Revert "Revert "[DEPLOY] Fix for microbes and GSE75083""

.circleci/config.yml

@@ -29,7 +29,6 @@ jobs:
 
       # Install Nomad
       - run: sudo ./scripts/install_nomad.sh
-
         # Start Nomad and register jobs.
       - run:
           command: sudo -E ./scripts/run_nomad.sh -e test
@@ -43,19 +42,21 @@ jobs:
       # Running these in the same job as the common tests is good
       # because their dockerfiles are very similar so a lot of the
       # build time is saved by only building those layers once.
+      - run: sudo chown -R circleci:circleci workers/test_volume/
       - run:
           command: .circleci/filter_tests.sh -t downloaders
           no_output_timeout: 1h
 
       # Run Foreman Tests
-      - run: mkdir -p test_volume && chmod -R a+rw test_volume
+      - run: mkdir -p test_volume && chmod -R a+rw test_volume && sudo chown -R circleci:circleci test_volume
 
       # The foreman includes the end-to-end tests, but some of these
       # require docker images which are not built in this
       # workflow. Therefore we exclude salmon, affymetrix, and
       # transcriptome and let those end-to-end tests get run in the
       # workflows that include building those images.
       - run: ./foreman/run_tests.sh --exclude-tag=salmon --exclude-tag=transcriptome --exclude-tag=affymetrix
+      - run: .circleci/upload_test_coverage.sh foreman
 
       # Run NO_OP tests
       - run: sudo chown -R circleci:circleci workers/test_volume/
@@ -90,7 +91,9 @@ jobs:
       - run: ./scripts/update_models.sh
 
       # Run Common Tests.
+      - run: mkdir -p test_volume && chmod -R a+rw test_volume && sudo chown -R circleci:circleci test_volume
       - run: ./common/run_tests.sh
+      - run: .circleci/upload_test_coverage.sh common
 
       - run: ./scripts/prepare_image.sh -i smasher -s workers -d localhost:5000
 
@@ -155,15 +158,16 @@ jobs:
       - run: ./scripts/rebuild_es_index.sh
 
       # Run API Tests.
+      - run: mkdir -p test_volume && chmod -R a+rw test_volume && sudo chown -R circleci:circleci test_volume
       - run: ./api/run_tests.sh
+      - run: .circleci/upload_test_coverage.sh api
 
       - run:
           command: .circleci/filter_tests.sh -t salmon
           no_output_timeout: 1h
 
       # Install Nomad
       - run: sudo ./scripts/install_nomad.sh
-
         # Start Nomad and register jobs.
       - run:
           command: sudo -E ./scripts/run_nomad.sh -e test
@@ -178,9 +182,9 @@ jobs:
       - run: docker push localhost:5000/dr_salmon
 
       # Containers run as a different user so we need to give them permission to the test directory.
-      - run: mkdir -p test_volume && chmod -R a+rw test_volume
-
+      - run: mkdir -p test_volume && chmod -R a+rw test_volume && sudo chown -R circleci:circleci test_volume
       - run: ./foreman/run_tests.sh --tag=salmon --tag=transcriptome
+      - run: .circleci/upload_test_coverage.sh foreman
 
   tx_illumina_tests:
     working_directory: ~/refinebio
@@ -262,7 +266,6 @@ jobs:
 
       # Install Nomad
       - run: sudo ./scripts/install_nomad.sh
-
         # Start Nomad and register jobs.
       - run:
           command: sudo -E ./scripts/run_nomad.sh -e test
@@ -279,12 +282,12 @@ jobs:
       - run: docker push localhost:5000/dr_affymetrix
 
       # Containers run as a different user so we need to give them permission to the test directory.
-      - run: mkdir -p test_volume && chmod -R a+rw test_volume
-
+      - run: mkdir -p test_volume && chmod -R a+rw test_volume && sudo chown -R circleci:circleci test_volume
       - run:
           command: ./foreman/run_tests.sh --tag=affymetrix
           # This takes more than 10 minutes, but not much.
           no_output_timeout: 20m
+      - run: .circleci/upload_test_coverage.sh foreman
 
   deploy:
     machine: true

.circleci/filter_tests.sh

@@ -9,3 +9,5 @@ else
 	echo "Running all tests..";
 	./workers/run_tests.sh "$@"
 fi
+
+./.circleci/upload_test_coverage.sh workers

