From 67af23cecafd21dd23b636fe7060c237dd4694d3 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Wed, 13 Oct 2021 10:13:50 +0100
Subject: [PATCH 01/19] auth jwt added to error message pipeline fail

---
 pipeline-runner/R/gem2s-3-run_emptydrops.R |  1 -
 pipeline-runner/R/handle_data.R            | 10 +++++++---
 pipeline-runner/R/qc-3-filter_high_mito.R  |  1 -
 pipeline-runner/init.R                     |  2 +-
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/pipeline-runner/R/gem2s-3-run_emptydrops.R b/pipeline-runner/R/gem2s-3-run_emptydrops.R
index 0195b2b7..600f8b4f 100644
--- a/pipeline-runner/R/gem2s-3-run_emptydrops.R
+++ b/pipeline-runner/R/gem2s-3-run_emptydrops.R
@@ -15,7 +15,6 @@ run_emptydrops <- function(input, pipeline_config, prev_out) {
   # destructure previous output
   counts_list <- prev_out$counts_list
   samples <- names(counts_list)
-
   edrops <- list()
   for (sample in samples) {
     message("\nSample --> ", sample)
diff --git a/pipeline-runner/R/handle_data.R b/pipeline-runner/R/handle_data.R
index 28bf7732..44ef74fe 100644
--- a/pipeline-runner/R/handle_data.R
+++ b/pipeline-runner/R/handle_data.R
@@ -83,11 +83,15 @@ send_gem2s_update_to_api <- function(pipeline_config, experiment_id, task_name,
   return(result$MessageId)
 }
 
-send_pipeline_fail_update <- function(pipeline_config, experiment_id, process_name, error_message) {
+send_pipeline_fail_update <- function(pipeline_config, input, error_message) {
+  process_name <- input$processName
+
   error_msg <- list()
-  error_msg$experimentId <- experiment_id
-  error_msg$response$error <- error_message
 
+  # todo - remove the duplicate experiment id from input response
+  error_msg$experimentId <- input$experimentId
+  error_msg$response$error <- process_name
+  error_msg$input <- input
   sns <- paws::sns(config = pipeline_config$aws_config)
 
   string_value <- ""
diff --git a/pipeline-runner/R/qc-3-filter_high_mito.R b/pipeline-runner/R/qc-3-filter_high_mito.R
index f6ca4218..b1939fb8 100644
--- a/pipeline-runner/R/qc-3-filter_high_mito.R
+++ b/pipeline-runner/R/qc-3-filter_high_mito.R
@@ -37,7 +37,6 @@ filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondri
     return(list(data = scdata, config = config, plotData = list()))
   }
   sample_subset <- subset(scdata, cells = barcode_names_this_sample)
-
   if (exists("auto", where = config)) {
     if (as.logical(toupper(config$auto))) {
       maxFraction <- generate_default_values_mitochondrialContent(sample_subset, config)
diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
index 4f667839..be9e1aa0 100644
--- a/pipeline-runner/init.R
+++ b/pipeline-runner/init.R
@@ -348,7 +348,7 @@ init <- function() {
                     cause = error_txt
                 )
 
-                send_pipeline_fail_update(pipeline_config, input_parse$experimentId, input_parse$processName, "Error message placeholder")
+                send_pipeline_fail_update(pipeline_config, input_parse, "Error message placeholder")
 
                 message("Sent task failure to state machine task: ", taskToken)
                 message("recovered from error:", e$message)

From 20ea4b9e36f53345df6dcec7b5b4cae9640d4f9c Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Wed, 20 Oct 2021 11:55:15 +0100
Subject: [PATCH 02/19] add input to gem2s message too

---
 pipeline-runner/R/handle_data.R              | 6 +++---
 pipeline-runner/R/qc-2-filter_low_cellsize.R | 1 -
 pipeline-runner/R/qc-3-filter_high_mito.R    | 2 +-
 pipeline-runner/init.R                       | 2 +-
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/pipeline-runner/R/handle_data.R b/pipeline-runner/R/handle_data.R
index 44ef74fe..faad010b 100644
--- a/pipeline-runner/R/handle_data.R
+++ b/pipeline-runner/R/handle_data.R
@@ -62,11 +62,11 @@ send_output_to_api <- function(pipeline_config, input, plot_data_keys, output) {
   return(result$MessageId)
 }
 
-send_gem2s_update_to_api <- function(pipeline_config, experiment_id, task_name, data, auth_JWT) {
+send_gem2s_update_to_api <- function(pipeline_config, experiment_id, task_name, data, input) {
   message("Sending to SNS topic ", pipeline_config$sns_topic)
   sns <- paws::sns(config = pipeline_config$aws_config)
-
-  msg <- c(data, taskName = list(task_name), experimentId = list(experiment_id), authJWT = list(auth_JWT))
+  # todo - remove duplicate authjwt in response
+  msg <- c(data, taskName = list(task_name), experimentId = list(experiment_id), authJWT = list(input$auth_JWT), input = list(input))
 
   result <- sns$publish(
     Message = RJSONIO::toJSON(msg),
diff --git a/pipeline-runner/R/qc-2-filter_low_cellsize.R b/pipeline-runner/R/qc-2-filter_low_cellsize.R
index 64b82351..6d53d830 100644
--- a/pipeline-runner/R/qc-2-filter_low_cellsize.R
+++ b/pipeline-runner/R/qc-2-filter_low_cellsize.R
@@ -19,7 +19,6 @@
 filter_low_cellsize <- function(scdata, config, sample_id, task_name = "cellSizeDistribution", num_cells_to_downsample = 6000) {
 
