.49931213589121,
+         -1.80460140377151,
+         -2.19055343583319,
+         -2.52135805259606,
+         -2.58599487577447
+      ],
+      "truncated.R.sq":[
+         0.768989700952805,
+         0.522025793450566,
+         0.329341226670409,
+         0.110265719555879,
+         0.0195649645183151,
+         -0.0503253079741786,
+         0.0507498358330625,
+         -0.0129255450167765,
+         -0.035717519210676,
+         -0.0807094793662766,
+         -0.0967803564932559,
+         0.00172686282662393,
+         -0.0340811003657508,
+         -0.0390284600100592,
+         -0.0489269837827069
+      ],
+      "mean.k.":[
+         4.20178789454309,
+         3.44556816856968,
+         2.98532344074325,
+         2.65297323828966,
+         2.39517682414009,
+         2.18846935370095,
+         2.01963258852289,
+         1.87999059876872,
+         1.76335304166057,
+         1.66510080962817,
+         1.51038968360321,
+         1.39583176924843,
+         1.30882729664563,
+         1.24120316437299,
+         1.18753154238216
+      ],
+      "median.k.":[
+         4.65733789933094,
+         4.13585224131512,
+         3.75980713552836,
+         3.43775457512904,
+         3.15305040369031,
+         2.89933881967523,
+         2.67225531456956,
+         2.46825611568646,
+         2.28437024155601,
+         2.118086531192,
+         1.83011067501282,
+         1.59073325345641,
+         1.38991168639473,
+         1.2201000051609,
+         1.07553194658444
+      ],
+      "max.k.":[
+         4.81522245318686,
+         4.21987143583501,
+         3.83876962723542,
+         3.55526976885104,
+         3.32904938849614,
+         3.14312441404036,
+         2.98828051379132,
+         2.85837136671219,
+         2.74879840851137,
+         2.65594228759455,
+         2.50929962297015,
+         2.40113981571731,
+         2.31993775805391,
+         2.25792900175825,
+         2.2098218130451
+      ]
+   },
+   "blockGenes":[
+      1,
+      2,
+      3,
+      4,
+      5,
+      6,
+      7
+   ],
+   "net_colors":{
+      "X1":"turquoise",
+      "X2":"turquoise",
+      "X3":"turquoise",
+      "X4":"turquoise",
+      "X5":"turquoise",
+      "X6":"turquoise",
+      "X7":"turquoise"
+   },
+   "net_unmerged":{
+      "X1":"turquoise",
+      "X2":"turquoise",
+      "X3":"turquoise",
+      "X4":"turquoise",
+      "X5":"turquoise",
+      "X6":"turquoise",
+      "X7":"turquoise"
+   },
+   "imageLoc":"/WGCNAoutput_1uujpTIpC.png"
+}
\ No newline at end of file
-- 
cgit v1.2.3


From fc335fa1394a39d1f9f397cb69c755040ecfc5e1 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:37:48 +0300
Subject: append input to output

---
 scripts/wgcna_analysis.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 86ddffb..ee749e9 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -20,19 +20,19 @@ if (length(args)==0) {
   json_file_path  = args[1]
 }
 
-results <- fromJSON(file = json_file_path)
+inputData <- fromJSON(file = json_file_path)
 
 
 # parse the json data input
 
-minModuleSize <-results$minModuleSize
+minModuleSize <-inputData$minModuleSize
 
-TOMtype <-results$TOMtype
+TOMtype <-inputData$TOMtype
 
-corType <-results$corType
+corType <-inputData$corType
 # 
 
-trait_sample_data <- do.call(rbind, results$trait_sample_data)
+trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
 
 dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
 # transform expressionData
@@ -102,12 +102,12 @@ addGuide = TRUE, guideHang = 0.05)
 
 
 
-json_data <- list(ModEigens=network$MEs,soft_threshold=sft$fitIndices,
+json_data <- list(input = inputData,output = list(ModEigens=network$MEs,soft_threshold=sft$fitIndices,
   blockGenes =network$blockGenes[[1]],
   net_colors =network$colors,
   net_unmerged=network$unmergedColors,
-  imageLoc=imageLoc)
+  imageLoc=imageLoc))
 
 json_data <- toJSON(json_data)
 