.circleci/upload_test_coverage.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# Script to upload code coverage to circleci
+
+project=$1
+if [[ $project == "" ]]
+then
+    echo "No project specified"
+    exit 1
+fi
+
+if [[ $project == "workers" ]]
+then
+    # the workers project uses it's own test_volume directory
+    test_volume="workers/test_volume"
+else
+    test_volume="test_volume"
+fi
+
+coverage_file="${test_volume}/coverage.xml"
+
+if [[ ! -f $coverage_file ]]
+then
+    echo "Coverage file wasn't found, were the tests run before?"
+    exit 0 # exit this script but don't fail the tests for this.
+fi
+
+output_file="${test_volume}/${project}_coverage.xml"
+
+# In the test coverage report, all file paths are relative to each project
+# folder. We need to be relative to the repo's root directory. That's why we
+# append the project folder name to each file path in coverage.xml
+sed "s/filename=\"/filename=\"$project\//g" $coverage_file > $output_file
+
+# codecov.sh is located at https://codecov.io/bash
+# we downloaded it for convenience
+./.circleci/codecov.sh -f "$output_file" -Z -F $project
+
+rm -f $coverage_file $output_file

.gitignore

@@ -29,6 +29,7 @@ infrastructure/.terraform/
 # We download a lot of files into the test_volume directory when
 # running tests, which we don't need to track.
 workers/test_volume/*
+!workers/test_volume/test_download_files
 # However for a couple tests we do store the data in the repo and need to track them.
 !workers/test_volume/raw/TEST/TRANSCRIPTOME_INDEX/aegilops_tauschii_short.gtf.gz
 !workers/test_volume/raw/TEST/NO_OP/test.txt

README.md

@@ -1,4 +1,4 @@
-# Refine.bio [![Build Status](https://circleci.com/gh/AlexsLemonade/refinebio/tree/dev.svg?&style=shield)](https://circleci.com/gh/AlexsLemonade/refinebio/)
+# Refine.bio [![Build Status](https://circleci.com/gh/AlexsLemonade/refinebio/tree/dev.svg?&style=shield)](https://circleci.com/gh/AlexsLemonade/refinebio/) [![codecov](https://codecov.io/gh/AlexsLemonade/refinebio/branch/master/graph/badge.svg)](https://codecov.io/gh/AlexsLemonade/refinebio)
 
 <!-- This section needs to be drastically improved -->
 Refine.bio harmonizes petabytes of publicly available biological data into

api/data_refinery_api/views.py

@@ -536,7 +536,6 @@ def perform_update(self, serializer):
                         requests.post(
                             settings.ENGAGEMENTBOT_WEBHOOK,
                             json={
-                                "channel": "ccdl-general",  # Move to robots when we get sick of these
                                 "username": "EngagementBot",
                                 "icon_emoji": ":halal:",
                                 "attachments": [

api/requirements.in

@@ -1,5 +1,5 @@
 coverage
-django==2.2.9
+django==2.2.10
 psycopg2-binary
 boto3
 requests>=2.20.0

api/requirements.txt

@@ -18,7 +18,7 @@ django-elasticsearch-dsl==6.4.2
 django-filter==2.0.0
 django-hstore==1.4.2      # via djangorestframework-hstore
 django-nine==0.2.2        # via django-elasticsearch-dsl-drf
-django==2.2.9
+django==2.2.10
 djangorestframework-hstore==1.3
 djangorestframework==3.9.4
 docutils==0.14            # via botocore

api/run_tests.sh

@@ -20,6 +20,13 @@ if ! [ "$(docker ps --filter name=drdb -q)" ]; then
     exit 1
 fi
 
+project_root=$(pwd) # "cd .." called above
+volume_directory="$project_root/test_volume"
+if [ ! -d "$volume_directory" ]; then
+    mkdir "$volume_directory"
+    chmod -R a+rwX "$volume_directory"
+fi
+
 ./scripts/prepare_image.sh -i api_local -s api
 