   minCellSize <- as.numeric(config$filterSettings$minCellSize)
-
   # extract plotting data of original data to return to plot slot later
   meta <- scdata@meta.data
   barcode_names_this_sample <- rownames(meta)[meta$samples == sample_id]
diff --git a/pipeline-runner/R/qc-3-filter_high_mito.R b/pipeline-runner/R/qc-3-filter_high_mito.R
index b1939fb8..e282db26 100644
--- a/pipeline-runner/R/qc-3-filter_high_mito.R
+++ b/pipeline-runner/R/qc-3-filter_high_mito.R
@@ -20,7 +20,6 @@
 #' @return a list with the filtered seurat object by mitochondrial content, the config and the plot values
 #'
 filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondrialContent", num_cells_to_downsample = 6000) {
-
   # Check if the experiment has MT-content
   if (!"percent.mt" %in% colnames(scdata@meta.data)) {
     # This return value breaks the step, no config data is returned!!!!
@@ -93,6 +92,7 @@ filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondri
     config = config,
     plotData = guidata
   )
+  stop('FAILURE!!')
   return(result)
 }
 
diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
index be9e1aa0..6257d701 100644
--- a/pipeline-runner/init.R
+++ b/pipeline-runner/init.R
@@ -197,7 +197,7 @@ call_gem2s <- function(task_name, input, pipeline_config) {
     c(data, task_out) %<-% run_gem2s_step(task_name, input, pipeline_config, prev_out)
     assign("prev_out", task_out, pos = ".GlobalEnv")
 
-    message_id <- send_gem2s_update_to_api(pipeline_config, experiment_id, task_name, data, input$authJWT)
+    message_id <- send_gem2s_update_to_api(pipeline_config, experiment_id, task_name, data, input)
 
     return(message_id)
 }

From 09ff91f6701fd683207053a0372e3f352a71587a Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Sun, 24 Oct 2021 16:53:29 +0100
Subject: [PATCH 03/19] test failing

---
 pipeline-runner/R/qc-3-filter_high_mito.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline-runner/R/qc-3-filter_high_mito.R b/pipeline-runner/R/qc-3-filter_high_mito.R
index e282db26..e67cc3cf 100644
--- a/pipeline-runner/R/qc-3-filter_high_mito.R
+++ b/pipeline-runner/R/qc-3-filter_high_mito.R
@@ -92,7 +92,6 @@ filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondri
     config = config,
     plotData = guidata
   )
-  stop('FAILURE!!')
   return(result)
 }
 

From 2ec860665a73a4aff5790e951c2f426b11f2a6da Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Tue, 26 Oct 2021 16:20:33 +0100
Subject: [PATCH 04/19] add removed lines for test coverage

---
 pipeline-runner/R/gem2s-3-run_emptydrops.R   | 1 +
 pipeline-runner/R/qc-2-filter_low_cellsize.R | 1 +
 pipeline-runner/R/qc-3-filter_high_mito.R    | 2 ++
 3 files changed, 4 insertions(+)

diff --git a/pipeline-runner/R/gem2s-3-run_emptydrops.R b/pipeline-runner/R/gem2s-3-run_emptydrops.R
index 600f8b4f..ad8c4d5e 100644
--- a/pipeline-runner/R/gem2s-3-run_emptydrops.R
+++ b/pipeline-runner/R/gem2s-3-run_emptydrops.R
@@ -15,6 +15,7 @@ run_emptydrops <- function(input, pipeline_config, prev_out) {
   # destructure previous output
   counts_list <- prev_out$counts_list
   samples <- names(counts_list)
+  
   edrops <- list()
   for (sample in samples) {
     message("\nSample --> ", sample)
diff --git a/pipeline-runner/R/qc-2-filter_low_cellsize.R b/pipeline-runner/R/qc-2-filter_low_cellsize.R
index 6d53d830..2e9b21a3 100644
--- a/pipeline-runner/R/qc-2-filter_low_cellsize.R
+++ b/pipeline-runner/R/qc-2-filter_low_cellsize.R
@@ -19,6 +19,7 @@
 filter_low_cellsize <- function(scdata, config, sample_id, task_name = "cellSizeDistribution", num_cells_to_downsample = 6000) {
 
   minCellSize <- as.numeric(config$filterSettings$minCellSize)
+  
   # extract plotting data of original data to return to plot slot later
   meta <- scdata@meta.data
   barcode_names_this_sample <- rownames(meta)[meta$samples == sample_id]
diff --git a/pipeline-runner/R/qc-3-filter_high_mito.R b/pipeline-runner/R/qc-3-filter_high_mito.R
index e67cc3cf..23410834 100644
--- a/pipeline-runner/R/qc-3-filter_high_mito.R
+++ b/pipeline-runner/R/qc-3-filter_high_mito.R
@@ -20,6 +20,7 @@
 #' @return a list with the filtered seurat object by mitochondrial content, the config and the plot values
 #'
 filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondrialContent", num_cells_to_downsample = 6000) {
+
   # Check if the experiment has MT-content
   if (!"percent.mt" %in% colnames(scdata@meta.data)) {
     # This return value breaks the step, no config data is returned!!!!
@@ -36,6 +37,7 @@ filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondri
     return(list(data = scdata, config = config, plotData = list()))
   }
   sample_subset <- subset(scdata, cells = barcode_names_this_sample)
+  
   if (exists("auto", where = config)) {
     if (as.logical(toupper(config$auto))) {
       maxFraction <- generate_default_values_mitochondrialContent(sample_subset, config)

From 211fe82df425b545651cb0c948072efc2130ec1f Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Tue, 26 Oct 2021 16:23:34 +0100
Subject: [PATCH 05/19] revert modified files

