more test json

4dn-dcic · Mar 6, 2019 · b958d78 · b958d78
1 parent d2e74b8
commit b958d78
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Showing 8 changed files with 235 additions and 26 deletions.
diff --git a/core/launch_utils.py b/core/launch_utils.py
@@ -35,7 +35,7 @@ def clear_awsem_template(awsem_template):
         del(awsem_template['_tibanna']['response'])
     if 'run_name' in awsem_template['_tibanna'] and len(awsem_template['_tibanna']['run_name']) > 40:
         awsem_template['_tibanna']['run_name'] = awsem_template['_tibanna']['run_name'][:-36]
-        awsem_template['config']['run_name'] = awsem_template['config']['run_name'][:-36]
+        awsem_template['config']['run_name'] = awsem_template['_tibanna']['run_name']
 
 
 def rerun(exec_arn, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME, override_config=None, app_name_filter=None, name=None):

diff --git a/test_json/pony/encode_atacseq-postaln5.json b/test_json/pony/encode_atacseq-postaln5.json
@@ -0,0 +1,45 @@
+{
+    "_tibanna": {
+      "run_type": "encode-atacseq-postaln-mergebedtest",
+      "env": "fourfront-webdev"
+    },
+    "app_name": "encode-atacseq-postaln",
+    "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+    "workflow_uuid": "4dn-dcic-lab:wf-encode-atacseq-postaln",
+    "parameters": { 
+        "atac.pipeline_type" : "atac",
+        "atac.paired_end" : true,
+        "atac.gensz" : "hs",
+        "atac.disable_ataqc": true,
+        "atac.enable_xcor": false
+    },
+    "input_files" : [
+       { 
+           "workflow_argument_name": "atac.tas", 
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-wfoutput",
+           "uuid": ["46147bfe-a9ed-4546-9b29-263c2cbc10f5", "b32b98ed-664d-4146-bbb9-4a533e4d1fb9"],
+           "object_key": ["4DNFIVQKKYUZ.bed.gz", "4DNFIPO7AHBE.bed.gz"],
+           "rename": ["4DNFIVQKKYUZ.tagAlign.gz", "4DNFIPO7AHBE.tagAlign.gz"]
+       },
+       { 
+           "workflow_argument_name": "atac.blacklist", 
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "9562ffbd-9f7a-4bd7-9c10-c335137d8966",
+           "object_key": "4DNFIZ1TGJZR.bed.gz"
+       },
+       { 
+           "workflow_argument_name": "atac.chrsz", 
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "9866d158-da3c-4d9b-96a9-1d59632eabeb",
+           "object_key": "4DNFIZJB62D1.chrom.sizes"
+       }
+  ],
+  "config": { 
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": "",
+    "email": true
+  },
+  "dependency": { "exec_arn": ["arn:aws:states:us-east-1:643366669028:execution:tibanna_pony:mergebed-test_fc11acaa-67f7-4da5-aade-0b42e5e5759b",
+                               "arn:aws:states:us-east-1:643366669028:execution:tibanna_pony:mergebed-test_7a501bb5-11f9-4afe-aa24-458455e284e7"]}
+}
diff --git a/test_json/pony/mergebed.2.json b/test_json/pony/mergebed.2.json
@@ -0,0 +1,26 @@
+{
+    "_tibanna": {
+      "run_type": "mergebed-test",
+      "env": "fourfront-webdev"
+    },
+    "app_name": "mergebed",
+    "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+    "workflow_uuid": "2b10e472-065e-43ed-992c-fccad6417b65",
+    "parameters" :  {"sortv": "0"},
+    "input_files" : [
+       {
+           "workflow_argument_name": "input_bed",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-wfoutput",
+           "object_key": ["4DNFIR8RTKAA.bed.gz"],
+           "uuid": ["a039c92b-67ff-4c90-9ebc-986ee76d7b5d"]
+       }
+  ],
+  "config": {
+    "ebs_type": "io1",
+    "ebs_iops": 500,
+    "shutdown_min": 30,
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": ""
+  }
+}
diff --git a/test_json/pony/mergebed.3.json b/test_json/pony/mergebed.3.json
@@ -0,0 +1,26 @@
+{
+    "_tibanna": {
+      "run_type": "mergebed-test",