 . ./scripts/common.sh
@@ -32,4 +39,5 @@ docker run \
        --add-host=nomad:"$HOST_IP" \
        --add-host=elasticsearch:"$ES_HOST_IP" \
        --env-file api/environments/test \
+       --volume "$volume_directory":/home/user/data_store \
        -it ccdlstaging/dr_api_local bash -c "$(run_tests_with_coverage "$@")"

common/data_refinery_common/constants.py

@@ -0,0 +1,10 @@
+from data_refinery_common.utils import get_env_variable
+
+LOCAL_ROOT_DIR = get_env_variable("LOCAL_ROOT_DIR", "/home/user/data_store")
+# We store what salmon ouptuts as its version, therefore for
+# comparisions or defaults we shouldn't just store the version string,
+# we need something with the pattern: 'salmon X.X.X'
+CURRENT_SALMON_VERSION = "salmon " + get_env_variable("SALMON_VERSION", "0.13.1")
+CHUNK_SIZE = 1024 * 256  # chunk_size is in bytes
+# Let this fail if SYSTEM_VERSION is unset.
+SYSTEM_VERSION = get_env_variable("SYSTEM_VERSION")

common/data_refinery_common/models/__init__.py

@@ -1,37 +1,55 @@
-from data_refinery_common.models.command_progress import (  # noqa
-    CdfCorrectedAccession,
-    SurveyedAccession,
-)
-from data_refinery_common.models.jobs import (  # noqa
-    DownloaderJob,
-    ProcessorJob,
-    SurveyJob,
-    SurveyJobKeyValue,
-)
-from data_refinery_common.models.models import (  # noqa
-    APIToken,
-    CompendiumResult,
+from data_refinery_common.models.api_token import APIToken  # noqa
+from data_refinery_common.models.associations.compendium_result_organism_association import (  # noqa
     CompendiumResultOrganismAssociation,
-    ComputationalResult,
-    ComputationalResultAnnotation,
-    ComputedFile,
-    Dataset,
+)
+from data_refinery_common.models.associations.downloaderjob_originalfile_association import (  # noqa
     DownloaderJobOriginalFileAssociation,
-    Experiment,
-    ExperimentAnnotation,
+)
+from data_refinery_common.models.associations.experiment_organism_association import (  # noqa
     ExperimentOrganismAssociation,
+)
+from data_refinery_common.models.associations.experiment_result_association import (  # noqa
     ExperimentResultAssociation,
+)
+from data_refinery_common.models.associations.experiment_sample_association import (  # noqa
     ExperimentSampleAssociation,
-    OrganismIndex,
-    OriginalFile,
+)
+from data_refinery_common.models.associations.original_file_sample_association import (  # noqa
     OriginalFileSampleAssociation,
-    Pipeline,
-    Processor,
+)
+from data_refinery_common.models.associations.processorjob_dataset_association import (  # noqa
     ProcessorJobDatasetAssociation,
+)
+from data_refinery_common.models.associations.processorjob_originalfile_association import (  # noqa
     ProcessorJobOriginalFileAssociation,
-    Sample,
-    SampleAnnotation,
+)
+from data_refinery_common.models.associations.sample_computed_file_association import (  # noqa
     SampleComputedFileAssociation,
+)
+from data_refinery_common.models.associations.sample_result_association import (  # noqa
     SampleResultAssociation,
 )
+from data_refinery_common.models.command_progress import (  # noqa
+    CdfCorrectedAccession,
+    SurveyedAccession,
+)
+from data_refinery_common.models.compendium_result import CompendiumResult  # noqa
+from data_refinery_common.models.computational_result import ComputationalResult  # noqa
+from data_refinery_common.models.computational_result_annotation import (  # noqa
+    ComputationalResultAnnotation,
+)
+from data_refinery_common.models.computed_file import ComputedFile  # noqa
+from data_refinery_common.models.dataset import Dataset  # noqa
+from data_refinery_common.models.experiment import Experiment  # noqa
+from data_refinery_common.models.experiment_annotation import ExperimentAnnotation  # noqa
+from data_refinery_common.models.jobs.downloader_job import DownloaderJob  # noqa
+from data_refinery_common.models.jobs.processor_job import ProcessorJob  # noqa
+from data_refinery_common.models.jobs.survey_job import SurveyJob  # noqa
+from data_refinery_common.models.jobs.survey_job_key_value import SurveyJobKeyValue  # noqa
 from data_refinery_common.models.organism import Organism  # noqa
+from data_refinery_common.models.organism_index import OrganismIndex  # noqa
+from data_refinery_common.models.original_file import OriginalFile  # noqa
+from data_refinery_common.models.pipeline import Pipeline  # noqa
+from data_refinery_common.models.processor import Processor  # noqa
+from data_refinery_common.models.sample import Sample  # noqa
+from data_refinery_common.models.sample_annotation import SampleAnnotation  # noqa