---
 pipeline-runner/R/qc-2-filter_low_cellsize.R | 2 +-
 pipeline-runner/R/qc-3-filter_high_mito.R    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipeline-runner/R/qc-2-filter_low_cellsize.R b/pipeline-runner/R/qc-2-filter_low_cellsize.R
index 2e9b21a3..64b82351 100644
--- a/pipeline-runner/R/qc-2-filter_low_cellsize.R
+++ b/pipeline-runner/R/qc-2-filter_low_cellsize.R
@@ -19,7 +19,7 @@
 filter_low_cellsize <- function(scdata, config, sample_id, task_name = "cellSizeDistribution", num_cells_to_downsample = 6000) {
 
   minCellSize <- as.numeric(config$filterSettings$minCellSize)
-  
+
   # extract plotting data of original data to return to plot slot later
   meta <- scdata@meta.data
   barcode_names_this_sample <- rownames(meta)[meta$samples == sample_id]
diff --git a/pipeline-runner/R/qc-3-filter_high_mito.R b/pipeline-runner/R/qc-3-filter_high_mito.R
index 23410834..f6ca4218 100644
--- a/pipeline-runner/R/qc-3-filter_high_mito.R
+++ b/pipeline-runner/R/qc-3-filter_high_mito.R
@@ -37,7 +37,7 @@ filter_high_mito <- function(scdata, config, sample_id, task_name = "mitochondri
     return(list(data = scdata, config = config, plotData = list()))
   }
   sample_subset <- subset(scdata, cells = barcode_names_this_sample)
-  
+
   if (exists("auto", where = config)) {
     if (as.logical(toupper(config$auto))) {
       maxFraction <- generate_default_values_mitochondrialContent(sample_subset, config)

From 7cf228e7c73461e4cdf8c619db8f6e4ec540ebbc Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Tue, 26 Oct 2021 16:24:21 +0100
Subject: [PATCH 06/19] forgotten file

---
 pipeline-runner/R/gem2s-3-run_emptydrops.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline-runner/R/gem2s-3-run_emptydrops.R b/pipeline-runner/R/gem2s-3-run_emptydrops.R
index ad8c4d5e..0195b2b7 100644
--- a/pipeline-runner/R/gem2s-3-run_emptydrops.R
+++ b/pipeline-runner/R/gem2s-3-run_emptydrops.R
@@ -15,7 +15,7 @@ run_emptydrops <- function(input, pipeline_config, prev_out) {
   # destructure previous output
   counts_list <- prev_out$counts_list
   samples <- names(counts_list)
-  
+
   edrops <- list()
   for (sample in samples) {
     message("\nSample --> ", sample)

From fcaaa0d8e70dcf68b24ae04901b494a22ecff911 Mon Sep 17 00:00:00 2001
From: alexvpickering <alexvpickering@gmail.com>
Date: Wed, 27 Oct 2021 11:45:16 +0100
Subject: [PATCH 07/19] init testing

---
 pipeline-runner/R/test-handle_data.R | 29 ++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 pipeline-runner/R/test-handle_data.R

diff --git a/pipeline-runner/R/test-handle_data.R b/pipeline-runner/R/test-handle_data.R
new file mode 100644
index 00000000..d6b07654
--- /dev/null
+++ b/pipeline-runner/R/test-handle_data.R
@@ -0,0 +1,29 @@
+sns <- paws::sns()
+
+# Create a topic to which we can send notifications.
+topic <- sns$create_topic("ExampleTopic")
+
+
+
+pipeline_config <- list(
+    sns_topic = 'ExampleTopic',
+    aws_config = NULL
+)
+
+
+send_gem2s_update_to_api(pipeline_config,
+                         experiment_id = 'dfgdfg',
+                         task_name = 'dsfdsdf',
+                         data = 1:5,
+                         input = 'blah')
+
+
+test_that("filter_gene_umi_outlier updates gam p.level in config if auto", {
+    scdata <- mock_scdata()
+    config <- mock_config()
+    config$filterSettings$regressionTypeSettings$gam$p.level <- 1
+    out <- filter_gene_umi_outlier(scdata, config, '123def')
+    new <- out$config$filterSettings$regressionTypeSettings$gam$p.level
+
+    expect_lt(new, 1)
+})

From 13f1a1f8cfcaa453440f38adfc98a34fa94a1a99 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Wed, 27 Oct 2021 12:32:20 +0100
Subject: [PATCH 08/19] test

---
 ..Rcheck/00check.log                 |  8 +++++++
 pipeline-runner/R/test-handle_data.R | 33 ++++++++++++++--------------
 2 files changed, 25 insertions(+), 16 deletions(-)
 create mode 100644 ..Rcheck/00check.log

diff --git a/..Rcheck/00check.log b/..Rcheck/00check.log
new file mode 100644
index 00000000..ef544aa9
--- /dev/null
+++ b/..Rcheck/00check.log
@@ -0,0 +1,8 @@
+* using log directory ‘/Users/grasp6/Desktop/work/biomage/pipeline/..Rcheck’
+* using R version 3.6.1 (2019-07-05)
+* using platform: x86_64-apple-darwin15.6.0 (64-bit)
+* using session charset: UTF-8
+* checking for file ‘./DESCRIPTION’ ... ERROR
+File DESCRIPTION does not exist
+* DONE
+Status: 1 ERROR
diff --git a/pipeline-runner/R/test-handle_data.R b/pipeline-runner/R/test-handle_data.R
index d6b07654..5854760d 100644
--- a/pipeline-runner/R/test-handle_data.R
+++ b/pipeline-runner/R/test-handle_data.R
@@ -10,20 +10,21 @@ pipeline_config <- list(
     aws_config = NULL
 )
 
