diff --git a/.gitignore b/.gitignore index 32eea3fe3..39d723d86 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,5 @@ db* scripts/*.json conda* input.json +scripts/*.json* *.swp diff --git a/Makefile b/Makefile index 58941b192..ec726a5fe 100644 --- a/Makefile +++ b/Makefile @@ -217,7 +217,7 @@ check-env: BEAGLE_AUTH_LDAP_SERVER_URI \ BEAGLE_LIMS_PASSWORD \ BEAGLE_LIMS_USERNAME; do \ - [ -z "$$(printenv BEAGLE_LIMS_USERNAME)" ] && echo ">>> env variable $$i is not set; some features may not work" || : ; done + [ -z "$$(printenv $$i)" ] && echo ">>> env variable $$i is not set; some features may not work" || : ; done # start the RabbitMQ server in the background rabbitmq-start: $(LOG_DIR_ABS) @@ -273,7 +273,7 @@ celery-start: # check that the Celery processes are running celery-check: - -ps auxww | grep 'celery' | grep -v 'grep' | grep -v 'make' | grep '$(CURDIR)' + ps auxww | grep 'celery' | grep -v 'grep' | grep -v 'make' | grep '$(CURDIR)' # kill all the Celery processes started from this dir celery-stop: @@ -291,11 +291,14 @@ start-services: check-env $(MAKE) celery-start stop-services: - $(MAKE) celery-stop - $(MAKE) rabbitmq-stop - $(MAKE) db-stop - + -$(MAKE) celery-stop + -$(MAKE) rabbitmq-stop + -$(MAKE) db-stop +check-services: + $(MAKE) celery-check + $(MAKE) db-check + $(MAKE) rabbitmq-check # ~~~~~ Set Up Django ~~~~~ # export DJANGO_BEAGLE_IP:=localhost @@ -311,15 +314,20 @@ export DJANGO_RIDGEBACK_IP:=localhost export DJANGO_RIDGEBACK_PORT:=7001 export BEAGLE_RIDGEBACK_URL=http://$(DJANGO_RIDGEBACK_IP):$(DJANGO_RIDGEBACK_PORT) export DJ_DEBUG_LOG:=$(LOG_DIR_ABS)/dj.debug.log - +export BEAGLE_LOG_PATH:=$(LOG_DIR_ABS)/beagle-server.log +export DUMP_JSON:=False # initialize the Django app in the database # do this after setting up the db above django-init: - python manage.py makemigrations --merge + python manage.py makemigrations # --merge python manage.py migrate + $(MAKE) django-load-fixtures python manage.py createsuperuser + +django-load-fixtures: python manage.py loaddata \ + beagle_etl.operator.json \ file_system.filegroup.json \ file_system.filetype.json \ file_system.storage.json \ @@ -336,6 +344,7 @@ test-lims: check-env # start the Django development server runserver: check-env + if $(MAKE) check-services ; then : ; else echo ">>> ERROR: some services are not started"; exit 1 ; fi python manage.py runserver $(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT) MIGRATION_ARGS?= @@ -377,9 +386,10 @@ REQID:=07264_G TOKEN:=IUzI1NiJ9.eyJ0 # import files data about samples in a request from the IGO LIMS import: + token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ curl -H "Content-Type: application/json" \ -X POST \ - -H "Authorization: Bearer $(TOKEN)" \ + -H "Authorization: Bearer $$token" \ --data '{"request_ids":["$(REQID)"]}' \ http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/etl/import-requests/ @@ -430,6 +440,7 @@ files-request: --data '{"request_ids":["$(REQID)"]}' \ http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/fs/files/ # python ./beagle_cli.py files list --metadata='requestId:$(REQID)' +# http://localhost:6991/v0/fs/files/?metadata=requestId:DemoRequest1 # get info on a single file REQFILE:=b37.fasta @@ -440,22 +451,26 @@ file-get: http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/fs/files/?filename=$(REQFILE) # start a Roslin run for a given request in the Beagle db -run-request: +PIPELINE:=roslin +run-request: $(AUTH_FILE) + token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ curl -H "Content-Type: application/json" \ -X POST \ - -H "Authorization: Bearer $(TOKEN)" \ - --data '{"request_ids":["$(REQID)"], "pipeline_name": "roslin"}' \ + -H "Authorization: Bearer $$token" \ + --data '{"request_ids":["$(REQID)"], "pipeline_name": "$(PIPELINE)"}' \ http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/run/request/ # send a pipeline input to the API to start running REQJSON:=fixtures/tests/run_roslin.json run-request-api: $(AUTH_FILE) - @token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ + token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ curl -H "Content-Type: application/json" \ -X POST \ -H "Authorization: Bearer $$token" \ --data @$(REQJSON) \ http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/run/api/ +# http://localhost:6991/v0/run/api/?metadata=requestId:10277_C +# http://localhost:6991/v0/run/api/?requestId%3D10277_C/ # make a demo Roslin input.json file from the template fixture; # need to update the fixture with the app ID of the demo pipeline that was loaded in the database @@ -471,12 +486,32 @@ $(DEMO_INPUT): $(INPUT_TEMPLATE) $(AUTH_FILE) .PHONY: $(DEMO_INPUT) # submit a demo Roslin run using the dev Roslin pipeline entry in the database -demo-run: register-dev-pipeline $(DEMO_INPUT) +# submit using the API endpoint; bypasses the Operator +demo-run-api: register-dev-pipeline $(DEMO_INPUT) @python manage.py loaddata fixtures/tests/juno_roslin_demo2.file.json @python manage.py loaddata fixtures/tests/juno_roslin_demo2.filemetadata.json @python manage.py loaddata fixtures/tests/roslin_reference_files.json @$(MAKE) run-request-api REQID=DemoRequest1 REQJSON=$(DEMO_INPUT) +demo-roslin-qc: + python manage.py loaddata fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json && \ + token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ + curl -H "Content-Type: application/json" \ + -X POST \ + -H "Authorization: Bearer $$token" \ + --data '{"request_ids":[], "run_ids":["ca18b090-03ad-4bef-acd3-52600f8e62eb"], "pipeline_name": "roslin-qc"}' \ + http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/run/request/ +# python manage.py loaddata fixtures/tests/8f44d2f8-15c0-4d97-a966-6ad0b916bb41.run.ALN-REQ-ID.json && \ + +# run the update-request endpoint for a request ID in order to update the metadata about a request +update-request: + @token=$$( jq -r '.token' "$(AUTH_FILE)" ) && \ + curl -H "Content-Type: application/json" \ + -X POST \ + -H "Authorization: Bearer $$token" \ + --data '{"request_ids":["$(REQID)"], "pipeline_name": "roslin"}' \ + http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/etl/update-requests/ + # check if the ports needed for services and servers are already in use on this system ifeq ($(UNAME), Darwin) # On macOS High Sierra, use this command: lsof -nP -i4TCP:$PORT | grep LISTEN @@ -514,5 +549,3 @@ PORT= port-check: ss -lntup | grep ':$(PORT)' endif - - diff --git a/beagle/settings.py b/beagle/settings.py index 738269fee..917ba882c 100644 --- a/beagle/settings.py +++ b/beagle/settings.py @@ -316,3 +316,5 @@ PROJECT_DIR = os.path.dirname(os.path.realpath(__file__)) ROOT_DIR = os.path.dirname(PROJECT_DIR) TEST_FIXTURE_DIR = os.path.join(ROOT_DIR, "fixtures", "tests") +FIXTURES_DIR = os.path.join(ROOT_DIR, "fixtures") +DUMP_JSON = os.environ.get('DUMP_JSON') == 'True' diff --git a/beagle_etl/fixtures/beagle_etl.operator.json b/beagle_etl/fixtures/beagle_etl.operator.json index 22c7f8dce..4af0d3b2c 100644 --- a/beagle_etl/fixtures/beagle_etl.operator.json +++ b/beagle_etl/fixtures/beagle_etl.operator.json @@ -38,5 +38,15 @@ "class_name": "CopyOutputsOperator", "slug": "copyOutputs" } + }, + { + "model": "beagle_etl.operator", + "pk": 5, + "fields": { + "active": true, + "recipes": "[]", + "class_name": "RoslinQcOperator", + "slug": "roslin-qc" + } } ] diff --git a/file_system/fixtures/file_system.filegroup.json b/file_system/fixtures/file_system.filegroup.json index fa4828340..7f6d71e67 100644 --- a/file_system/fixtures/file_system.filegroup.json +++ b/file_system/fixtures/file_system.filegroup.json @@ -1,90 +1,90 @@ [ -{ - "model": "file_system.filegroup", - "pk": "0221fdb7-6cf8-41d7-9432-8cbbccfd08fe", - "fields": { - "created_date": "2019-12-06T19:20:43.437Z", - "modified_date": "2019-12-06T19:20:43.437Z", - "name": "Origin Unknown", - "slug": "origin-unknown", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + { + "model": "file_system.filegroup", + "pk": "0221fdb7-6cf8-41d7-9432-8cbbccfd08fe", + "fields": { + "created_date": "2019-12-06T19:20:43.437Z", + "modified_date": "2019-12-06T19:20:43.437Z", + "name": "Origin Unknown", + "slug": "origin-unknown", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "0abb8733-dd3e-46d1-b147-def516f125f4", + "fields": { + "created_date": "2019-12-02T22:11:05.490Z", + "modified_date": "2019-12-02T22:11:05.490Z", + "name": "junk", + "slug": "junk", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "1552617b-3b06-46de-921a-a000a9129385", + "fields": { + "created_date": "2020-01-22T19:19:05.790Z", + "modified_date": "2020-01-22T19:19:05.790Z", + "name": "Pooled Normal", + "slug": "pooled-normal", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", + "fields": { + "created_date": "2019-10-01T20:52:31.890Z", + "modified_date": "2019-10-01T20:52:31.890Z", + "name": "LIMS", + "slug": "lims", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "4616ef88-103c-4cf4-baab-f3a247bc2172", + "fields": { + "created_date": "2019-10-23T19:44:01.317Z", + "modified_date": "2019-10-23T19:44:01.317Z", + "name": "reference_files", + "slug": "reference_files", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "a66f03b4-ce43-40d0-9134-d5a3575cabae", + "fields": { + "created_date": "2019-11-05T20:13:29.923Z", + "modified_date": "2019-11-05T20:13:29.923Z", + "name": "outputs", + "slug": "outputs", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "a975f490-1b02-4575-abae-a4f8e3667733", + "fields": { + "created_date": "2019-11-18T17:44:56.345Z", + "modified_date": "2019-11-18T17:44:56.345Z", + "name": "roslin_pair_sv_outputs", + "slug": "roslin_pair_sv_outputs", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } + }, + { + "model": "file_system.filegroup", + "pk": "d9015037-cd6b-4cb6-87a8-16d355482461", + "fields": { + "created_date": "2019-11-19T20:02:12.221Z", + "modified_date": "2019-11-19T20:02:12.221Z", + "name": "access_m1_output", + "slug": "access_m1_output", + "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" + } } -}, -{ - "model": "file_system.filegroup", - "pk": "0abb8733-dd3e-46d1-b147-def516f125f4", - "fields": { - "created_date": "2019-12-02T22:11:05.490Z", - "modified_date": "2019-12-02T22:11:05.490Z", - "name": "junk", - "slug": "junk", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "1552617b-3b06-46de-921a-a000a9129385", - "fields": { - "created_date": "2020-01-22T19:19:05.790Z", - "modified_date": "2020-01-22T19:19:05.790Z", - "name": "Pooled Normal", - "slug": "pooled-normal", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", - "fields": { - "created_date": "2019-10-01T20:52:31.890Z", - "modified_date": "2019-10-01T20:52:31.890Z", - "name": "LIMS", - "slug": "lims", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "4616ef88-103c-4cf4-baab-f3a247bc2172", - "fields": { - "created_date": "2019-10-23T19:44:01.317Z", - "modified_date": "2019-10-23T19:44:01.317Z", - "name": "reference_files", - "slug": "reference_files", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "a66f03b4-ce43-40d0-9134-d5a3575cabae", - "fields": { - "created_date": "2019-11-05T20:13:29.923Z", - "modified_date": "2019-11-05T20:13:29.923Z", - "name": "outputs", - "slug": "outputs", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "a975f490-1b02-4575-abae-a4f8e3667733", - "fields": { - "created_date": "2019-11-18T17:44:56.345Z", - "modified_date": "2019-11-18T17:44:56.345Z", - "name": "roslin_pair_sv_outputs", - "slug": "roslin_pair_sv_outputs", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -}, -{ - "model": "file_system.filegroup", - "pk": "d9015037-cd6b-4cb6-87a8-16d355482461", - "fields": { - "created_date": "2019-11-19T20:02:12.221Z", - "modified_date": "2019-11-19T20:02:12.221Z", - "name": "access_m1_output", - "slug": "access_m1_output", - "storage": "0cd14133-0f6a-413d-a498-495bf48546c0" - } -} ] diff --git a/fixtures/runs/aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json b/fixtures/runs/aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json new file mode 100644 index 000000000..d77409d95 --- /dev/null +++ b/fixtures/runs/aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json @@ -0,0 +1,6290 @@ +[ + { + "model": "runner.run", + "pk": "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2", + "fields": { + "created_date": "2020-03-03T15:51:28.999Z", + "modified_date": "2020-03-03T16:36:07.390Z", + "name": "ROSLIN ALN-REQ-ID, 1 of 1 (03/03/2020, 15:51:28)", + "app": "c7849f2b-9a4f-4352-acde-1d993af379d8", + "status": 4, + "execution_id": "46b17469-330b-4fbf-a83a-da72e1dc09db", + "job_statuses": {}, + "output_metadata": {}, + "tags": { + "requestId": "ALN-REQ-ID", + "labHeadName": "", + "labHeadEmail": "", + "sampleNameTumor": "s_C_ALLANT_T001_d", + "sampleNameNormal": "s_C_ALLANT_N002_d" + } + } + }, + { + "model": "runner.port", + "pk": "0de3037b-f83a-4333-919c-d491eaefeb38", + "fields": { + "created_date": "2020-03-03T15:51:33.058Z", + "modified_date": "2020-03-03T16:36:07.037Z", + "run": "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2", + "name": "db_files", + "port_type": 0, + "schema": { + "type": "record", + "fields": { + "refseq": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "vep_data": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "vep_path": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "custom_enst": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "facets_snps": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "hotspot_vcf": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "fp_genotypes": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "fp_intervals": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "hotspot_list": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "bait_intervals": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "conpair_markers": { + "type": [ + "null", + "array" + ], + "items": "string" + }, + "hotspot_list_maf": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "target_intervals": { + "type": [ + "null", + "array" + ], + "items": "File" + }, + "conpair_markers_bed": { + "type": [ + "null", + "array" + ], + "items": "string" + } + } + }, + "secondary_files": [], + "db_value": { + "refseq": { + "class": "File", + "location": "bid://3814d1da-e507-4e7d-b65b-b4ae7e07ec61" + }, + "vep_data": "/var/cache", + "vep_path": "/usr/bin/vep", + "custom_enst": "/usr/bin/vcf2maf/data/isoform_overrides_at_mskcc", + "facets_snps": { + "class": "File", + "location": "bid://584079c8-13af-4816-9ad3-50ce86e13934" + }, + "hotspot_vcf": "/usr/bin/basicfiltering/data/hotspot-list-union-v1-v2.vcf", + "fp_genotypes": { + "class": "File", + "location": "bid://3f2fcb1e-cdf4-4d71-8369-04197b5ef7ff" + }, + "fp_intervals": { + "class": "File", + "location": "bid://d058dd8e-6097-4556-b7e7-7c2184789036" + }, + "hotspot_list": "/usr/bin/ngs-filters/data/hotspot-list-union-v1-v2.txt", + "delly_exclude": { + "class": "File", + "location": "bid://e0e6283e-24ba-466f-9ec6-b6d9d85b2acd" + }, + "bait_intervals": { + "class": "File", + "location": "bid://14b45ffc-8797-40dd-b456-669bf79c22bb" + }, + "conpair_markers": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt", + "hotspot_list_maf": { + "class": "File", + "location": "bid://92bff766-15fd-4316-8977-77afcef97dae" + }, + "target_intervals": { + "class": "File", + "location": "bid://dce51627-5764-429b-ba52-f9cab17d967d" + }, + "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed" + }, + "value": { + "refseq": { + "path": "/juno/work/ci/resources/request_files/refseq/refGene_b37.sorted.txt", + "class": "File" + }, + "vep_data": "/var/cache", + "vep_path": "/usr/bin/vep", + "custom_enst": "/usr/bin/vcf2maf/data/isoform_overrides_at_mskcc", + "facets_snps": { + "path": "/juno/work/ci/resources/genomes/GRCh37/facets_snps/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf.gz", + "class": "File" + }, + "hotspot_vcf": 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"/juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" + { + "class": "File", + "location": "juno:///juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" + } ], "R2": [ - "/juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz" + { + "class": "File", + "location": "juno:///juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz" + } ], "bam": [], "zR1": [], @@ -332,10 +338,16 @@ "PU": [ ], "R1": [ - "/juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" + { + "class": "File", + "location": "juno:///juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" + } ], "R2": [ - "/juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz" + { + "class": "File", + "location": "juno:///juno/work/ci/roslin-pipelines/variant/2.6.0/workspace/test_data/examples/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz" + } ], "bam": [], "zR1": [], diff --git a/runner/fixtures/runner.pipeline.json b/runner/fixtures/runner.pipeline.json index 54bb11fc5..9858dfaed 100644 --- a/runner/fixtures/runner.pipeline.json +++ b/runner/fixtures/runner.pipeline.json @@ -10,7 +10,8 @@ "version": "0.1.0", "entrypoint": "align_sort_bam.cwl", "output_file_group": "a66f03b4-ce43-40d0-9134-d5a3575cabae", - "output_directory": null + "output_directory": null, + "operator": null } }, { @@ -24,18 +25,49 @@ "version": "0.1.1", "entrypoint": "fastq_to_bam.cwl", "output_file_group": "d9015037-cd6b-4cb6-87a8-16d355482461", - "output_directory": "/work/pi/beagle/output/access_m1" + "output_directory": "/work/pi/beagle/output/access_m1", + "operator": null } }, { "model": "runner.pipeline", - "pk": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", + "pk": "ee5f19d6-f8bf-401f-8cbc-1dd81af10e67", + "fields": { + "created_date": "2019-11-07T21:50:16.747Z", + "modified_date": "2019-12-05T04:34:27.747Z", + "name": "flatbush", + "github": "https://github.com/mskcc-cwl/flatbush", + "version": "master", + "entrypoint": "flatbush.cwl", + "output_file_group": "a66f03b4-ce43-40d0-9134-d5a3575cabae", + "output_directory": "/juno/work/pi/beagle/output/flatbush", + "operator": null + } + }, + { + "model": "runner.pipeline", + "pk": "9b7f2ac8-03a5-4c44-ae87-1d9f6500d19a", "fields": { "created_date": "2019-11-18T17:46:45.118Z", "modified_date": "2019-12-05T01:12:39.854Z", - "name": "roslin", + "name": "roslin-qc", "github": "https://github.com/mskcc/roslin-cwl", "version": "1.0.0-rc5", + "entrypoint": "modules/project/generate-qc.cwl", + "output_file_group": "a975f490-1b02-4575-abae-a4f8e3667733", + "output_directory": "/juno/work/pi/beagle/output/roslin-qc", + "operator": null + } + }, + { + "model": "runner.pipeline", + "pk": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", + "fields": { + "created_date": "2019-11-18T17:46:45.118Z", + "modified_date": "2020-02-26T22:22:30.099Z", + "name": "roslin", + "github": "https://github.com/mskcc/roslin-cwl", + "version": "feature/3.0.0_release", "entrypoint": "workflows/pair-workflow-sv.cwl", "output_file_group": "a975f490-1b02-4575-abae-a4f8e3667733", "output_directory": "/juno/work/pi/beagle/output/roslin_pair_sv", @@ -44,31 +76,32 @@ }, { "model": "runner.pipeline", - "pk": "ee5f19d6-f8bf-401f-8cbc-1dd81af10e67", + "pk": "06792b3f-f9dc-4ad1-80a7-2a7af300f000", "fields": { - "created_date": "2019-11-07T21:50:16.747Z", - "modified_date": "2019-12-05T04:34:27.747Z", - "name": "flatbush", - "github": "https://github.com/mskcc-cwl/flatbush", - "version": "master", - "entrypoint": "flatbush.cwl", - "output_file_group": "a66f03b4-ce43-40d0-9134-d5a3575cabae", - "output_directory": "/juno/work/pi/beagle/output/flatbush" + "created_date": "2020-02-25T17:04:46.410Z", + "modified_date": "2020-03-03T15:12:51.891Z", + "name": "roslin-dev", + "github": "https://github.com/mskcc/roslin-cwl", + "version": "3.0.0", + "entrypoint": "workflows/pair-workflow-sv.cwl", + "output_file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", + "output_directory": "/juno/work/ci/kellys5/projects/beagle-dev/beagle-dev4/output/roslin-dev", + "operator": 5 } }, { "model": "runner.pipeline", - "pk": "65419097-a2b8-4d57-a8ab-c4c4cddcbea8", + "pk": "c7849f2b-9a4f-4352-acde-1d993af379d8", "fields": { - "created_date": "2019-11-18T17:46:45.118Z", - "modified_date": "2019-12-05T01:12:39.854Z", - "name": "copy_outputs", + "created_date": "2020-01-22T18:15:20.875Z", + "modified_date": "2020-03-02T17:43:21.328Z", + "name": "roslin-pair-workflow", "github": "https://github.com/mskcc/roslin-cwl", - "version": "1.0.0", - "entrypoint": "workflows/copy_outputs.cwl", + "version": "feature/3.0.0_release", + "entrypoint": "workflows/pair-workflow.cwl", "output_file_group": "a975f490-1b02-4575-abae-a4f8e3667733", - "output_directory": "/juno/work/pi/beagle/output/copy_outputs", - "operator": 4 + "output_directory": "/juno/work/pi/beagle/output/roslin_pair_workflow", + "operator": 3 } } ] diff --git a/runner/operator/operator_factory.py b/runner/operator/operator_factory.py index 150259845..724a5590c 100644 --- a/runner/operator/operator_factory.py +++ b/runner/operator/operator_factory.py @@ -1,15 +1,16 @@ from .tempo_operator import TempoOperator from .roslin_operator import RoslinOperator from .access_operator import AccessOperator +from .roslin_qc_operator import RoslinQcOperator from .copy_outputs_operator import CopyOutputsOperator - class OperatorFactory(object): operators = { "TempoOperator": TempoOperator, "RoslinOperator": RoslinOperator, "AccessOperator": AccessOperator, + "RoslinQcOperator": RoslinQcOperator, "CopyOutputsOperator": CopyOutputsOperator } diff --git a/runner/operator/roslin_operator/roslin_operator.py b/runner/operator/roslin_operator/roslin_operator.py index 470685733..ae433e8a4 100644 --- a/runner/operator/roslin_operator/roslin_operator.py +++ b/runner/operator/roslin_operator/roslin_operator.py @@ -6,7 +6,6 @@ from .bin.pair_request import compile_pairs from .bin.make_sample import build_sample - class RoslinOperator(Operator): def get_jobs(self): files = self.files.filter(filemetadata__metadata__requestId=self.request_id, filemetadata__metadata__igocomplete=True).all() @@ -43,11 +42,18 @@ def get_jobs(self): assay = job['assay'] pi = job['pi'] pi_email = job['pi_email'] - roslin_jobs.append((APIRunCreateSerializer( - data={'app': self.get_pipeline_id(), 'inputs': roslin_inputs, 'name': name, - 'tags': {'requestId': self.request_id, - 'sampleNameTumor': tumor_sample_name, - 'sampleNameNormal': normal_sample_name, - 'labHeadName': pi, - 'labHeadEmail': pi_email}}), job)) + data = { + 'app': self.get_pipeline_id(), + 'inputs': roslin_inputs, + 'name': name, + 'tags': { + 'requestId': self.request_id, + 'sampleNameTumor': tumor_sample_name, + 'sampleNameNormal': normal_sample_name, + 'labHeadName': pi, + 'labHeadEmail': pi_email + } + } + run = APIRunCreateSerializer(data = data) + roslin_jobs.append((run, job)) return roslin_jobs diff --git a/runner/operator/roslin_qc_operator/__init__.py b/runner/operator/roslin_qc_operator/__init__.py new file mode 100644 index 000000000..0941c50e5 --- /dev/null +++ b/runner/operator/roslin_qc_operator/__init__.py @@ -0,0 +1 @@ +from .roslin_qc_operator import RoslinQcOperator diff --git a/runner/operator/roslin_qc_operator/bin/__init__.py b/runner/operator/roslin_qc_operator/bin/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/runner/operator/roslin_qc_operator/bin/input.py b/runner/operator/roslin_qc_operator/bin/input.py new file mode 100644 index 000000000..95d6a50e1 --- /dev/null +++ b/runner/operator/roslin_qc_operator/bin/input.py @@ -0,0 +1,410 @@ +""" +Module for generating input dataset for use with Roslin QC operator + +Example input datastructure format: + +db_files: + fp_genotypes: db_files['value']['fp_genotypes'] + hotspot_list_maf: db_files['value']['hotspot_list_maf'] + conpair_markers: db_files['value']['conpair_markers'] +runparams: + project_prefix: runparams['value']['project_prefix'] + genome: runparams['value']['genome'] + scripts_bin: runparams['value']['scripts_bin'] + assay: ---MISSING--- + pi: ---MISSING--- + pi_email: ---MISSING--- +ref_fasta: ref_fasta +clstats1: [clstats1] +clstats2: [clstats2] +md_metrics: [md_metrics] +hs_metrics: [hs_metrics] +insert_metrics: [insert_metrics] +per_target_coverage: [per_target_coverage] +qual_metrics: [qual_metrics] +doc_basecounts: [doc_basecounts] +conpair_pileups: [conpair_pileups] +pairs: [pair] +""" +import os +import json +import urllib +from file_system.models import FileMetadata, File +from runner.models import Port +import urllib.parse + +def build_sample(filemetadata_instance, company_name = "MSKCC", platform = "Illumina"): + """ + Create base Roslin CWL sample datastructure from the FileMetadata + """ + sample = {} + sample['CN'] = company_name + sample['PL'] = platform + sample['PU'] = filemetadata_instance.metadata['flowCellId'] + sample['LB'] = filemetadata_instance.metadata['libraryId'] + sample['tumor_type'] = filemetadata_instance.metadata['tumorOrNormal'] + sample['ID'] = '_'.join([filemetadata_instance.metadata['sampleName'], filemetadata_instance.metadata['flowCellId']]) + sample['SM'] = filemetadata_instance.metadata['sampleName'] + sample['species'] = filemetadata_instance.metadata['species'] + sample['patient_id'] = filemetadata_instance.metadata['patientId'] + sample['bait_set'] = filemetadata_instance.metadata['baitSet'] + sample['igo_id'] = filemetadata_instance.metadata['sampleId'] + sample['run_date'] = filemetadata_instance.metadata['runDate'] + sample['specimen_type'] = filemetadata_instance.metadata['specimenType'] + sample['request_id'] = filemetadata_instance.metadata['requestId'] + return(sample) + +def file_to_cwl(file_instance): + """ + Convert a Beagle File instance into a dict in CWL File format dict + + example: + {'class': 'File', 'path': '/path/to/foo.txt'} + """ + d = { + 'class': 'File', + 'path': file_instance.path + } + return(d) + +def file_to_job_data(file_instance): + """ + Convert a Beagle File instance into a dict that will be used in the Job submitted to Beagle + NOTE: this is not the same as the CWL output format + + example: + {'class': 'File', 'location': 'juno://path/to/foo.txt'} + """ + d = { + 'class': 'File', + 'location': 'juno://%s' % file_instance.path + } + return(d) + +def path_to_cwl(filepath): + """ + Convert a filepath string into a CWL File format dict + """ + d = { + 'class': 'File', + 'path': filepath + } + return(d) + +def path_to_job_data(filepath): + """ + Convert a filepath to a string representation for Job submission data` + NOTE: not the same format as CWL representation + """ + d = { + 'class': 'File', + 'location': 'juno://%s' % filepath + } + return(d) + +def create_files_data_from_ports_with_names(ports): + """ + Retrieve the File entries for each Port entry, while keeping the associated Port.name attribute + """ + # list of dicts for File and 'name' + # TODO: use a Django query instead of iteration + files = [] + for port in ports: + # arbitrary ordering to force a test-able output + for file in port.files.all().order_by('path'): + file_cwl = file_to_job_data(file) + d = { 'name': port.name, 'file': file_cwl } + files.append(d) + return(files) + +def parse_pairs_from_ports(ports_queryset): + """ + Search the set of Ports for "pair" entries and format them into a list of tumor normal pair entries + """ + pair_ports = ports_queryset.filter(name = "pair") + pairs = [] + + # get the tumor and normal R1 and R2 items from FileMetadata assocaited with File's associated with each Port + all_pair_items = [] + for port in pair_ports: + pair_items = [] + # all the Files assocaited with a Port + files = port.files.all() + for file in files: + # get the highest 'version' number FileMetadata instance for the File + filemetata_instance = file.filemetadata_set.first() + R1_or_R2 = filemetata_instance.metadata['R'] + tumor_or_normal = filemetata_instance.metadata['tumorOrNormal'] + pair_items.append( {'filemetadata': filemetata_instance, 'R1_or_R2': R1_or_R2, 'tumor_or_normal': tumor_or_normal } ) + all_pair_items.append(pair_items) + + # parse the entries into a sensible mapping of tumor and normal R1 and R2 + for pair_items in all_pair_items: + pair_set = {} + pair_set['tumor'] = {} + pair_set['normal'] = {} + # TODO: how to handle case where wrong number of items are associated? Should be 1 of each tumor/normal + R1/R2 + for item in pair_items: + if item['tumor_or_normal'] == 'Tumor' and item['R1_or_R2'] == 'R1': + pair_set['tumor']['R1'] = item['filemetadata'] + elif item['tumor_or_normal'] == 'Tumor' and item['R1_or_R2'] == 'R2': + pair_set['tumor']['R2'] = item['filemetadata'] + elif item['tumor_or_normal'] == 'Normal' and item['R1_or_R2'] == 'R1': + pair_set['normal']['R1'] = item['filemetadata'] + elif item['tumor_or_normal'] == 'Normal' and item['R1_or_R2'] == 'R2': + pair_set['normal']['R2'] = item['filemetadata'] + pairs.append(pair_set) + return pairs + +def parse_bams_from_ports(ports_queryset): + """ + Search a set of Ports for the 'bams' entries and format them into a list of tumor normal pair entries + + TODO: what to do if there are multiple 'normal_bam' and 'tumor_bam'? + """ + normal_bam_port = ports_queryset.filter(name = "normal_bam").first() + tumor_bam_port = ports_queryset.filter(name = "tumor_bam").first() + + # each Port has two files; the .bam and .bai + # based on just the foreign key in Port.files, you cannot tell which is the .bam and which is the .bai + # so we need to check the file extension and sort them out + normal_items = {} + tumor_items = {} + for file_instance in normal_bam_port.files.all(): + # file_name might end up being a URI + filepath = urllib.parse.urlsplit(file_instance.file_name).path + filename, file_extension = os.path.splitext(filepath) + normal_items[file_extension] = file_instance + for file_instance in tumor_bam_port.files.all(): + filepath = urllib.parse.urlsplit(file_instance.file_name).path + filename, file_extension = os.path.splitext(filepath) + tumor_items[file_extension] = file_instance + + # now make a sensible output mapping to the files + output_items = { + 'normal_bam' : normal_items['.bam'], + 'normal_bai' : normal_items['.bai'], + 'tumor_bam' : tumor_items['.bam'], + 'tumor_bai' : tumor_items['.bai'] + } + + return(output_items) + +def pair_to_cwl(pair): + """ + Convert a single tumor normal pair dict to CWL format datastructure + + pair = { + 'normal': { + 'R1': FileMetadata, + 'R2': FileMetadata + }, + 'tumor': { + 'R1': FileMetadata, + 'R2': FileMetadata + } + """ + # get the base