-write(json_data,"./output.json")
\ No newline at end of file
+write(json_data,file= json_file_path)
\ No newline at end of file
-- 
cgit v1.2.3


From 9c221e0d89603acd5412be95650a469824e2ab99 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 15:10:16 +0300
Subject: check for na powerEst and use a default value

---
 scripts/wgcna_analysis.R | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index ee749e9..c3b1ac8 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -62,13 +62,21 @@ enableWGCNAThreads()
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 
+# check the power estimate
+
+if (is.na(sft$powerEstimate)){
+  powerEst = 1
+}else{
+  powerEst = sft$powerEstimate
+}
+
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
                   corType = corType,
                   #adjacency  matrix options
 
-                  power = 5,
+                  power = powerEst,
                   networkType = "unsigned",
                   #TOM options
                   TOMtype =  TOMtype,
-- 
cgit v1.2.3


From 1c392b4b2786d196af6b882e80270b8cb839f554 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 15:38:50 +0300
Subject: read generated files from r and return output

---
 gn3/computations/wgcna.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index f0f0fa2..689bc2d 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -22,7 +22,7 @@ def dump_wgcna_data(request_data: dict):
 
 def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     """function to componse wgcna cmd"""
-    cmd = f"Rscript {rscript_path}  {temp_file_path}"
+    cmd = f"Rscript ./scripts/{rscript_path}  {temp_file_path}"
     return cmd
 
 
@@ -32,6 +32,9 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
     cmd = compose_wgcna_cmd(rscript_path, generated_file)
 
     try:
-        return run_cmd(cmd)
+
+        run_cmd(cmd)
+        with open(generated_file, "r") as outputfile:
+            return results
     except Exception as error:
         raise error
-- 
cgit v1.2.3


From 0ca5f01422883d97e42dd37e59ffacdcf9a65af9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 15:58:25 +0300
Subject: Return r error if returncode!=0

---
 gn3/computations/wgcna.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 689bc2d..e9b76e8 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -22,6 +22,7 @@ def dump_wgcna_data(request_data: dict):
 
 def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     """function to componse wgcna cmd"""
+    # (todo):issue relative paths to abs paths
     cmd = f"Rscript ./scripts/{rscript_path}  {temp_file_path}"
     return cmd
 
@@ -33,8 +34,16 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
 
     try:
 
-        run_cmd(cmd)
+        run_cmd_results = run_cmd(cmd)
+
         with open(generated_file, "r") as outputfile:
-            return results
+
+            if run_cmd_results["code"] != 0:
+                return run_cmd_results
+            return {
+                "data": json.load(outputfile),
+                **run_cmd_results
+            }
+            # return json.load(outputfile)
     except Exception as error:
         raise error
-- 
cgit v1.2.3


From 62a5047be6cee5f692d44f97410cab11a01e3396 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 16:05:17 +0300
Subject: minor fixes for endpoint

---
 gn3/api/wgcna.py          | 3 +++
 gn3/computations/wgcna.py | 1 -
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index 89784c4..fa044cf 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -19,4 +19,7 @@ def run_wgcna():
 
     results = call_wgcna_script(wgcna_script, wgcna_data)
 
+    if results.get("data") is None:
+        return jsonify(results), 401
+
     return jsonify(results), 200
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index e9b76e8..436a888 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -44,6 +44,5 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
                 "data": json.load(outputfile),
                 **run_cmd_results
             }
-            # return json.load(outputfile)
     except Exception as error:
         raise error
-- 
cgit v1.2.3


From 3062aee581560ae1928d8e6077366fc072646677 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 21:27:42 +0300
Subject: add traits as columns names and pass as json input

---
 scripts/wgcna_analysis.R     | 18 +++++++++++-------
 scripts/wgcna_test_data.json |  3 ++-
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index c3b1ac8..e641652 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -53,6 +53,8 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 ## network constructions and modules
 
+names(dataExpr) = inputData$trait_names
+
 # Allow multi-threading within WGCNA
 enableWGCNAThreads()
 