-
-send_gem2s_update_to_api(pipeline_config,
-                         experiment_id = 'dfgdfg',
-                         task_name = 'dsfdsdf',
-                         data = 1:5,
-                         input = 'blah')
-
-
-test_that("filter_gene_umi_outlier updates gam p.level in config if auto", {
-    scdata <- mock_scdata()
-    config <- mock_config()
-    config$filterSettings$regressionTypeSettings$gam$p.level <- 1
-    out <- filter_gene_umi_outlier(scdata, config, '123def')
-    new <- out$config$filterSettings$regressionTypeSettings$gam$p.level
-
-    expect_lt(new, 1)
+mock_sns <- function(){
+    return(
+        list(publish=function(){
+            return(list(MessageId = 'ok'))
+        }
+    ))
+}
+
+test_that("send_gem2s_update_to_api completes successfully", {
+    stub(send_gem2s_update_to_api, 'paws::sns', mock_sns)
+
+    response <- send_gem2s_update_to_api(pipeline_config,
+                            experiment_id = 'dfgdfg',
+                            task_name = 'dsfdsdf',
+                            data = 1:5,
+                            input = list(auth_JWT='ayylmao'))
+    expect_true(response$MessageId=='ok')
 })

From 8f6a90e0ac30acf85bfe4a4b85f52cc8c3b42fc8 Mon Sep 17 00:00:00 2001
From: alexvpickering <alexvpickering@gmail.com>
Date: Wed, 27 Oct 2021 12:52:01 +0100
Subject: [PATCH 09/19] init mockery stub

---
 pipeline-runner/R/test-handle_data.R          | 30 -------------------
 .../tests/testthat/test-handle_data.R         | 27 +++++++++++++++++
 2 files changed, 27 insertions(+), 30 deletions(-)
 delete mode 100644 pipeline-runner/R/test-handle_data.R
 create mode 100644 pipeline-runner/tests/testthat/test-handle_data.R

diff --git a/pipeline-runner/R/test-handle_data.R b/pipeline-runner/R/test-handle_data.R
deleted file mode 100644
index 5854760d..00000000
--- a/pipeline-runner/R/test-handle_data.R
+++ /dev/null
@@ -1,30 +0,0 @@
-sns <- paws::sns()
-
-# Create a topic to which we can send notifications.
-topic <- sns$create_topic("ExampleTopic")
-
-
-
-pipeline_config <- list(
-    sns_topic = 'ExampleTopic',
-    aws_config = NULL
-)
-
-mock_sns <- function(){
-    return(
-        list(publish=function(){
-            return(list(MessageId = 'ok'))
-        }
-    ))
-}
-
-test_that("send_gem2s_update_to_api completes successfully", {
-    stub(send_gem2s_update_to_api, 'paws::sns', mock_sns)
-
-    response <- send_gem2s_update_to_api(pipeline_config,
-                            experiment_id = 'dfgdfg',
-                            task_name = 'dsfdsdf',
-                            data = 1:5,
-                            input = list(auth_JWT='ayylmao'))
-    expect_true(response$MessageId=='ok')
-})
diff --git a/pipeline-runner/tests/testthat/test-handle_data.R b/pipeline-runner/tests/testthat/test-handle_data.R
new file mode 100644
index 00000000..9567fe2d
--- /dev/null
+++ b/pipeline-runner/tests/testthat/test-handle_data.R
@@ -0,0 +1,27 @@
+
+mock_sns <- function(config) {
+    print('hello mock!')
+    return(
+        list(publish = function (Message, TopicArn, MessageAttributes) {
+            return (list(MessageId = 'ok'))
+        }
+    ))
+}
+
+test_that("send_gem2s_update_to_api completes successfully", {
+    pipeline_config <- list(
+        sns_topic = 'ExampleTopic',
+        aws_config = NULL
+    )
+
+    mockery::stub(send_gem2s_update_to_api, 'paws::sns', mock_sns)
+
+    response <- send_gem2s_update_to_api(pipeline_config,
+                            experiment_id = 'dfgdfg',
+                            task_name = 'dsfdsdf',
+                            data = 1:5,
+                            input = list(auth_JWT='ayylmao'))
+
+
+    expect_true(response == 'ok')
+})

From d02d66a5200a95ef10e2cce960983386b5beb929 Mon Sep 17 00:00:00 2001
From: alexvpickering <alexvpickering@gmail.com>
Date: Wed, 27 Oct 2021 12:53:59 +0100
Subject: [PATCH 10/19] remove Rcheck logs

---
 ..Rcheck/00check.log | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 ..Rcheck/00check.log

diff --git a/..Rcheck/00check.log b/..Rcheck/00check.log
deleted file mode 100644
index ef544aa9..00000000
--- a/..Rcheck/00check.log
+++ /dev/null
@@ -1,8 +0,0 @@
-* using log directory ‘/Users/grasp6/Desktop/work/biomage/pipeline/..Rcheck’
-* using R version 3.6.1 (2019-07-05)
-* using platform: x86_64-apple-darwin15.6.0 (64-bit)
-* using session charset: UTF-8
-* checking for file ‘./DESCRIPTION’ ... ERROR
-File DESCRIPTION does not exist
-* DONE
-Status: 1 ERROR

From d21b02651bdd31bf34513493d042cdbe682f3d15 Mon Sep 17 00:00:00 2001
From: alexvpickering <alexvpickering@gmail.com>
Date: Wed, 27 Oct 2021 13:20:23 +0100
Subject: [PATCH 11/19] add mockery to lockfile

---
 pipeline-runner/renv.lock | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pipeline-runner/renv.lock b/pipeline-runner/renv.lock
index 7b741910..be4e0745 100644
--- a/pipeline-runner/renv.lock
+++ b/pipeline-runner/renv.lock
@@ -931,6 +931,13 @@
       "Repository": "CRAN",
       "Hash": "fec5f52652d60615fdb3957b3d74324a"
     },
+    "mockery": {
+      "Package": "mockery",
+      "Version": "0.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "313fa6504824ba5aab9308412135fb5f"
+    },
     "munsell": {
       "Package": "munsell",
       "Version": "0.5.0",