datastructure dict for each R1 and R2 + normal_r1 = build_sample(pair['normal']['R1']) + normal_r2 = build_sample(pair['normal']['R2']) + tumor_r1 = build_sample(pair['tumor']['R1']) + tumor_r2 = build_sample(pair['tumor']['R2']) + + # merge the dict's; the second dict will overwrite args from the first + normal = {**normal_r1, **normal_r2} + normal['R1'] = file_to_cwl(pair['normal']['R1'].file) + normal['R2'] = file_to_cwl(pair['normal']['R2'].file) + + tumor = {**tumor_r1, **tumor_r2} + tumor['R1'] = file_to_cwl(pair['tumor']['R1'].file) + tumor['R2'] = file_to_cwl(pair['tumor']['R2'].file) + + output = (tumor, normal) + return(output) + +def pair_to_job_data(pair): + """ + Convert a single tumor normal pair dict to Job submission data format + NOTE: not the same as CWL format + + pair = { + 'normal': { + 'R1': FileMetadata, + 'R2': FileMetadata + }, + 'tumor': { + 'R1': FileMetadata, + 'R2': FileMetadata + } + """ + # get the base datastructure dict for each R1 and R2 + normal_r1 = build_sample(pair['normal']['R1']) + normal_r2 = build_sample(pair['normal']['R2']) + tumor_r1 = build_sample(pair['tumor']['R1']) + tumor_r2 = build_sample(pair['tumor']['R2']) + + # merge the dict's; the second dict will overwrite args from the first + normal = {**normal_r1, **normal_r2} + normal['R1'] = file_to_job_data(pair['normal']['R1'].file) + normal['R2'] = file_to_job_data(pair['normal']['R2'].file) + + tumor = {**tumor_r1, **tumor_r2} + tumor['R1'] = file_to_job_data(pair['tumor']['R1'].file) + tumor['R2'] = file_to_job_data(pair['tumor']['R2'].file) + + output = (tumor, normal) + return(output) + +def bams_to_job_data(bams): + """ + Convert the set of bam files into the datastructure needed for the Job JSON + + bams = { + 'normal_bam' : File.objects.get(...), + 'normal_bai' : File.objects.get(...), + 'tumor_bam' : File.objects.get(...), + 'tumor_bai' : File.objects.get(...) + } + """ + job_data = [] + job_data.append(file_to_job_data(bams['tumor_bam'])) + job_data.append(file_to_job_data(bams['normal_bam'])) + return(job_data) + +def parse_runparams_from_ports(ports_queryset): + """ + Get the runparams from a Port queryset + """ + # TODO: how to ensure the correct number of Port items? Should be 1 + # TODO: how to handle multiple sets of runparams in the ports queryset???? + param_port = ports_queryset.filter(name = "runparams").first() + runparams = {} + runparams['project_prefix'] = param_port.value['project_prefix'] + runparams['genome'] = param_port.value['genome'] + runparams['scripts_bin'] = param_port.value['scripts_bin'] + runparams['assay'] = param_port.value['assay'] + + # at the time of writing these, 'pi' and 'pi_email' were not output by Roslin pipeline but were needed by Roslin QC pipeline + if 'pi' not in runparams: + runparams['pi'] = "NA" + if 'pi_email' not in runparams: + runparams['pi_email'] = "NA" + return(runparams) + +def get_baits_and_targets(assay): + """ + get a assay label that matches the known keys in roslin_resources.json + + copy paste'd from Roslin QC Operator; https://github.com/mskcc/beagle/blob/032b7aeb5abedfdae6e6b434c4f231f5645a2df8/runner/operator/roslin_operator/construct_roslin_pair.py#L94 + """ + if assay.find("IMPACT410") > -1: + return("IMPACT410_b37") + if assay.find("IMPACT468") > -1: + return("IMPACT468_b37") + if assay.find("IMPACT341") > -1: + return("IMPACT341_b37") + if assay.find("IDT_Exome_v1_FP") > -1: + return("IDT_Exome_v1_FP_b37") + if assay.find("IMPACT468+08390") > -1: + return("IMPACT468_08390") + if assay.find("IMPACT468+Poirier_RB1_intron_V2") > -1: + return("IMPACT468_08050") + +def get_db_files(assay, references_json = "runner/operator/roslin_operator/reference_jsons/roslin_resources.json"): + """ + Return a dict with the required reference file paths + """ + # assay does not actually always match the key needed to figure out the reference files + better_assay = get_baits_and_targets(assay) + references = json.load(open(references_json)) + db_files = {} + db_files['fp_genotypes'] = references["targets"][better_assay]['FP_genotypes'] + db_files['hotspot_list_maf'] = references["request_files"]['hotspot_list_maf'] + db_files['conpair_markers'] = references["request_files"]['conpair_markers'] + db_files['ref_fasta'] = references["request_files"]['ref_fasta'] + + # need to resolve some items to URI's + for key in ['fp_genotypes', 'hotspot_list_maf', 'ref_fasta']: + value = db_files[key] + if value.startswith('juno:///'): + parts = urllib.parse.urlsplit(value) + db_files[key] = path_to_job_data(parts.path) + elif value.startswith('/'): + db_files[key] = path_to_job_data(db_files[key]) + return(db_files) + +def parse_outputs_files_data(files_data): + """ + Generate an input dataset from a list of dicts of File objects and their associated Port.name value + Uses items that came from a pipeline output + + files_data = [{ 'name': Port.name, 'file': {'class': 'File', 'path': '/path/to/foo.txt'} }, ... ] + """ + # initialize the output data to use for starting QC pipeline + qc_input = {} + qc_input['clstats1'] = [] + qc_input['clstats2'] = [] + qc_input['md_metrics'] = [] + qc_input['hs_metrics'] = [] + qc_input['insert_metrics'] = [] + qc_input['per_target_coverage'] = [] + qc_input['qual_metrics'] = [] + qc_input['doc_basecounts'] = [] + qc_input['conpair_pileups'] = [] + + for item in files_data: + item_type = item['name'] + file_data = item['file'] + + # append values for known keys + # TODO: do we need to enforce unique-ness here? Do we need to enfore unique on file basename as well? + if item_type in qc_input: + if file_data not in qc_input[item_type]: + qc_input[item_type].append(file_data) + return(qc_input) + +def build_inputs_from_runs(run_queryset): + """ + Build the Roslin QC pipeline inputs data structure from a set of Roslin Voyager pipeline Run instances + """ + # get the input and output Ports of the run + ports = Port.objects.filter(run__in = run_queryset).order_by('created_date') # arbitrary ordering to force a test-able output + + # get the list of tumor normal pairs out of the Ports + pairs = parse_pairs_from_ports(ports) + + # convert the pairs to CWL format datastructure + pairs_job_data = [] + for pair_set in pairs: + job_data = pair_to_job_data(pair_set) + pairs_job_data.append(job_data) + + # get the File entries while keeping Port.name; needed for later parsing + files_data = create_files_data_from_ports_with_names(ports) + input_files = parse_outputs_files_data(files_data) + + # find the Port with 'runparams' needed for QC input + runparams = parse_runparams_from_ports(ports) + + # get the correct reference files based on assay type + db_files = get_db_files(runparams['assay']) + ref_fasta = db_files.pop('ref_fasta') + + # get the .bam files needed for QC input + bams = parse_bams_from_ports(ports) + + # convert to CWL output format + bams_job_data = bams_to_job_data(bams) + + # build the final data dict for QC input + qc_input = {} + qc_input['db_files'] = db_files + qc_input['runparams'] = runparams + qc_input['pairs'] = pairs_job_data + qc_input['ref_fasta'] = ref_fasta + qc_input['bams'] = bams_job_data + qc_input['directories'] = [] + qc_input['files'] = [] + qc_input = {**qc_input, **input_files} + + return(qc_input) diff --git a/runner/operator/roslin_qc_operator/roslin_qc_operator.py b/runner/operator/roslin_qc_operator/roslin_qc_operator.py new file mode 100644 index 000000000..23649d2d7 --- /dev/null +++ b/runner/operator/roslin_qc_operator/roslin_qc_operator.py @@ -0,0 +1,78 @@ +from runner.operator.operator import Operator +from runner.models import Run, Pipeline, Run, RunStatus +from runner.serializers import APIRunCreateSerializer +from .bin import input +import datetime + +class RoslinQcOperator(Operator): + """ + Operator for Roslin QC pipeline + """ + + def __init__(self, model, request_id = None, run_ids = None): + self.run_ids = run_ids + self.runs = None + if self.run_ids != None: + self.runs = Run.objects.filter(id__in = self.run_ids) + # TODO: add support for things like FileMetadata's + # TODO: add support for multiple request ids + + Operator.__init__(self, model, request_id = request_id, run_ids = run_ids) + + def get_pipeline_id(self): + return "9b7f2ac8-03a5-4c44-ae87-1d9f6500d19a" + + def get_input_data(self): + """ + Build up the data to use for input to QC pipeline + Needs to match the datastructure expected by the CWL pipeline input + + TODO: fill this in with handling of more types of input criteria; runs, requests, FileMetadata's, etc + """ + input_data = {} + if self.runs != None: + input_data = input.build_inputs_from_runs(self.runs) + # TODO: add methods here to add data from other items like requests, FileMetadata, etc + return(input_data) + + def get_output_metadata(self): + """ + Implement methods here to generate output metadata values that might need to be passed + """ + return({}) + + def get_data_for_serializer(self, input_data, output_metadata, create_date = None, name = None, tags = None, pipeline_id = None): + """ + Put together the data that will be sent to the serializer for run creation + """ + if create_date == None: + create_date = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S") + + if name == None: + name = "Roslin QC {create_date}".format(create_date = create_date) + + if tags == None: + tags = {} + if self.request_id: + tags['request_id'] = self.request_id + if self.run_ids: + tags['run_ids'] = self.run_ids + + if pipeline_id == None: + pipeline_id = self.get_pipeline_id() + + serializer_data = { + 'app': pipeline_id, + 'inputs': input_data, + 'name': name, + 'tags': tags, + 'output_metadata': output_metadata + } + return(serializer_data) + + def get_jobs(self): + input_data = self.get_input_data() + output_metadata = self.get_output_metadata() + serializer_data = self.get_data_for_serializer(input_data, output_metadata) + run = APIRunCreateSerializer(data = serializer_data) + return([(run, input_data)]) diff --git a/runner/tasks.py b/runner/tasks.py index 9df0e3398..304618915 100644 --- a/runner/tasks.py +++ b/runner/tasks.py @@ -2,6 +2,7 @@ import uuid import logging import requests +import json