common/data_refinery_common/models/api_token.py

@@ -0,0 +1,32 @@
+import uuid
+
+from django.conf import settings
+from django.db import models
+from django.utils import timezone
+
+
+class APIToken(models.Model):
+    """ Required for starting a smash job """
+
+    # ID
+    id = models.UUIDField(primary_key=True, default=uuid.uuid4, editable=False)
+
+    # Activation
+    is_activated = models.BooleanField(default=False)
+
+    # Common Properties
+    created_at = models.DateTimeField(editable=False, default=timezone.now)
+    last_modified = models.DateTimeField(default=timezone.now)
+
+    def save(self, *args, **kwargs):
+        """ On save, update timestamps """
+        current_time = timezone.now()
+        if not self.id:
+            self.created_at = current_time
+        self.last_modified = current_time
+        return super(APIToken, self).save(*args, **kwargs)
+
+    @property
+    def terms_and_conditions(self):
+        """ """
+        return settings.TERMS_AND_CONDITIONS

common/data_refinery_common/models/associations/compendium_result_organism_association.py

@@ -0,0 +1,16 @@
+from django.db import models
+
+from data_refinery_common.models.compendium_result import CompendiumResult
+from data_refinery_common.models.organism import Organism
+
+
+class CompendiumResultOrganismAssociation(models.Model):
+
+    compendium_result = models.ForeignKey(
+        CompendiumResult, blank=False, null=False, on_delete=models.CASCADE
+    )
+    organism = models.ForeignKey(Organism, blank=False, null=False, on_delete=models.CASCADE)
+
+    class Meta:
+        db_table = "compendium_result_organism_associations"
+        unique_together = ("compendium_result", "organism")

common/data_refinery_common/models/associations/downloaderjob_originalfile_association.py

@@ -0,0 +1,18 @@
+from django.db import models
+
+from data_refinery_common.models.jobs.downloader_job import DownloaderJob
+from data_refinery_common.models.original_file import OriginalFile
+
+
+class DownloaderJobOriginalFileAssociation(models.Model):
+
+    downloader_job = models.ForeignKey(
+        DownloaderJob, blank=False, null=False, on_delete=models.CASCADE
+    )
+    original_file = models.ForeignKey(
+        OriginalFile, blank=False, null=False, on_delete=models.CASCADE
+    )
+
+    class Meta:
+        db_table = "downloaderjob_originalfile_associations"
+        unique_together = ("downloader_job", "original_file")

common/data_refinery_common/models/associations/experiment_organism_association.py

@@ -0,0 +1,14 @@
+from django.db import models
+
+from data_refinery_common.models.experiment import Experiment
+from data_refinery_common.models.organism import Organism
+
+
+class ExperimentOrganismAssociation(models.Model):
+
+    experiment = models.ForeignKey(Experiment, blank=False, null=False, on_delete=models.CASCADE)
+    organism = models.ForeignKey(Organism, blank=False, null=False, on_delete=models.CASCADE)
+
+    class Meta:
+        db_table = "experiment_organism_associations"
+        unique_together = ("experiment", "organism")

common/data_refinery_common/models/associations/experiment_result_association.py

@@ -0,0 +1,16 @@
+from django.db import models
+
+from data_refinery_common.models.computational_result import ComputationalResult
+from data_refinery_common.models.experiment import Experiment
+
+
+class ExperimentResultAssociation(models.Model):
+
+    experiment = models.ForeignKey(Experiment, blank=False, null=False, on_delete=models.CASCADE)
+    result = models.ForeignKey(
+        ComputationalResult, blank=False, null=False, on_delete=models.CASCADE
+    )
+
+    class Meta:
+        db_table = "experiment_result_associations"
+        unique_together = ("result", "experiment")