From c0d645275ee92ccd02ef640efb7bd0174aca12d4 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Sat, 30 Oct 2021 12:35:44 +0100
Subject: [PATCH 12/19] comment fixes

---
 pipeline-runner/R/handle_data.R                   | 5 +++--
 pipeline-runner/tests/testthat/test-handle_data.R | 1 -
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pipeline-runner/R/handle_data.R b/pipeline-runner/R/handle_data.R
index faad010b..e64aab8e 100644
--- a/pipeline-runner/R/handle_data.R
+++ b/pipeline-runner/R/handle_data.R
@@ -65,7 +65,7 @@ send_output_to_api <- function(pipeline_config, input, plot_data_keys, output) {
 send_gem2s_update_to_api <- function(pipeline_config, experiment_id, task_name, data, input) {
   message("Sending to SNS topic ", pipeline_config$sns_topic)
   sns <- paws::sns(config = pipeline_config$aws_config)
-  # todo - remove duplicate authjwt in response
+  # TODO -REMOVE DUPLICATE AUTHJWT IN RESPONSE
   msg <- c(data, taskName = list(task_name), experimentId = list(experiment_id), authJWT = list(input$auth_JWT), input = list(input))
 
   result <- sns$publish(
@@ -88,7 +88,8 @@ send_pipeline_fail_update <- function(pipeline_config, input, error_message) {
 
   error_msg <- list()
 
-  # todo - remove the duplicate experiment id from input response
+  # TODO - REMOVE THE DUPLICATE EXPERIMETN ID FROM INPUT RESPONSE
+  
   error_msg$experimentId <- input$experimentId
   error_msg$response$error <- process_name
   error_msg$input <- input
diff --git a/pipeline-runner/tests/testthat/test-handle_data.R b/pipeline-runner/tests/testthat/test-handle_data.R
index 9567fe2d..d55bdf5d 100644
--- a/pipeline-runner/tests/testthat/test-handle_data.R
+++ b/pipeline-runner/tests/testthat/test-handle_data.R
@@ -1,6 +1,5 @@
 
 mock_sns <- function(config) {
-    print('hello mock!')
     return(
         list(publish = function (Message, TopicArn, MessageAttributes) {
             return (list(MessageId = 'ok'))

From 7094593f2db3d6210b7d8a22f2845e4b42d17af7 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Tue, 9 Nov 2021 16:51:18 +0000
Subject: [PATCH 13/19] well i cant crash test because tests fail :/

---
 pipeline-runner/R/qc-5-filter_doublets.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline-runner/R/qc-5-filter_doublets.R b/pipeline-runner/R/qc-5-filter_doublets.R
index f7e88083..b99bf9ce 100644
--- a/pipeline-runner/R/qc-5-filter_doublets.R
+++ b/pipeline-runner/R/qc-5-filter_doublets.R
@@ -80,7 +80,6 @@ filter_doublets <- function(scdata, config, sample_id, cells_id, task_name = "do
     config = config,
     plotData = guidata
   )
-  stop('TEST CRASH PIPELINE!!')
   return(result)
 }
 

From 47991adb26544854a5a75ba0a665f57805b1bf4e Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Tue, 9 Nov 2021 18:16:24 +0000
Subject: [PATCH 14/19] test fail

---
 pipeline-runner/R/qc-5-filter_doublets.R      |   1 +
 .../testthat/test-qc-5-filter_doublets.R      | 180 +++++++++---------
 2 files changed, 91 insertions(+), 90 deletions(-)

diff --git a/pipeline-runner/R/qc-5-filter_doublets.R b/pipeline-runner/R/qc-5-filter_doublets.R
index b99bf9ce..f293f282 100644
--- a/pipeline-runner/R/qc-5-filter_doublets.R
+++ b/pipeline-runner/R/qc-5-filter_doublets.R
@@ -80,6 +80,7 @@ filter_doublets <- function(scdata, config, sample_id, cells_id, task_name = "do
     config = config,
     plotData = guidata
   )
+  stop("TEST FAIL")
   return(result)
 }
 