from celery import shared_task from django.conf import settings from runner.run.objects.run_object import RunObject @@ -101,6 +102,9 @@ def process_triggers(): @shared_task def create_run_task(run_id, inputs, output_directory=None): logger.info("Creating and validating Run") + if settings.DUMP_JSON: + output_file_name = "{}.job.inputs.json".format(run_id) + print(json.dumps(inputs, indent = 4), file = open(output_file_name, "w")) try: run = RunObject.from_cwl_definition(run_id, inputs) run.ready() @@ -131,6 +135,11 @@ def submit_job(run_id, output_directory=None): inputs = dict() for port in run.port_set.filter(port_type=PortType.INPUT).all(): inputs[port.name] = port.value + + if settings.DUMP_JSON: + output_file_name = "{}.job.inputs-cwl.json".format(run_id) + print(json.dumps(inputs, indent = 4), file = open(output_file_name, "w")) + if not output_directory: output_directory = os.path.join(run.app.output_directory, str(run_id)) job = { @@ -138,6 +147,11 @@ def submit_job(run_id, output_directory=None): 'inputs': inputs, 'root_dir': output_directory } + + if settings.DUMP_JSON: + output_file_name = "{}.job.json".format(run_id) + print(json.dumps(job, indent = 4), file = open(output_file_name, "w")) + logger.info("Job %s ready for submitting" % run_id) response = requests.post(settings.RIDGEBACK_URL + '/v0/jobs/', json=job) if response.status_code == 201: diff --git a/runner/tests/operator/roslin_qc_operator/__init__.py b/runner/tests/operator/roslin_qc_operator/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/runner/tests/operator/roslin_qc_operator/test_input.py b/runner/tests/operator/roslin_qc_operator/test_input.py new file mode 100644 index 000000000..d87969655 --- /dev/null +++ b/runner/tests/operator/roslin_qc_operator/test_input.py @@ -0,0 +1,323 @@ +""" +Tests for Roslin QC input parsing methods +""" +import os +import json +from uuid import UUID +from django.test import TestCase +from django.conf import settings +from django.core.management import call_command +from file_system.models import File, FileMetadata, FileGroup +from runner.models import Run, Port, PortType +from runner.operator.roslin_qc_operator.bin.input import parse_outputs_files_data +from runner.operator.roslin_qc_operator.bin.input import parse_pairs_from_ports +from runner.operator.roslin_qc_operator.bin.input import parse_runparams_from_ports +from runner.operator.roslin_qc_operator.bin.input import get_db_files +from runner.operator.roslin_qc_operator.bin.input import get_baits_and_targets +from runner.operator.roslin_qc_operator.bin.input import build_inputs_from_runs +from runner.operator.roslin_qc_operator.bin.input import file_to_cwl +from runner.operator.roslin_qc_operator.bin.input import path_to_cwl +from runner.operator.roslin_qc_operator.bin.input import path_to_job_data +from runner.operator.roslin_qc_operator.bin.input import build_sample +from runner.operator.roslin_qc_operator.bin.input import pair_to_cwl +from runner.operator.roslin_qc_operator.bin.input import parse_bams_from_ports +from runner.operator.roslin_qc_operator.bin.input import file_to_job_data +from runner.operator.roslin_qc_operator.bin.input import pair_to_job_data + +class TestInput(TestCase): + fixtures = [ + "file_system.filegroup.json", + "file_system.filetype.json", + "file_system.storage.json", + "runner.pipeline.json", + "beagle_etl.operator.json" + ] + + def test_file_to_cwl1(self): + """ + Test conversion of a File instance to an equivalent CWL entry + + """ + file_instance = File.objects.create( + file_group = FileGroup.objects.first(), + path = "/path/to/foo.txt") + file_cwl = file_to_cwl(file_instance) + expected_file_cwl = {'class': 'File', 'path': '/path/to/foo.txt'} + self.assertEqual(file_cwl, expected_file_cwl) + + job_data = file_to_job_data(file_instance) + expected_job_data = {'class': 'File', 'location': 'juno:///path/to/foo.txt'} + self.assertEqual(job_data, expected_job_data) + + def test_path_to_cwl1(self): + """ + Test conversion of a string based file path into CWL File format dict + """ + file_cwl = path_to_cwl('/path/to/foo.txt') + expected_file_cwl = {'class': 'File', 'path': '/path/to/foo.txt'} + self.assertEqual(file_cwl, expected_file_cwl) + + job_data = path_to_job_data('/path/to/foo.txt') + expected_job_data = {'class': 'File', 'location': 'juno:///path/to/foo.txt'} + self.assertEqual(job_data, expected_job_data) + + def test_build_sample1(self): + """ + Test building of the base dict datastructure to be used later in Roslin CWL output + """ + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + file_instance = File.objects.get(file_name = 'DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz') + filemetadata_instance = FileMetadata.objects.filter(file = file_instance).order_by('-version').first() + sample = build_sample(filemetadata_instance = filemetadata_instance) + expected_sample = {'CN': 'MSKCC', + 'PL': 'Illumina', + 'PU': 'MyFlowCellId', + 'LB': 'MyLibraryId', + 'tumor_type': 'Tumor', + 'ID': 'C-ALLANT-T001-d_MyFlowCellId', + 'SM': 'C-ALLANT-T001-d', + 'species': 'Human', + 'patient_id': 'C-ALLANT', + 'bait_set': 'IMPACT468_BAITS', + 'igo_id': 'ALN-TEST-01', + 'run_date': None, + 'specimen_type': 'Blood', + 'request_id': 'ALN-REQ-ID'} + self.assertEqual(sample, expected_sample) + + def test_parse_pairs_from_ports1(self): + """ + Test that pairs are properly constructed from Port objects + """ + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + run_instance = Run.objects.first() + ports = run_instance.port_set.all() + pairs = parse_pairs_from_ports(ports) + + tumor_R2 = FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz")) + turmor_R1 = FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz")) + normal_R2 = FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz")) + normal_R1 = FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz")) + + expected_pairs = [{ + 'normal': { + 'R1': normal_R1, + 'R2': normal_R2 + }, + 'tumor': { + 'R1': turmor_R1, + 'R2': tumor_R2 + } + }] + self.assertEqual(pairs, expected_pairs) + + def test_parse_bams_from_ports1(self): + """ + Test that the 'bams' entries are constructed correctly from the Port objects + """ + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + run_instance = Run.objects.first() + ports = run_instance.port_set.all() + bams = parse_bams_from_ports(ports) + expected_bams = { + 'normal_bam' : File.objects.get(file_name = 's_C_ALLANT_N002_d.rg.md.abra.printreads.bam'), + 'normal_bai' : File.objects.get(file_name = 's_C_ALLANT_N002_d.rg.md.abra.printreads.bai'), + 'tumor_bam' : File.objects.get(file_name = 's_C_ALLANT_T001_d.rg.md.abra.printreads.bam'), + 'tumor_bai' : File.objects.get(file_name = 's_C_ALLANT_T001_d.rg.md.abra.printreads.bai') + } + self.assertEqual(bams, expected_bams) # TODO: need to figure out how this will be handled; need the sample metadata associated with .bam files + + def test_pair_to_job_data(self): + """ + Test that a pair dict is correctly converted to Job data for submission + """ + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + pair = { + 'normal': { + 'R1': FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz")), + 'R2': FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz")) + }, + 'tumor': { + 'R1': FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz")), + 'R2': FileMetadata.objects.get(file = File.objects.get(file_name = "DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz")) + } + } + + job_data = pair_to_job_data(pair) + expected_job_data = ({ + "CN": "MSKCC", + "PL": "Illumina", + "PU": "MyFlowCellId", + "LB": "MyLibraryId", + "tumor_type": "Tumor", + "ID": "C-ALLANT-T001-d_MyFlowCellId", + "SM": "C-ALLANT-T001-d", + "species": "Human", + "patient_id": "C-ALLANT", + "bait_set": "IMPACT468_BAITS", + "igo_id": "ALN-TEST-01", + "run_date": None, + "specimen_type": "Blood", + "request_id": "ALN-REQ-ID", + "R1": { + "class": "File", + "location": "juno:///juno/work/pi/prototypes/register_fastqs/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" + }, + "R2": { + "class": "File", + "location": "juno:///juno/work/pi/prototypes/register_fastqs/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz" + } + }, + { + "CN": "MSKCC", + "PL": "Illumina", + "PU": "MyFlowCellId", + "LB": "MyLibraryId", + "tumor_type": "Normal", + "ID": "C-ALLANT-N002-d_MyFlowCellId", + "SM": "C-ALLANT-N002-d", + "species": "Human", + "patient_id": "C-ALLANT", + "bait_set": "IMPACT468_BAITS", + "igo_id": "ALN-TEST-02", + "run_date": None, + "specimen_type": "Blood", + "request_id": "ALN-REQ-ID", + "R1": { + "class": "File", + "location": "juno:///juno/work/pi/prototypes/register_fastqs/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" + }, + "R2": { + "class": "File", + "location": "juno:///juno/work/pi/prototypes/register_fastqs/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz" + } + }) + + self.assertEqual(job_data, expected_job_data) + + def test_parse_runparams_from_ports1(self): + """ + Test that runparams are correctly parsed from Port queryset + """ + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + run_instance = Run.objects.first() + ports = run_instance.port_set.all() + runparams = parse_runparams_from_ports(ports) + expected_runparams = {'genome': 'GRCh37', + 'pi': 'NA', + 'pi_email': 'NA', + 'project_prefix': 'ALN-REQ-ID', + 'scripts_bin': '/usr/bin', + 'assay': 'IMPACT468_BAITS'} + self.assertEqual(runparams, expected_runparams) + + def test_get_baits_and_targets1(self): + """ + Test that give a certain assay label, the correct one is returned + """ + self.assertEqual(get_baits_and_targets("IMPACT468_BAITS"), "IMPACT468_b37") + + def test_get_db_files(self): + """ + Test that db_files are returned correctly + """ + assay = "IDT_Exome_v1_FP_b37" + db_files = get_db_files(assay) + expected_db_files = { + 'conpair_markers': '/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt', + 'fp_genotypes': { + 'class': 'File', + 'location': 'juno:///juno/work/ci/resources/roslin_resources/targets/IDT_Exome_v1_FP/b37/FP_tiling_genotypes.txt' + }, + 'hotspot_list_maf': { + 'class': 'File', + 'location': 