@@ -82,6 +84,7 @@ network <- blockwiseModules(dataExpr,
                   TOMtype =  TOMtype,
 
                   #module indentification
+                  verbose = 3,
 
                   minmodulesSize = minModuleSize,
                   deepSplit = 3,
@@ -108,13 +111,14 @@ dendroLabels = FALSE, hang = 0.03,
 addGuide = TRUE, guideHang = 0.05)
 
 
-
-
-json_data <- list(input = inputData,output = list(ModEigens=network$MEs,soft_threshold=sft$fitIndices,
-  blockGenes =network$blockGenes[[1]],
-  net_colors =network$colors,
-  net_unmerged=network$unmergedColors,
-  imageLoc=imageLoc))
+json_data <- list(input = inputData,
+  output = list(ModEigens=network$MEs,
+   soft_threshold=sft$fitIndices,
+   blockGenes =network$blockGenes[[1]],
+   net_colors =network$colors,
+   power_used_for_analy=powerEst,
+   net_unmerged=network$unmergedColors,
+   imageLoc=imageLoc))
 
 json_data <- toJSON(json_data)
 
diff --git a/scripts/wgcna_test_data.json b/scripts/wgcna_test_data.json
index 7348b4e..1d469f4 100644
--- a/scripts/wgcna_test_data.json
+++ b/scripts/wgcna_test_data.json
@@ -1,4 +1,5 @@
 {
+  "trait_names":["1455537_at","1425637_at","1449593_at","1421945_a_at","1450423_s_at","1423841_at","1451144_at"],
    "trait_sample_data":[
   {
     "129S1/SvImJ": 7.142,
@@ -61,4 +62,4 @@
    "minModuleSize": 30,
    "corType": "pearson"
 
-}
\ No newline at end of file
+}
-- 
cgit v1.2.3


From 7dbb0e6d27cdb0923e94685cf44d244dd8a2e105 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sat, 25 Sep 2021 18:33:12 +0300
Subject: minor fixes for unittests

---
 tests/integration/test_wgcna.py       | 2 +-
 tests/unit/computations/test_wgcna.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
index 65763c1..39dabb2 100644
--- a/tests/integration/test_wgcna.py
+++ b/tests/integration/test_wgcna.py
@@ -33,5 +33,5 @@ class WgcnaIntegrationTest(TestCase):
         response = self.app.post("/api/wgcna/run_wgcna",
                                  json=request_data, follow_redirects=True)
 
-        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.status_code, 401)
         self.assertEqual(response.get_json(), wgcna_api_data)
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index fd90732..64f6c14 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -25,9 +25,9 @@ class TestWgcna(TestCase):
     def test_compose_wgcna_cmd(self):
         """test for composing wgcna cmd"""
         wgcna_cmd = compose_wgcna_cmd(
-            "/wgcna.r", "/tmp/wgcna.json")
+            "wgcna.r", "/tmp/wgcna.json")
         self.assertEqual(
-            wgcna_cmd, "Rscript /wgcna.r  /tmp/wgcna.json")
+            wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
 
     @skip("to  update tests")
     def test_create_json_file(self):
-- 
cgit v1.2.3


From 6f25b8e2b1d1a34c054d325b1c37b303529b8827 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 15:15:28 +0300
Subject: remove unnecessary comments and variables

---
 scripts/wgcna_analysis.R | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index e641652..17b3537 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -23,24 +23,14 @@ if (length(args)==0) {
 inputData <- fromJSON(file = json_file_path)
 
 
-# parse the json data input
-
-minModuleSize <-inputData$minModuleSize
-
-TOMtype <-inputData$TOMtype
-
-corType <-inputData$corType
-# 
-
 trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
 
 dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
 # transform expressionData
 
 dataExpr <- data.frame(t(dataExpr))
-gsg = goodSamplesGenes(dataExpr, verbose = 3);
+gsg = goodSamplesGenes(dataExpr, verbose = 3)
 