diff --git a/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R b/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
index 21ac5ca0..7b6750de 100644
--- a/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
+++ b/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
@@ -1,90 +1,90 @@
-mock_config <- function(thr = 0.1, auto = FALSE, enabled = TRUE) {
-  config <- list(
-    auto = auto,
-    enabled = enabled,
-    filterSettings = list(
-      probabilityThreshold = thr
-    )
-  )
-  return(config)
-}
-
-
-mock_scdata <- function() {
-  pbmc_raw <- read.table(
-    file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
-    as.is = TRUE
-  )
-
-  scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
-  scdata$cells_id <- 0:(ncol(scdata) - 1)
-
-  # add doublet scores and class
-  scdata@meta.data$doublet_scores <- 0.01
-  scdata@meta.data$doublet_scores[1:10] <- 0.9
-
-  scdata@meta.data$doublet_class <- rep("singlet", 80)
-  scdata@meta.data$doublet_class[1:10] <- rep("doublet", 10)
-
-  # add samples
-  scdata$samples <- rep(c("123abc", "123def"), each = 40)
-  scdata <- Seurat::RenameCells(scdata, paste(scdata$samples, colnames(scdata), sep = ""))
-  return(scdata)
-}
-
-
-
-test_that("filter_doublets filters based on threshold", {
-  scdata <- mock_scdata()
-  cells_id <- mock_ids()
-  # should filter first 10 cells
-  config <- mock_config(0.5)
-
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(ncol(out$data), 80)
-  expect_equal(out$new_ids$`123abc`, 10:39)
-})
-
-test_that("filter_doublets is sample aware", {
-  scdata <- mock_scdata()
-  cells_id <- mock_ids()
-  scdata@meta.data$doublet_scores[71:80] <- 0.9
-  config <- mock_config(0.5)
-
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(ncol(out$data), 80)
-  expect_equal(out$new_ids$`123abc`, 10:39)
-  expect_equal(out$new_ids$`123def`, 40:79)
-
-  out <- filter_doublets(out$data, config, "123def", out$new_ids)
-  expect_equal(ncol(out$data), 80)
-  expect_equal(out$new_ids$`123abc`, 10:39)
-  expect_equal(out$new_ids$`123def`, 40:69)
-})
-
-test_that("filter_doublets filters works with auto", {
-  scdata <- mock_scdata()
-  cells_id <- mock_ids()
-  # should filter first 10 cells
-  config <- mock_config(0.001, auto = TRUE)
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(out$new_ids$`123abc`, 10:39)
-
-  config <- mock_config(0.001, auto = FALSE)
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(length(out$new_ids$`123abc`), 0)
-})
-
-test_that("filter_doublets can be disabled", {
-  scdata <- mock_scdata()
-  cells_id <- mock_ids()
-  config <- mock_config(0.5, enabled = FALSE)
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(out$new_ids$`123abc`, 0:39)
-  expect_equal(out$new_ids$`123def`, 40:79)
-
-  config <- mock_config(0.5, enabled = TRUE)
-  out <- filter_doublets(scdata, config, "123abc", cells_id)
-  expect_equal(out$new_ids$`123abc`, 10:39)
-  expect_equal(out$new_ids$`123def`, 40:79)
-})
+# mock_config <- function(thr = 0.1, auto = FALSE, enabled = TRUE) {
+#   config <- list(
+#     auto = auto,
+#     enabled = enabled,
+#     filterSettings = list(
+#       probabilityThreshold = thr
+#     )
+#   )
+#   return(config)
+# }
+
+
+# mock_scdata <- function() {
+#   pbmc_raw <- read.table(
+#     file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
+#     as.is = TRUE
+#   )
+
+#   scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
+#   scdata$cells_id <- 0:(ncol(scdata) - 1)
+
+#   # add doublet scores and class
+#   scdata@meta.data$doublet_scores <- 0.01
+#   scdata@meta.data$doublet_scores[1:10] <- 0.9
+
+#   scdata@meta.data$doublet_class <- rep("singlet", 80)
+#   scdata@meta.data$doublet_class[1:10] <- rep("doublet", 10)
+
+#   # add samples
+#   scdata$samples <- rep(c("123abc", "123def"), each = 40)
+#   scdata <- Seurat::RenameCells(scdata, paste(scdata$samples, colnames(scdata), sep = ""))
+#   return(scdata)
+# }
+
+
+
+# test_that("filter_doublets filters based on threshold", {
+#   scdata <- mock_scdata()
+#   cells_id <- mock_ids()
+#   # should filter first 10 cells
+#   config <- mock_config(0.5)
+
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(ncol(out$data), 80)
+#   expect_equal(out$new_ids$`123abc`, 10:39)
+# })
+
+# test_that("filter_doublets is sample aware", {
+#   scdata <- mock_scdata()
+#   cells_id <- mock_ids()
+#   scdata@meta.data$doublet_scores[71:80] <- 0.9
+#   config <- mock_config(0.5)
+
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(ncol(out$data), 80)
+#   expect_equal(out$new_ids$`123abc`, 10:39)
+#   expect_equal(out$new_ids$`123def`, 40:79)
+
+#   out <- filter_doublets(out$data, config, "123def", out$new_ids)
+#   expect_equal(ncol(out$data), 80)
+#   expect_equal(out$new_ids$`123abc`, 10:39)
+#   expect_equal(out$new_ids$`123def`, 40:69)
+# })
+
+# test_that("filter_doublets filters works with auto", {
+#   scdata <- mock_scdata()
+#   cells_id <- mock_ids()
+#   # should filter first 10 cells
+#   config <- mock_config(0.001, auto = TRUE)
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(out$new_ids$`123abc`, 10:39)
+
+#   config <- mock_config(0.001, auto = FALSE)
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(length(out$new_ids$`123abc`), 0)
+# })
+
+# test_that("filter_doublets can be disabled", {
+#   scdata <- mock_scdata()
+#   cells_id <- mock_ids()
+#   config <- mock_config(0.5, enabled = FALSE)
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(out$new_ids$`123abc`, 0:39)
+#   expect_equal(out$new_ids$`123def`, 40:79)
+
+#   config <- mock_config(0.5, enabled = TRUE)
+#   out <- filter_doublets(scdata, config, "123abc", cells_id)
+#   expect_equal(out$new_ids$`123abc`, 10:39)
+#   expect_equal(out$new_ids$`123def`, 40:79)
+# })

From 212d5a6710e84df50a6989f3da5c42f445455677 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Wed, 10 Nov 2021 11:01:22 +0000
Subject: [PATCH 15/19] commit without exporter roles

---
 .../kubernetes-event-exporter-roles.yaml       | 18 ------------------
 1 file changed, 18 deletions(-)
 delete mode 100644 chart-infra/templates/kubernetes-event-exporter-roles.yaml

diff --git a/chart-infra/templates/kubernetes-event-exporter-roles.yaml b/chart-infra/templates/kubernetes-event-exporter-roles.yaml
deleted file mode 100644
index 2f8a30bb..00000000
--- a/chart-infra/templates/kubernetes-event-exporter-roles.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-apiVersion: v1
-kind: ServiceAccount
-metadata:
-  namespace: {{.Release.Namespace}}
-  name: event-exporter
----
-apiVersion: rbac.authorization.k8s.io/v1
-kind: ClusterRoleBinding
-metadata:
-  name: event-exporter
-roleRef:
-  apiGroup: rbac.authorization.k8s.io
-  kind: ClusterRole
-  name: view
-subjects:
-  - kind: ServiceAccount
-    namespace: {{.Release.Namespace}}
-    name: event-exporter
\ No newline at end of file