'juno:///juno/work/ci/resources/roslin-qc/hotspot-list-union-v1-v2.maf' + }, + 'ref_fasta': { + 'class': 'File', + 'location': 'juno:///juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta' + } + } + self.assertEqual(db_files, expected_db_files) + + def test_parse_outputs_files_data1(self): + """ + Test that a series of files are correctly organized into dict for QC input + """ + files_data = [ + {'name': 'clstats1', 'file': {'class': 'File', 'path': '/path/to/clstats1.txt'} }, + {'name': 'clstats2', 'file': {'class': 'File', 'path': '/path/to/clstats2.txt'} }, + {'name': 'md_metrics', 'file': {'class': 'File', 'path': '/path/to/md_metrics.txt'} }, + {'name': 'hs_metrics', 'file': {'class': 'File', 'path': '/path/to/hs_metrics.txt'} }, + {'name': 'insert_metrics', 'file': {'class': 'File', 'path': '/path/to/insert_metrics.txt'} }, + {'name': 'per_target_coverage', 'file': {'class': 'File', 'path': '/path/to/per_target_coverage.txt'} }, + {'name': 'qual_metrics', 'file': {'class': 'File', 'path': '/path/to/qual_metrics.txt'} }, + {'name': 'doc_basecounts', 'file': {'class': 'File', 'path': '/path/to/doc_basecounts.txt'} }, + {'name': 'conpair_pileups', 'file': {'class': 'File', 'path': '/path/to/conpair_pileups.txt'} } + ] + qc_input = parse_outputs_files_data(files_data) + expected_qc_input = { + 'clstats1': [{'class': 'File', 'path': '/path/to/clstats1.txt'}], + 'clstats2': [{'class': 'File', 'path': '/path/to/clstats2.txt'}], + 'md_metrics': [{'class': 'File', 'path': '/path/to/md_metrics.txt'}], + 'hs_metrics': [{'class': 'File', 'path': '/path/to/hs_metrics.txt'}], + 'insert_metrics': [{'class': 'File', 'path': '/path/to/insert_metrics.txt'}], + 'per_target_coverage': [{'class': 'File', 'path': '/path/to/per_target_coverage.txt'}], + 'qual_metrics': [{'class': 'File', 'path': '/path/to/qual_metrics.txt'}], + 'doc_basecounts': [{'class': 'File', 'path': '/path/to/doc_basecounts.txt'}], + 'conpair_pileups': [{'class': 'File', 'path': '/path/to/conpair_pileups.txt'}], + } + self.assertEqual(qc_input, expected_qc_input) + + + def test_build_inputs_from_run_and_ports1(self): + """ + Test generation of Roslin QC input from Roslin pipeline output Run and Port instances + """ + # load test pipeline Run output fixtures + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "dfefc47b-3ee4-4867-890f-9bab87c7f53f.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + + run_queryset = Run.objects.all() + + qc_input = build_inputs_from_runs(run_queryset) + # print(">>> printing qc_input to file") + # print(json.dumps(qc_input, indent = 4), file = open("qc_input.json", 'w')) + + # TODO: how to test output format? + self.assertEqual(len(qc_input['pairs']), 2) + self.assertEqual(len(qc_input['pairs'][0]), 2) + self.assertEqual(len(qc_input['bams']), 2) + self.assertEqual(len(qc_input['bams'][0]), 2) + + def test_load_extra_fixtures(self): + """ + Sanity test to ensure that our fixtures have not changed + """ + self.assertEqual(len(Run.objects.all()), 0) + self.assertEqual(len(Port.objects.all()), 0) + self.assertEqual(len(File.objects.all()), 0) + self.assertEqual(len(FileMetadata.objects.all()), 0) + + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + + self.assertEqual(len(Run.objects.all()), 1) + self.assertEqual(len(Port.objects.all()), 51) + self.assertEqual(len(File.objects.all()), 114) + self.assertEqual(len(FileMetadata.objects.all()), 114) + + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "dfefc47b-3ee4-4867-890f-9bab87c7f53f.run.json") + call_command('loaddata', test_files_fixture, verbosity=0) + + self.assertEqual(len(Run.objects.all()), 2) + self.assertEqual(len(Port.objects.all()), 102) + self.assertEqual(len(File.objects.all()), 168) + self.assertEqual(len(FileMetadata.objects.all()), 168) diff --git a/runner/tests/operator/roslin_qc_operator/test_roslin_qc_operator.py b/runner/tests/operator/roslin_qc_operator/test_roslin_qc_operator.py new file mode 100644 index 000000000..a439063d5 --- /dev/null +++ b/runner/tests/operator/roslin_qc_operator/test_roslin_qc_operator.py @@ -0,0 +1,96 @@ +""" +Tests for Roslin QC Operator class +""" +import os +import json +from mock import patch +from django.test import TestCase +from runner.operator.operator_factory import OperatorFactory +from runner.operator.roslin_qc_operator.roslin_qc_operator import RoslinQcOperator +from beagle_etl.models import Operator +from django.conf import settings +from django.core.management import call_command +from runner.models import Pipeline, Run +from runner.tasks import create_run_task +from pprint import pprint + +class TestRoslinQcOperator(TestCase): + fixtures = [ + "file_system.filegroup.json", + "file_system.filetype.json", + "file_system.storage.json", + "runner.pipeline.json", + "beagle_etl.operator.json" + ] + + def test_create_operator1(self): + """ + Test that a Roslin QC operator instance can be created + """ + pipeline_type = "roslin-qc" + request_id = "foo" + roslin_qc_model = Operator.objects.get(slug="roslin-qc") + operator = RoslinQcOperator(roslin_qc_model, request_id = request_id) + self.assertTrue(isinstance(operator, RoslinQcOperator)) + self.assertTrue( operator.request_id == "foo") + self.assertTrue( operator._jobs == []) + self.assertTrue( len(operator.files) == 0) + + # disable job submission to Ridgeback + @patch('runner.tasks.submit_job') + def test_direct_operator_creation(self, submit_job): + """ + Test direct Operator instantiation without Operator Factory and try to create valid jobs + """ + # self.maxDiff = None + test_files_fixture = os.path.join(settings.FIXTURES_DIR, "runs", "aa0694f1-0109-4205-a6b2-63e3e1d7c0a2.run.json") + # test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json") + call_command('loaddata', test_files_fixture, verbosity=0) + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "roslin_reference_files.json") + call_command('loaddata', test_files_fixture, verbosity=0) + + # create the operator instance + roslin_qc_model = Operator.objects.get(slug="roslin-qc") + operator = RoslinQcOperator(roslin_qc_model, run_ids = ['aa0694f1-0109-4205-a6b2-63e3e1d7c0a2']) + + # check its attributes + self.assertEqual(operator.run_ids, ['aa0694f1-0109-4205-a6b2-63e3e1d7c0a2']) + self.assertEqual(operator.get_pipeline_id(), "9b7f2ac8-03a5-4c44-ae87-1d9f6500d19a") + + # create the data for the operator run + input_data = operator.get_input_data() + # TODO: need way to recreate this for testing + # expected_input_data = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "ca18b090-03ad-4bef-acd3-52600f8e62eb.roslin-qc.input.json"))) + + output_metadata = operator.get_output_metadata() + serializer_data = operator.get_data_for_serializer(input_data, output_metadata, name = "foo name") + # pprint(serializer_data, indent = 4, stream = open('roslin-qc-job.json', "w")) + # print(json.dumps(serializer_data, indent = 4), file = open('roslin-qc-job.json', "w")) + + # check qualities of the data generated + # need to pass data through JSON because loaded JSON fixtures do not represent Python tuples embedded in data + # self.assertEqual(json.loads(json.dumps(input_data)), expected_input_data) + # self.assertEqual(output_metadata, {}) + + expected_serializer_data = { + 'app': "9b7f2ac8-03a5-4c44-ae87-1d9f6500d19a", + 'inputs': input_data, + 'name': "foo name", + 'tags': {'run_ids':['aa0694f1-0109-4205-a6b2-63e3e1d7c0a2']}, + 'output_metadata': output_metadata + } + self.assertEqual(serializer_data, expected_serializer_data) + + # create a run with the data + # make sure only 1 run exists before starting + self.assertEqual(len(Run.objects.all()), 1) + + # create and validate the jobs then use them to create Runs + jobs = operator.get_jobs() + for job in jobs: + if job[0].is_valid(): + run = job[0].save() + create_run_task(str(run.id), job[1], None) + + # make sure that a Run was made + self.assertEqual(len(Run.objects.all()), 2) diff --git a/runner/tests/operator/test_operator_factory.py b/runner/tests/operator/test_operator_factory.py index 24faa9f20..a50dff8e9 100755 --- a/runner/tests/operator/test_operator_factory.py +++ b/runner/tests/operator/test_operator_factory.py @@ -12,4 +12,4 @@ def test_operator_factory_invalid_pipeline1(self): """ pipeline_type = "foo" request_id = "bar" - self.assertRaises(Exception, OperatorFactory.get_by_model, pipeline_type, request_id=request_id) + self.assertRaises(Exception, OperatorFactory.get_by_model, pipeline_type, request_id = request_id) diff --git a/runner/tests/serializers/__init__.py b/runner/tests/serializers/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/runner/tests/serializers/test_serializers.py b/runner/tests/serializers/test_serializers.py new file mode 100644 index 000000000..b9fb9238f --- /dev/null +++ b/runner/tests/serializers/test_serializers.py @@ -0,0 +1,64 @@ +""" +Tests for serialzers +""" +from django.test import TestCase +from uuid import UUID +from runner.serializers import APIRunCreateSerializer +from runner.models import Run + +class TestSerializers(TestCase): + fixtures = [ + "file_system.filegroup.json", + "file_system.filetype.json", + "file_system.storage.json", + "runner.pipeline.json", + "beagle_etl.operator.json" + ] + + def test_create_run_serializer1(self): + """ + Test that the API Run Create Serializer works and creates a Run + """ + # start with 0 runs in the database + self.assertEqual(len(Run.objects.all()), 0) + + # data to pass to serializer + data = { + 'app': 'cb5d793b-e650-4b7d-bfcd-882858e29cc5', + 'inputs': [], + 'name': 'ROSLIN 10075_D, 1 of 1', + 'tags': {'requestId': '10075_D'} + } + + # run the serialzer + serializer = APIRunCreateSerializer(data = data) + serializer.is_valid() + run = serializer.save() + + # should be a Run in the database now + self.assertEqual(len(Run.objects.all()), 1) + + run_instance = Run.objects.all()[0] + self.assertEqual(run_instance.app_id, UUID('cb5d793b-e650-4b7d-bfcd-882858e29cc5')) + self.assertTrue(run_instance.name.startswith(data['name'])) + self.assertEqual(run_instance.tags, {'requestId': '10075_D'}) + self.assertEqual(run_instance.status, 0) + + def test_create_run_with_output_metadata1(self): + """ + Test that output_metadata propagates to the Run instance created + """ + data = { + 'app': 'cb5d793b-e650-4b7d-bfcd-882858e29cc5', + 'inputs': [], + 'name': 'foo Run', + 'output_metadata': {'assay':'IMPACT486'} + } + serializer = APIRunCreateSerializer(data = data) + serializer.is_valid() + run = serializer.save() + run_instance = Run.objects.all()[0] + self.assertEqual(run_instance.app_id, UUID('cb5d793b-e650-4b7d-bfcd-882858e29cc5')) + self.assertTrue(run_instance.name.startswith(data['name'])) + self.assertEqual(run_instance.status, 0) + self.assertEqual(run_instance.output_metadata, data['output_metadata']) diff --git a/runner/tests/views/test_run_api_view.py b/runner/tests/views/test_run_api_view.py index b91a6bb82..f5a56f6e7 100644 --- a/runner/tests/views/test_run_api_view.py +++ b/runner/tests/views/test_run_api_view.py @@ -3,7 +3,6 @@ """ import os from mock import patch -from unittest.mock import Mock from django.test import TestCase from runner.views.run_api_view import OperatorViewSet from runner.models import Run diff --git a/runner/views/run_api_view.py b/runner/views/run_api_view.py index 028175838..f2b28eb50 100644 --- a/runner/views/run_api_view.py +++ b/runner/views/run_api_view.py @@ -18,7 +18,8 @@ from rest_framework.response import Response from rest_framework.viewsets import GenericViewSet from runner.tasks import create_jobs_from_request - +from beagle_etl.models import Operator +from runner.operator.roslin_qc_operator.roslin_qc_operator import RoslinQcOperator class RunApiViewSet(mixins.ListModelMixin, mixins.CreateModelMixin, @@ -92,13 +93,25 @@ class OperatorViewSet(GenericAPIView): logger = logging.getLogger(__name__) def post(self, request): - request_ids = request.data['request_ids'] + request_ids = request.data.get('request_ids', None) + run_ids = request.data.get('run_ids', None) pipeline_name = request.data['pipeline_name'] pipeline = get_object_or_404(Pipeline, name=pipeline_name) - for request_id in request_ids: - logging.info("Submitting requestId %s to pipeline %s" % (request_id, pipeline_name)) - create_jobs_from_request.delay(request_id, pipeline.operator_id) + if pipeline_name == "roslin-qc": + logging.info("Got roslin-qc pipeline for: request_ids: {request_ids}, run_ids: {run_ids}".format(request_ids = request_ids, run_ids = run_ids)) + # create the operator instance + roslin_qc_model = Operator.objects.get(slug="roslin-qc") + operator = RoslinQcOperator(roslin_qc_model, request_id = None, run_ids = run_ids) # TODO: need to handle all request_ids + jobs = operator.get_jobs() + for job in jobs: + if job[0].is_valid(): + run = job[0].save() + create_run_task.delay(str(run.id), job[1], None) + else: + for request_id in request_ids: + logging.info("Submitting requestId %s to pipeline %s" % (request_id, pipeline_name)) + create_jobs_from_request.delay(request_id, pipeline.operator_id) # tempo_operator = TempoOperator(request_id) # jobs = tempo_operator.get_jobs() # result = [] diff --git a/scripts/complete-run-from-CWL-output.py b/scripts/complete-run-from-CWL-output.py new file mode 100755 index 000000000..55ae73425 --- /dev/null +++ b/scripts/complete-run-from-CWL-output.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +Script to mark a Beagle Run as "complete" using a pre-made JSON representing the CWL output +Use this by first creating a Run using; + + +curl -H "Content-Type: application/json" \ +-X POST \ +-H "Authorization: Bearer $$token" \ +--data '{"request_ids":["$(REQID)"], "pipeline_name": "$(PIPELINE)"}' \ +http://$(DJANGO_BEAGLE_IP):$(DJANGO_BEAGLE_PORT)/v0/run/request/ + +then, get the Run ID for the created Run (from Admin panel or other) and feed it the pre-made JSON output here to +populate all the Ports and Files for the run output +""" +import os +import sys +import django +import json + +# import django app from parent dir +parentdir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) +sys.path.insert(0, parentdir) +os.environ.setdefault("DJANGO_SETTINGS_MODULE", "beagle.settings") +django.setup() +from runner.run.objects.run_object import RunObject +sys.path.pop(0) + +run_id = sys.argv[1] +input_json = sys.argv[2] + +cwl_output = json.load(open(input_json)) +run_obj = RunObject.from_db(run_id = run_id) +run_obj.complete(outputs = cwl_output) +run_obj.to_db() diff --git a/scripts/dump_db_fixtures.py b/scripts/dump_db_fixtures.py index daffab62a..79b7e88d9 100755 --- a/scripts/dump_db_fixtures.py +++ b/scripts/dump_db_fixtures.py @@ -17,6 +17,8 @@ $ dump_db_fixtures.py port_files fd41534c-71eb-4b1b-b3af-e3b1ec3aecde +$ dump_db_fixtures.py run --onefile ca18b090-03ad-4bef-acd3-52600f8e62eb + Output ------ @@ -34,7 +36,7 @@ import json import argparse import django -from django.db.models import Prefetch +from django.db.models import Prefetch, Max from django.core import serializers from pprint import pprint @@ -44,9 +46,20 @@ os.environ.setdefault("DJANGO_SETTINGS_MODULE", "beagle.settings") django.setup() from file_system.models import File, FileMetadata, FileGroup, FileType -from runner.models import Run, RunStatus, Port, PortType, Pipeline +from runner.models import Run, RunStatus, Port, PortType, Pipeline, OperatorRun sys.path.pop(0) +def get_file_filemetadata_from_port(port_instance): + """ + Get the queryset of all File and FileMetadata entries for a given Port entry + returns a tuple of type (files_queryset, filemetadata_queryset) + """ + files_queryset = port_instance.files.all() + # filemetadata_queryset = FileMetadata.objects.filter(file__in = [i for i in files_queryset]) + filemetata_instances = [] + for file in files_queryset: + filemetata_instances.append(FileMetadata.objects.filter(file = file).order_by('-version').first()) + return(files_queryset, filemetata_instances) def dump_request(**kwargs): """ @@ -73,22 +86,75 @@ def dump_run(**kwargs): Dump re-loadable Django database fixtures for a Run entry and its associated input and output Port entries """ runID = kwargs.pop('runID') + onefile = kwargs.pop('onefile') output_run_file = "{}.run.json".format(runID) - output_port_input_file = "{}.port.input.json".format(runID) - output_port_output_file = "{}.port.output.json".format(runID) + output_port_input_file = "{}.run.port.input.json".format(runID) + output_port_output_file = "{}.run.port.output.json".format(runID) + output_port_file_input_file = "{}.run.port_file.input.json".format(runID) + output_port_filemetadata_input_file = "{}.run.port_filemetadata.input.json".format(runID) + output_port_file_output_file = "{}.run.port_file.output.json".format(runID) + output_port_filemetadata_output_file = "{}.run.port_filemetadata.output.json".format(runID) + output_operator_run_file = "{}.run.operator_run.json".format(runID) + + all_data = [] + input_files = [] + input_filemetadatas = [] + output_files = [] + output_filemetadatas = [] # get the parent Run instance run_instance = Run.objects.get(id = runID) - print(json.dumps(json.loads(serializers.serialize('json', [run_instance])), indent=4), file = open(output_run_file, "w")) - # get the Run input and output Port instances - input_queryset = run_instance.port_set.filter(port_type=PortType.INPUT) - print(json.dumps(json.loads(serializers.serialize('json', input_queryset.all())), indent=4), file = open(output_port_input_file, "w")) + operator_run_instance = run_instance.operator_run - output_queryset = run_instance.port_set.filter(port_type=PortType.OUTPUT) - print(json.dumps(json.loads(serializers.serialize('json', output_queryset.all())), indent=4), file = open(output_port_output_file, "w")) - for item in output_queryset: - pprint((item, item.files.all())) + # get the Run input and output Port instances + input_port_queryset = run_instance.port_set.filter(port_type=PortType.INPUT) + output_port_queryset = run_instance.port_set.filter(port_type=PortType.OUTPUT) + + for item in input_port_queryset: + files_queryset, filemetata_instances = get_file_filemetadata_from_port(item) + for file in files_queryset: + input_files.append(file) + for filemetadata in filemetata_instances: + input_filemetadatas.append(filemetadata) + + for item in output_port_queryset: + files_queryset, filemetata_instances = get_file_filemetadata_from_port(item) + for file in files_queryset: + output_files.append(file) + for filemetadata in filemetata_instances: + output_filemetadatas.append(filemetadata) + + # save each set of items to individual files by default + if onefile == False: + print(json.dumps(json.loads(serializers.serialize('json', [run_instance])), indent=4), file = open(output_run_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', [operator_run_instance])), indent=4), file = open(output_operator_run_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', input_port_queryset.all())), indent=4), file = open(output_port_input_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', output_port_queryset.all())), indent=4), file = open(output_port_output_file, "w")) + + print(json.dumps(json.loads(serializers.serialize('json', input_files)), indent=4), file = open(output_port_file_input_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', input_filemetadatas)), indent=4), file = open(output_port_filemetadata_input_file, "w")) + + print(json.dumps(json.loads(serializers.serialize('json', output_files)), indent=4), file = open(output_port_file_output_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', output_filemetadatas)), indent=4), file = open(output_port_filemetadata_output_file, "w")) + + # save all items to a single file + if onefile == True: + all_data.append(run_instance) + all_data.append(operator_run_instance) + for item in input_port_queryset: + all_data.append(item) + for item in output_port_queryset: + all_data.append(item) + for item in input_files: + all_data.append(item) + for item in input_filemetadatas: + all_data.append(item) + for item in output_files: + all_data.append(item) + for item in output_filemetadatas: + all_data.append(item) + print(json.dumps(json.loads(serializers.serialize('json', all_data)), indent=4), file = open(output_run_file, "w")) def dump_port_files(**kwargs): @@ -113,13 +179,23 @@ def dump_pipeline(**kwargs): Dump re-loadable Django database fixtures for Pipeline entries and related table fixtures """ pipelineName = kwargs.pop('pipelineName') - output_pipeline_file = "{}.pipeline.json".format(pipelineName) - output_pipeline_filegroup_file = "{}.pipeline.output_file_group.json".format(pipelineName) + if pipelineName == "all": + output_pipeline_file = "all_pipeline.json".format(pipelineName) + output_pipeline_filegroup_file = "all_pipeline.output_file_group.json".format(pipelineName) + + pipelines = Pipeline.objects.all() + print(json.dumps(json.loads(serializers.serialize('json', pipelines)), indent=4), file = open(output_pipeline_file, "w")) + + file_groups = FileGroup.objects.all() + print(json.dumps(json.loads(serializers.serialize('json', file_groups)), indent=4), file = open(output_pipeline_filegroup_file, "w")) + else: + output_pipeline_file = "{}.pipeline.json".format(pipelineName) + output_pipeline_filegroup_file = "{}.pipeline.output_file_group.json".format(pipelineName) - pipeline_instance = Pipeline.objects.get(name = pipelineName) - print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance])), indent=4), file = open(output_pipeline_file, "w")) + pipeline_instance = Pipeline.objects.get(name = pipelineName) + print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance])), indent=4), file = open(output_pipeline_file, "w")) - print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance.output_file_group])), indent=4), file = open(output_pipeline_filegroup_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance.output_file_group])), indent=4), file = open(output_pipeline_filegroup_file, "w")) def get_files(value, type): """ @@ -178,6 +254,14 @@ def dump_file(**kwargs): output_file = "all.file_filemetadata.json" print(json.dumps(all_data, indent=4), file = open(output_file, "w")) +def dump_file_group(**kwargs): + """ + Dump the FileGroup fixtures + """ + fileGroupId = kwargs.pop('fileGroupID') + output_file_group_file = "{}.file_group.json".format(fileGroupId) + filegroup_instance = FileGroup.objects.get(id = fileGroupId) + print(json.dumps(json.loads(serializers.serialize('json', [filegroup_instance])), indent=4), file = open(output_file_group_file, "w")) def parse(): """ @@ -193,6 +277,7 @@ def parse(): run = subparsers.add_parser('run', help = 'Dump output data for pipeline run') run.add_argument('runID', help = 'Run ID to dump items for') + run.add_argument('--onefile', action = "store_true", help = 'Put all the outputs into a single file ') run.set_defaults(func = dump_run) pipeline = subparsers.add_parser('pipeline', help = 'Dump pipeline fixture') @@ -210,6 +295,10 @@ def parse(): port_files.add_argument('portID', help = 'Port ID to dump files for') port_files.set_defaults(func = dump_port_files) + file_group = subparsers.add_parser('filegroup', help = 'Dump filegroup fixture') + file_group.add_argument('fileGroupID', help = 'FileGroup ID ID to dump items for') + file_group.set_defaults(func = dump_file_group) + args = parser.parse_args() args.func(**vars(args)) diff --git a/scripts/duplicate_fixtures.py b/scripts/duplicate_fixtures.py new file mode 100755 index 000000000..152098619 --- /dev/null +++ b/scripts/duplicate_fixtures.py @@ -0,0 +1,198 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +Script to use for creating a modified, non-conflicting duplicate of an existing database fixture +Use this after you have dumped some fixtures to a .json file using `dump_db_fixtures.py`, and now you +want another fixture set that has different UUIDs and identifiers so you can load both at once in a dev database +in order to get work done with them. + +Input: .json file produced by dump_db_fixtures.py + +Output: a new .json file with updated key values + +Usage +----- + ./duplicate_fixtures.py ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json + +Notes +----- +The input .json file must have been produced with 'indent = 4' or have equivalent indenting, or this script will probably not work +""" +import os +import sys +import json +import uuid +import copy +import re +import time +import argparse + +def get_unique_id(): + """ + Get a unique ID + maybe replace with with uuid4? + uuid1 has a lower chance of duplicate id's being generated + + TODO: see what Sinisa thinks about this later + """ + return(uuid.uuid1()) + +def replace_primary_keys(input_file, no_change_files): + """ + Replaces all primary keys in the file with new values + """ + # get all primary keys that need to be changed + all_pk = [] + with open(input_file) as f: + for item in json.load(f): + # do not change the pk's on 'File' objects because that causes unique constraint issues on file path + if item['model'] != 'file_system.file': + all_pk.append(item['pk']) + elif item['model'] == 'file_system.file': + if no_change_files == True: + pass + elif no_change_files == False: + all_pk.append(item['pk']) + + # sort unique based on descending length + # this makes sure we replace the longer pattern first in the next steps + all_pk = sorted(list(set(all_pk)), key = len, reverse=True) + + # load all lines of text from the file + lines = open(input_file).readlines() + + # make a copy for editing + output_lines = copy.deepcopy(lines) + + editted_lines = [] + + # search for every primary key in every line of text ... !! Yes, we are doing this + for old_pk in all_pk: + new_pk = str(get_unique_id()) + for i, old_line in enumerate(lines): + if old_pk in old_line: + # I think this only replaces first intance of the pattern? shouldnt matter for this if you printed JSON with indent = 4 + new_line = re.sub(old_pk, new_pk, output_lines[i]) + output_lines[i] = new_line + + # each line should only get editted one time doing this otherwise something is wrong + if i not in editted_lines: + editted_lines.append(i) + else: + print("ERROR: line {} is about to get editted twice; that is not supposed to happen something is wrong".format(i)) + raise + return(output_lines) + +def get_field_values(input_lines, field_name): + """ + Finds a list of all unique values for a given field in the file lines + + examples: + + "runId": "PITT_0390", + >>> ["PITT_0390"] + + "requestId": "09670_D_1581808018", + "sampleId": "09670_D_1", + "patientId": "C-K2902H", + "sampleName": "C-K2902H-P001-d", + "externalSampleId": "S16-68609", + "investigatorSampleId": "S16-68609", + """ + all_values = set() + search_pattern = '.*"{field_name}": "(.*)"'.format(field_name = field_name) + for line in input_lines: + match = re.search(search_pattern, line) + if match != None: + value = match.group(1) + all_values.add(value) + + # return reverse sorted on length to ensure sub-patterns do not get replaced first later + all_values = sorted(list(set(all_values)), key = len, reverse=True) + return(all_values) + +def replace_field_value(input_lines, field_name, old_value, new_value): + """ + Replace the old value for a field with the new value in all file lines + """ + # make a copy for editing + output_lines = copy.deepcopy(input_lines) + + fieldname_search_pattern = '"{field_name}":'.format(field_name = field_name) + + # search for the field label in all lines and replace the value if found + for i, line in enumerate(input_lines): + # check that its a line with the desired field name in it + line_match = re.search(fieldname_search_pattern, line) + if line_match != None: + # check that the desired value to be changed is present + id_match = re.search(old_value, line) + if id_match != None: + # replace the old value with the new value + new_line = re.sub(old_value, new_value, output_lines[i]) + output_lines[i] = new_line + return(output_lines) + +def main(**kwargs): + """ + Main function for editing a fixtures file to replace all old primary keys with new keys + So that both old and new fixtures sets can be loaded into the database at the same time + """ + input_file = kwargs.pop('input_file') + output_file = kwargs.pop('output_file', None) + no_change_files = kwargs.pop('output_file', False) + + if output_file == None: + output_file_name = "{}.duplicated.json".format(input_file) + else: + output_file_name = output_file + + # generate a timestamp string to use for new unique identifiers + timestamp_str = str(int(time.time())) + + # replace all the primary keys with new values; need special handling for pk's because they do not always have a field label in the file + output_lines = replace_primary_keys(input_file, no_change_files) + + # replace the values for all of these other desired fields; these fields are always clearly labeled in the file so they are easy to find + fields_to_change = [ + 'runId', + 'requestId', + 'sampleId', + 'patientId', + 'sampleName', + 'externalSampleId', + 'investigatorSampleId', + 'file_name', + 'path' + ] + for field_name in fields_to_change: + all_values = get_field_values(input_lines = output_lines, field_name = field_name) + for old_value in all_values: + # make a new value by appending the timestamp + if field_name in ['file_name', 'path']: + # special handling for adding timestamp to file paths + name, ext = os.path.splitext(old_value) + new_value = name + '.' + timestamp_str + ext + else: + new_value = old_value + '_' + timestamp_str + output_lines = replace_field_value(input_lines = output_lines, field_name = field_name, old_value = old_value, new_value = new_value) + + # save the output files + with open(output_file_name, "w") as fout: + fout.writelines(output_lines) + +def parse(): + """ + Parses script args + Script arg parsing will go here as this script grows + """ + parser = argparse.ArgumentParser(description = 'Duplicate database fixtures that were previously dumped in json format with indentation') + parser.add_argument('input_file', help = "Input file containing fixtures") + parser.add_argument('--output-file', dest = "output_file", default = None, help = "Name of output file to write to") + parser.add_argument('--no-change-files', dest = "no_change_files", action = 'store_true', help = "Dont change the File items' primary keys and paths") + + args = parser.parse_args() + main(**vars(args)) + +if __name__ == '__main__': + parse()