-# https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
 if (!gsg$allOK)
 {
 if (sum(!gsg$goodGenes)>0)
@@ -75,18 +65,18 @@ if (is.na(sft$powerEstimate)){
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
-                  corType = corType,
+                  corType = inputData$corType,
                   #adjacency  matrix options
 
                   power = powerEst,
                   networkType = "unsigned",
                   #TOM options
-                  TOMtype =  TOMtype,
+                  TOMtype =  inputData$TOMtype,
 
                   #module indentification
                   verbose = 3,
 
-                  minmodulesSize = minModuleSize,
+                  minmodulesSize = inputData$minModuleSize,
                   deepSplit = 3,
                   PamRespectsDendro = FALSE
                 )
-- 
cgit v1.2.3


From f51a09e2c5f594425531fe26e8237b09fb6909ae Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 17:29:27 +0300
Subject: return str error for exception

---
 gn3/computations/wgcna.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 436a888..1ee55f5 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -45,4 +45,7 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
                 **run_cmd_results
             }
     except Exception as error:
-        raise error
+        # relook  at handling errors gn3
+        return {
+            "output": str(error)
+        }
-- 
cgit v1.2.3


From 0d60b01476e49b094944c1ba4136e4cc8c28aaba Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 17:30:32 +0300
Subject: add tests for calling wgcna_script

---
 tests/unit/computations/test_wgcna.py | 96 ++++++++++++++++++++++++++++++++---
 1 file changed, 89 insertions(+), 7 deletions(-)

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 64f6c14..57224b3 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -11,16 +11,98 @@ from gn3.computations.wgcna import call_wgcna_script
 class TestWgcna(TestCase):
     """test class for wgcna"""
 
+    @mock.patch("gn3.computations.wgcna.run_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
-    def test_call_wgcna_script(self, mock_dump):
-        """call wgcna script"""
+    def test_call_wgcna_script(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+        """test for calling wgcna script"""
+        mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
-        mock_dump.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+        mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
-        results = call_wgcna_script(
-            "/home/kabui/project/genenetwork3/scripts/wgcna_analysis.R", {})
+        request_data = {
+            "trait_names": ["1455537_at", "1425637_at", "1449593_at", "1421945_a_at", "1450423_s_at", "1423841_at", "1451144_at"],
+            "trait_sample_data": [
+                {
+                    "129S1/SvImJ": 7.142,
+                    "A/J": 7.31,
+                    "AKR/J": 7.49,
+                    "B6D2F1": 6.899,
+                    "BALB/cByJ": 7.172,
+                    "BALB/cJ": 7.396
+                },
+                {
+                    "129S1/SvImJ": 7.071,
+                    "A/J": 7.05,
+                    "AKR/J": 7.313,
+                    "B6D2F1": 6.999,
+                    "BALB/cByJ": 7.293,
+                    "BALB/cJ": 7.117
+                }]}
 
-        self.assertEqual(results, "dsedf")
+        mock_run_cmd_results = {
+
+            "code": 0,
+            "output": "Flagging genes and samples with too many missing values...\n  ..step 1\nAllowing parallel execution with up to 3 working processes.\npickSoftThreshold: will use block size 7.\n pickSoftThreshold: calculating connectivity for given powers...\n   ..working on genes 1 through 7 of 7\n   Flagging genes and samples with too many missing values...\n    ..step 1\n ..Working on block 1 .\n    TOM calculation: adjacency..\n    ..will not use multithreading.\nclustering..\n ....detecting modules..\n ....calculating module eigengenes..\n ....checking kME in modules..\n ..merging modules that are too close..\n     mergeCloseModules: Merging modules whose distance is less than 0.15\n     mergeCloseModules: less than two proper modules.\n      ..color levels are turquoise\n      ..there is nothing to merge.\n       Calculating new MEs...\n"
+        }
+
+        json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"outputdata\":{\"eigengenes\":[],\"colors\":[]}}"
+
+        expected_output = {
+
+            "data": {
+                "inputdata": {
+                    "trait_sample_data ": {},
+                    "minModuleSize": 30,
+                    "TOMtype": "unsigned"
+                },
+
+                "outputdata": {
+                    "eigengenes": [],
+                    "colors": []
+                }
+            },
+
+            **mock_run_cmd_results
+
+        }
+
+        with mock.patch("builtins.open", mock.mock_open(read_data=json_output)) as mock_file:
+
+            mock_run_cmd.return_value = mock_run_cmd_results
+
+            results = call_wgcna_script(
+                "Rscript/GUIX_PATH/scripts/r_file.R", request_data)
+
+            mock_dumping_data.assert_called_once_with(request_data)
+
+            mock_compose_wgcna.assert_called_once_with(
+                "Rscript/GUIX_PATH/scripts/r_file.R", "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+            mock_run_cmd.assert_called_once_with(
+                "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+            self.assertEqual(results, expected_output)
+
+    @mock.patch("gn3.computations.wgcna.run_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+    @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+    def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+        """test for calling wgcna script fails and generates the expected error"""
+        mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        expected_error = {
+            "code": 127,
+            "output": "could not read the json file"
+        }
+
+        with mock.patch("builtins.open", mock.mock_open(read_data="")) as mock_file:
+
+            mock_run_cmd.return_value = expected_error
+            self.assertEqual(call_wgcna_script(
+                "input_file.R", ""), expected_error)
 