From f21859dbf9ad9126a6c48b58d2d80968d00c3295 Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Wed, 10 Nov 2021 12:57:56 +0000
Subject: [PATCH 16/19] trying to test fail again

---
 pipeline-runner/R/qc-5-filter_doublets.R      |   1 -
 pipeline-runner/init.R                        |   7 +-
 .../testthat/test-qc-5-filter_doublets.R      | 180 +++++++++---------
 3 files changed, 95 insertions(+), 93 deletions(-)

diff --git a/pipeline-runner/R/qc-5-filter_doublets.R b/pipeline-runner/R/qc-5-filter_doublets.R
index f293f282..b99bf9ce 100644
--- a/pipeline-runner/R/qc-5-filter_doublets.R
+++ b/pipeline-runner/R/qc-5-filter_doublets.R
@@ -80,7 +80,6 @@ filter_doublets <- function(scdata, config, sample_id, cells_id, task_name = "do
     config = config,
     plotData = guidata
   )
-  stop("TEST FAIL")
   return(result)
 }
 
diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
index 008e62cf..39ff9459 100644
--- a/pipeline-runner/init.R
+++ b/pipeline-runner/init.R
@@ -332,8 +332,11 @@ init <- function() {
         }
 
         tryCatchLog({
+                input_parse <- RJSONIO::fromJSON(input, simplify = FALSE)
                 wrapper(input)
-
+                if(input_parse$taskName == "mitochondrialContent"){
+                    stop("TEST STOPPING!!!")
+                }
                 message('Send task success\n------\n')
                 states$send_task_success(
                     taskToken = taskToken,
@@ -358,7 +361,7 @@ init <- function() {
                     cause = error_txt
                 )
 
-                send_pipeline_fail_update(pipeline_config, input_parse$experimentId, input_parse$processName, error_txt)
+                send_pipeline_fail_update(pipeline_config, input_parse, error_txt)
 
                 message("Sent task failure to state machine task: ", taskToken)
                 message("recovered from error:", e$message)
diff --git a/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R b/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
index 7b6750de..21ac5ca0 100644
--- a/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
+++ b/pipeline-runner/tests/testthat/test-qc-5-filter_doublets.R
@@ -1,90 +1,90 @@
-# mock_config <- function(thr = 0.1, auto = FALSE, enabled = TRUE) {
-#   config <- list(
-#     auto = auto,
-#     enabled = enabled,
-#     filterSettings = list(
-#       probabilityThreshold = thr
-#     )
-#   )
-#   return(config)
-# }
-
-
-# mock_scdata <- function() {
-#   pbmc_raw <- read.table(
-#     file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
-#     as.is = TRUE
-#   )
-
-#   scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
-#   scdata$cells_id <- 0:(ncol(scdata) - 1)
-
-#   # add doublet scores and class
-#   scdata@meta.data$doublet_scores <- 0.01
-#   scdata@meta.data$doublet_scores[1:10] <- 0.9
-
-#   scdata@meta.data$doublet_class <- rep("singlet", 80)
-#   scdata@meta.data$doublet_class[1:10] <- rep("doublet", 10)
-
-#   # add samples
-#   scdata$samples <- rep(c("123abc", "123def"), each = 40)
-#   scdata <- Seurat::RenameCells(scdata, paste(scdata$samples, colnames(scdata), sep = ""))
-#   return(scdata)
-# }
-
-
-
-# test_that("filter_doublets filters based on threshold", {
-#   scdata <- mock_scdata()
-#   cells_id <- mock_ids()
-#   # should filter first 10 cells
-#   config <- mock_config(0.5)
-
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(ncol(out$data), 80)
-#   expect_equal(out$new_ids$`123abc`, 10:39)
-# })
-
-# test_that("filter_doublets is sample aware", {
-#   scdata <- mock_scdata()
-#   cells_id <- mock_ids()
-#   scdata@meta.data$doublet_scores[71:80] <- 0.9
-#   config <- mock_config(0.5)
-
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(ncol(out$data), 80)
-#   expect_equal(out$new_ids$`123abc`, 10:39)
-#   expect_equal(out$new_ids$`123def`, 40:79)
-
-#   out <- filter_doublets(out$data, config, "123def", out$new_ids)
-#   expect_equal(ncol(out$data), 80)
-#   expect_equal(out$new_ids$`123abc`, 10:39)
-#   expect_equal(out$new_ids$`123def`, 40:69)
-# })
-
-# test_that("filter_doublets filters works with auto", {
-#   scdata <- mock_scdata()
-#   cells_id <- mock_ids()
-#   # should filter first 10 cells
-#   config <- mock_config(0.001, auto = TRUE)
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(out$new_ids$`123abc`, 10:39)
-
-#   config <- mock_config(0.001, auto = FALSE)
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(length(out$new_ids$`123abc`), 0)
-# })
-
-# test_that("filter_doublets can be disabled", {
-#   scdata <- mock_scdata()
-#   cells_id <- mock_ids()
-#   config <- mock_config(0.5, enabled = FALSE)
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(out$new_ids$`123abc`, 0:39)
-#   expect_equal(out$new_ids$`123def`, 40:79)
-
-#   config <- mock_config(0.5, enabled = TRUE)
-#   out <- filter_doublets(scdata, config, "123abc", cells_id)
-#   expect_equal(out$new_ids$`123abc`, 10:39)
-#   expect_equal(out$new_ids$`123def`, 40:79)
-# })
+mock_config <- function(thr = 0.1, auto = FALSE, enabled = TRUE) {
+  config <- list(
+    auto = auto,
+    enabled = enabled,
+    filterSettings = list(
+      probabilityThreshold = thr
+    )
+  )
+  return(config)
+}
+
+
+mock_scdata <- function() {
+  pbmc_raw <- read.table(
+    file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
+    as.is = TRUE
+  )
+
+  scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
+  scdata$cells_id <- 0:(ncol(scdata) - 1)
+
+  # add doublet scores and class
+  scdata@meta.data$doublet_scores <- 0.01
+  scdata@meta.data$doublet_scores[1:10] <- 0.9
+
+  scdata@meta.data$doublet_class <- rep("singlet", 80)
+  scdata@meta.data$doublet_class[1:10] <- rep("doublet", 10)
+
+  # add samples
+  scdata$samples <- rep(c("123abc", "123def"), each = 40)
+  scdata <- Seurat::RenameCells(scdata, paste(scdata$samples, colnames(scdata), sep = ""))
+  return(scdata)
+}
+
+
+
+test_that("filter_doublets filters based on threshold", {
+  scdata <- mock_scdata()
+  cells_id <- mock_ids()
+  # should filter first 10 cells
+  config <- mock_config(0.5)
+
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(ncol(out$data), 80)
+  expect_equal(out$new_ids$`123abc`, 10:39)
+})
+
+test_that("filter_doublets is sample aware", {
+  scdata <- mock_scdata()
+  cells_id <- mock_ids()
+  scdata@meta.data$doublet_scores[71:80] <- 0.9
+  config <- mock_config(0.5)
+
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(ncol(out$data), 80)
+  expect_equal(out$new_ids$`123abc`, 10:39)
+  expect_equal(out$new_ids$`123def`, 40:79)
+
+  out <- filter_doublets(out$data, config, "123def", out$new_ids)
+  expect_equal(ncol(out$data), 80)
+  expect_equal(out$new_ids$`123abc`, 10:39)
+  expect_equal(out$new_ids$`123def`, 40:69)
+})
+
+test_that("filter_doublets filters works with auto", {
+  scdata <- mock_scdata()
+  cells_id <- mock_ids()
+  # should filter first 10 cells
+  config <- mock_config(0.001, auto = TRUE)
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(out$new_ids$`123abc`, 10:39)
+
+  config <- mock_config(0.001, auto = FALSE)
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(length(out$new_ids$`123abc`), 0)
+})
+
+test_that("filter_doublets can be disabled", {
+  scdata <- mock_scdata()
+  cells_id <- mock_ids()
+  config <- mock_config(0.5, enabled = FALSE)
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(out$new_ids$`123abc`, 0:39)
+  expect_equal(out$new_ids$`123def`, 40:79)
+
+  config <- mock_config(0.5, enabled = TRUE)
+  out <- filter_doublets(scdata, config, "123abc", cells_id)
+  expect_equal(out$new_ids$`123abc`, 10:39)
+  expect_equal(out$new_ids$`123def`, 40:79)
+})

