#!/bin/bash -eo pipefail 
source ~/miniconda/bin/activate root 
conda activate base 
source activate merlin_env 
cd ~/MERlin 
mkdir ~/test-reports 
pytest --cov --cov-report=xml 
 
============================= test session starts ==============================
 
platform linux -- Python 3.6.10, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
rootdir: /home/circleci/MERlin
 plugins: cov-2.10.0
 collecting ... collecting 71 items                                                            collecting 96 items                                                            collected 96 items                                                             
 
test/test_barcode_database.py ..........                                 [ 10%]
 test/test_binary_utils.py ..                                             [ 12%]
test/test_codebook.py ...........                                        [ 23%]
test/test_core.py .....................                                  [ 45%]
test/test_dataorganization.py ..........                                 [ 56%]
 test/test_dataportal.py ............                                     [ 68%]
test/test_dataset.py ...                                                 [ 71%]
 test/test_image_reader.py .                                              [ 72%]
  
Too long with no output (exceeded 10m0s): context deadline exceeded 

[lsepulvedaduran@boslogin03 MERlin]$ git rebase master machine_learning_segmentation
First, rewinding head to replay your work on top of it...
Applying: Adding _get_membrane_mask and _get_nuclei_mask functions to WatershedSegmentNucleiCV2 class
...
Applying: add george's modifications to dataportal
Using index info to reconstruct a base tree...
M       requirements.txt
M       test/test_dataportal.py
Falling back to patching base and 3-way merge...
Auto-merging requirements.txt
Applying: adding additional modifications to aws
Using index info to reconstruct a base tree...
M       merlin/util/dataportal.py
Falling back to patching base and 3-way merge...
Auto-merging merlin/util/dataportal.py
CONFLICT (content): Merge conflict in merlin/util/dataportal.py
Failed to merge in the changes.
Patch failed at 0066 adding additional modifications to aws
The copy of the patch that failed is found in:
   /n/home06/lsepulvedaduran/Software/MERlin/.git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase --abort".

[lsepulvedaduran@boslogin03 MERlin]$

_[lsepulvedaduran@boslogin03 rebase-apply]$ more 0066
From 60acd7246a1a06562dd50a0147ccfb3d810dd35e Mon Sep 17 00:00:00 2001
From: leonardosepulveda <[email protected]>
Date: Sat, 15 Feb 2020 09:38:38 -0500
Subject: adding additional modifications to aws

---
 merlin/util/dataportal.py | 37 ++++++++++++++++++++++++++++++++++---
 1 file changed, 34 insertions(+), 3 deletions(-)

diff --git a/merlin/util/dataportal.py b/merlin/util/dataportal.py
index e3d0f6e832b69a6491bee876abd741b44844ddb9..9fcd4631bcb603feeeddee777b1f1d9b3f8ffb0e 100644
--- a/merlin/util/dataportal.py
+++ b/merlin/util/dataportal.py
@@ -2,9 +2,11 @@ import os
 import boto3
 import botocore
 from google.cloud import storage
+from google.cloud import exceptions
 from urllib import parse
 from abc import abstractmethod, ABC
 from typing import List
+from time import sleep


 class DataPortal(ABC):
@@ -340,12 +342,41 @@ class GCloudFilePortal(FilePortal):
         return GCloudFilePortal(
             self._exchange_extension(newExtension), self._client)

+    def _error_tolerant_access(self, request, attempts = 5, wait = 60):
+        while attempts > 0:
+            try:
+                file = self._fileHandle.download_as_string()
+                return file
+            except (exceptions.GatewayTimeout, exceptions.ServiceUnavailable):
+                attempts -= 1
+                sleep(60)
+                if attempts == 0:
+                    raise
+
     def read_as_text(self):
-        return self._fileHandle.download_as_string().decode('utf-8')
+         backoffSeries= [1,2,4,8,16,32,64,128,256]
+        for sleepDuration in backoffSeries:
+            try:
+                file = self._fileHandle.download_as_string().decode('utf-8')
+                return file
+            except (exceptions.GatewayTimeout, exceptions.ServiceUnavailable):
+                if sleepDuration == backoffSeries[-1]:
+                    raise
+                else:
+                    sleep(sleepDuration)

     def read_file_bytes(self, startByte, endByte):
-        return self._fileHandle.download_as_string(
-            start=startByte, end=endByte-1)
+        backoffSeries= [1,2,4,8,16,32,64,128,256]
+            for sleepDuration in backoffSeries:
+            try:
+                file = self._fileHandle.download_as_string(start=startByte,
+                                                           end=endByte-1)
+                return file
+            except (exceptions.GatewayTimeout, exceptions.ServiceUnavailable):
+                if sleepDuration == backoffSeries[-1]:
+                    raise
+                else:
+                    sleep(sleepDuration)

     def close(self) -> None:
         pass
--
1.8.3.1_

FileNotFoundError: [Errno 2] No such file or directory: '/home/circleci/MERlin/test_analysis_parameters/test_analysis_segmentation_cellpose.json'
 
FileNotFoundError: [Errno 2] No such file or directory: '/home/circleci/MERlin/test_analysis_parameters/test_analysis_segmentation_cv2.json'

______________________________ test_cv2_2d_local _______________________________

simple_merfish_data = <merlin.core.dataset.MERFISHDataSet object at 0x7f4636cba978>
     
    @pytest.mark.fullrun
    @pytest.mark.slowtest
    def test_cv2_2d_local(simple_merfish_data):
       	with open(os.sep.join([merlin.ANALYSIS_PARAMETERS_HOME,
                               'test_analysis_segmentation_cv2.json']), 'r') as f:
            snakefilePath = m.generate_analysis_tasks_and_snakefile(
                simple_merfish_data, f)
>           m.run_with_snakemake(simple_merfish_data, snakefilePath, 5)
 
test/test_segmentation_cv2.py:15: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
merlin/merlin.py:194: in run_with_snakemake
    for t in dataSet.get_analysis_tasks()}
 
merlin/merlin.py:194: in <dictcomp>
    for t in dataSet.get_analysis_tasks()}
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _  
 
self = <merlin.core.dataset.MERFISHDataSet object at 0x7f4636cba978>
analysisTaskName = 'RandomNumberParallelAnalysisTask'
    def load_analysis_task(self, analysisTaskName: str) \
            -> analysistask.AnalysisTask:
        loadName = os.sep.join([self.get_task_subdirectory(
            analysisTaskName), 'task.json'])
        print(loadName)
>       with open(loadName, 'r') as inFile:
E       FileNotFoundError: [Errno 2] No such file or directory: '/home/circleci/MERlin/test_analysis/merfish_test/RandomNumberParallelAnalysisTask/tasks/task.json'

merlin/core/dataset.py:620: FileNotFoundError