     def test_compose_wgcna_cmd(self):
         """test for composing wgcna cmd"""
@@ -29,7 +111,7 @@ class TestWgcna(TestCase):
         self.assertEqual(
             wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
 
-    @skip("to  update tests")
+    @ skip("to  update tests")
     def test_create_json_file(self):
         """test for writing the data to a csv file"""
         # # All the traits we have data for (should not contain duplicates)
-- 
cgit v1.2.3


From b6097cff6431e50c132f46dc0d3e1b841897da0f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 19:14:58 +0300
Subject: add file not found exception

---
 gn3/computations/wgcna.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 1ee55f5..fd508fa 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -44,8 +44,8 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
                 "data": json.load(outputfile),
                 **run_cmd_results
             }
-    except Exception as error:
+    except FileNotFoundError:
         # relook  at handling errors gn3
         return {
-            "output": str(error)
+            "output": "output file not found"
         }
-- 
cgit v1.2.3


From a2da1f5dbc49b0137ef6b8ee9e234178521935f3 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 19:15:23 +0300
Subject: modify  integration tests

---
 tests/integration/test_wgcna.py | 60 ++++++++++++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 12 deletions(-)

diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
index 39dabb2..078449d 100644
--- a/tests/integration/test_wgcna.py
+++ b/tests/integration/test_wgcna.py
@@ -13,25 +13,61 @@ class WgcnaIntegrationTest(TestCase):
         self.app = create_app().test_client()
 
     @mock.patch("gn3.api.wgcna.call_wgcna_script")
-    def test_wgcna_endpoint(self, mock_wgcna_api):
+    def test_wgcna_endpoint(self, mock_wgcna_script):
         """test /api/wgcna/run_wgcna endpoint"""
 
-        wgcna_api_data = {
-            "eigengenes": ["1224_at", "121412_at", "32342342-at"],
-            "dendrogram_file_location": "/tmp/dend1.png"
-
+        wgcna_output_data = {
+            "code": 0,
+            "output": "run script successfully",
+            "data": {
+                "ModEigens": {
+                    "MEturquoise": [
+                        0.0646677768085351,
+                        0.137200224277058,
+                        0.63451113720732,
+                        -0.544002665501479,
+                        -0.489487590361863,
+                        0.197111117570427
+                    ]
+                },
+                "net_colors": {
+                    "X1": "turquoise",
+                    "X2": "turquoise",
+                    "X3": "turquoise",
+                    "X4": "turquoise"
+                },
+                "imageLoc": "/WGCNAoutput_1uujpTIpC.png"
+            }
         }
-        mock_wgcna_api.return_value = wgcna_api_data
 
         request_data = {
-
-            "trait_sample_data": [],
-
-
+            "trait_names": [
+                "1455537_at",
+                "1425637_at"
+            ],
+            "trait_sample_data": [
+                {
+                    "129S1/SvImJ": 6.142,
+                    "A/J": 5.31,
+                    "AKR/J": 3.49,
+                    "B6D2F1": 2.899,
+                    "BALB/cByJ": 1.172,
+                    "BALB/cJ": 7.396
+                },
+                {
+                    "129S1/SvImJ": 1.42,
+                    "A/J": 2.31,
+                    "AKR/J": 5.49,
+                    "B6D2F1": 3.899,
+                    "BALB/cByJ": 1.172,
+                    "BALB/cJ": 7.396
+                }
+            ]
         }
+        mock_wgcna_script.return_value = wgcna_output_data
 
         response = self.app.post("/api/wgcna/run_wgcna",
                                  json=request_data, follow_redirects=True)
 