From 4ab6158bb040b9079e993198d5eb861accde276b Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Thu, 11 Nov 2021 10:02:31 +0000
Subject: [PATCH 17/19] change fail

---
 pipeline-runner/init.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
index 39ff9459..c9cc403c 100644
--- a/pipeline-runner/init.R
+++ b/pipeline-runner/init.R
@@ -333,10 +333,12 @@ init <- function() {
 
         tryCatchLog({
                 input_parse <- RJSONIO::fromJSON(input, simplify = FALSE)
-                wrapper(input)
+                message("current step name ", input_parse$taskName)
                 if(input_parse$taskName == "mitochondrialContent"){
                     stop("TEST STOPPING!!!")
                 }
+                wrapper(input)
+
                 message('Send task success\n------\n')
                 states$send_task_success(
                     taskToken = taskToken,

From 75bbbfc33732db915b4e5ecb1846743e0d4fb547 Mon Sep 17 00:00:00 2001
From: Pol Alvarez <pol.avms@gmail.com>
Date: Thu, 11 Nov 2021 15:16:07 +0100
Subject: [PATCH 18/19] added taskName to fail pipeline message

---
 pipeline-runner/R/handle_data.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pipeline-runner/R/handle_data.R b/pipeline-runner/R/handle_data.R
index 9ee3dbeb..fa8cd0f7 100644
--- a/pipeline-runner/R/handle_data.R
+++ b/pipeline-runner/R/handle_data.R
@@ -130,8 +130,9 @@ send_pipeline_fail_update <- function(pipeline_config, input, error_message) {
   error_msg <- list()
 
   # TODO - REMOVE THE DUPLICATE EXPERIMETN ID FROM INPUT RESPONSE
-  
+
   error_msg$experimentId <- input$experimentId
+  error_msg$taskName <- input$taskName
   error_msg$response$error <- process_name
   error_msg$input <- input
   sns <- paws::sns(config = pipeline_config$aws_config)

From 8a79b1dc9ba2d3d55e810f2a933f437105636abd Mon Sep 17 00:00:00 2001
From: stefanbabukov <stefanbabukov98@gmail.com>
Date: Thu, 11 Nov 2021 14:46:32 +0000
Subject: [PATCH 19/19] remove stopping

---
 pipeline-runner/init.R | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
index c9cc403c..b2d37e9c 100644
--- a/pipeline-runner/init.R
+++ b/pipeline-runner/init.R
@@ -332,11 +332,6 @@ init <- function() {
         }
 
         tryCatchLog({
-                input_parse <- RJSONIO::fromJSON(input, simplify = FALSE)
-                message("current step name ", input_parse$taskName)
-                if(input_parse$taskName == "mitochondrialContent"){
-                    stop("TEST STOPPING!!!")
-                }
                 wrapper(input)
 
                 message('Send task success\n------\n')