-        self.assertEqual(response.status_code, 401)
-        self.assertEqual(response.get_json(), wgcna_api_data)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.get_json(), wgcna_output_data)
-- 
cgit v1.2.3


From 16235188d4ee2ad21a667832baf6cbbea6d8856a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 19:15:46 +0300
Subject: modify unittests

---
 tests/unit/computations/test_wgcna.py | 40 ++++++++++++++++++++++++-----------
 1 file changed, 28 insertions(+), 12 deletions(-)

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 57224b3..ec81d94 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -1,5 +1,4 @@
 """module contains python code for wgcna"""
-from unittest import skip
 from unittest import TestCase
 from unittest import mock
 
@@ -14,8 +13,13 @@ class TestWgcna(TestCase):
     @mock.patch("gn3.computations.wgcna.run_cmd")
     @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
-    def test_call_wgcna_script(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+    def test_call_wgcna_script(self,
+                               mock_dumping_data,
+                               mock_compose_wgcna,
+                               mock_run_cmd):
         """test for calling wgcna script"""
+
+        # pylint: disable = line-too-long
         mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
         mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
@@ -67,7 +71,7 @@ class TestWgcna(TestCase):
 
         }
 
-        with mock.patch("builtins.open", mock.mock_open(read_data=json_output)) as mock_file:
+        with mock.patch("builtins.open", mock.mock_open(read_data=json_output)):
 
             mock_run_cmd.return_value = mock_run_cmd_results
 
@@ -77,7 +81,8 @@ class TestWgcna(TestCase):
             mock_dumping_data.assert_called_once_with(request_data)
 
             mock_compose_wgcna.assert_called_once_with(
-                "Rscript/GUIX_PATH/scripts/r_file.R", "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+                "Rscript/GUIX_PATH/scripts/r_file.R",
+                "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
 
             mock_run_cmd.assert_called_once_with(
                 "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
@@ -88,17 +93,19 @@ class TestWgcna(TestCase):
     @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
     def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
-        """test for calling wgcna script fails and generates the expected error"""
+        """test for calling wgcna script\
+        fails and generates the expected error"""
+        # pylint: disable = line-too-long,
         mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
         mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
         expected_error = {
-            "code": 127,
+            "code": 2,
             "output": "could not read the json file"
         }
 
-        with mock.patch("builtins.open", mock.mock_open(read_data="")) as mock_file:
+        with mock.patch("builtins.open", mock.mock_open(read_data="")):
 
             mock_run_cmd.return_value = expected_error
             self.assertEqual(call_wgcna_script(
@@ -111,8 +118,9 @@ class TestWgcna(TestCase):
         self.assertEqual(
             wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
 
-    @ skip("to  update tests")
-    def test_create_json_file(self):
+    @mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp")
+    @mock.patch("gn3.computations.wgcna.uuid.uuid4")
+    def test_create_json_file(self, file_name_generator):
         """test for writing the data to a csv file"""
         # # All the traits we have data for (should not contain duplicates)
         # All the strains we have data for (contains duplicates)
@@ -138,7 +146,15 @@ class TestWgcna(TestCase):
             "minModuleSize": 30
         }
 
-        results = dump_wgcna_data(
-            expected_input)
+        with mock.patch("builtins.open", mock.mock_open()) as file_handler:
+
+            file_name_generator.return_value = "facb73ff-7eef-4053-b6ea-e91d3a22a00c"
+
+            results = dump_wgcna_data(
+                expected_input)
+
+            file_handler.assert_called_once_with(
+                "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w')
 
-        self.assertEqual(results, {})
+            self.assertEqual(
+                results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json")
-- 
cgit v1.2.3