+      "env": "fourfront-webdev"
+    },
+    "app_name": "mergebed",
+    "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+    "workflow_uuid": "2b10e472-065e-43ed-992c-fccad6417b65",
+    "parameters" :  {"sortv": "0"},
+    "input_files" : [
+       {
+           "workflow_argument_name": "input_bed",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-wfoutput",
+           "object_key": ["4DNFI5RC8NP6.bed.gz"],
+           "uuid": ["009f9282-9c9e-4608-8b94-60410af34d05"]
+       }
+  ],
+  "config": {
+    "ebs_type": "io1",
+    "ebs_iops": 500,
+    "shutdown_min": 30,
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": ""
+  }
+}
diff --git a/test_json/pony/repliseq_parta-pony.v16.pe.json b/test_json/pony/repliseq_parta-pony.v16.pe.json
@@ -0,0 +1,44 @@
+{
+  "_tibanna": {
+    "env": "fourfront-webdev",
+    "run_type": "repliseq-parta"
+  },
+  "app_name": "repliseq-parta",
+  "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+  "workflow_uuid": "4dn-dcic-lab:wf-repliseq-parta-v16",
+  "parameters" :  { "nthreads": 4, "memperthread": "2G" },
+  "input_files" : [
+       {
+           "object_key": "4DNFIZQZ39L9.bwaIndex.tgz",
+           "workflow_argument_name": "bwaIndex",
+           "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+       },
+       { 
+           "workflow_argument_name": "fastq", 
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "a6ffb820-c600-4c32-9d99-249ed8029022",
+           "object_key": "4DNFI2ZDNVFL.fastq.gz"
+       },
+       { 
+           "workflow_argument_name": "fastq2", 
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "a6ffb820-c600-4c32-9d99-249ed8029022",
+           "object_key": "4DNFI2ZDNVFL.fastq.gz"
+       },
+       {
+           "object_key": "4DNFI823LSII.chrom.sizes",
+           "workflow_argument_name": "chromsizes",
+           "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+      }
+  ],
+  "config": {
+    "ebs_type": "io1",
+    "ebs_iops": 500,
+    "shutdown_min": "now",
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": ""
+  }
+}
diff --git a/test_json/pony/repliseq_parta-pony.v16.pe2.json b/test_json/pony/repliseq_parta-pony.v16.pe2.json
@@ -0,0 +1,44 @@
+{
+  "_tibanna": {
+    "env": "fourfront-webdev",
+    "run_type": "repliseq-parta"
+  },
+  "app_name": "repliseq-parta",
+  "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+  "workflow_uuid": "4dn-dcic-lab:wf-repliseq-parta-v16",
+  "parameters" :  { "nthreads": 4, "memperthread": "2G" },
+  "input_files" : [
+       {
+           "object_key": "4DNFIZQZ39L9.bwaIndex.tgz",
+           "workflow_argument_name": "bwaIndex",
+           "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+       },
+       {
+           "workflow_argument_name": "fastq",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "a6ffb820-c600-4c32-9d99-249ed8029022",
+           "object_key": "4DNFI2ZDNVFL.fastq.gz"
+       },
+       {
+           "workflow_argument_name": "fastq2",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "17ef719b-8b68-418e-8c39-776022b31585",
+           "object_key": "4DNFIB7L4NFG.fastq.gz"
+       },
+       {
+           "object_key": "4DNFI823LSII.chrom.sizes",
+           "workflow_argument_name": "chromsizes",
+           "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+      }
+  ],
+  "config": {
+    "ebs_type": "io1",
+    "ebs_iops": 500,
+    "shutdown_min": "now",
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": ""
+  }
+}
diff --git a/test_json/pony/repliseq_parta-pony.v16.se.json b/test_json/pony/repliseq_parta-pony.v16.se.json
@@ -0,0 +1,38 @@
+{
+  "_tibanna": {
+    "env": "fourfront-webdev",
+    "run_type": "repliseq-parta"
+  },
+  "app_name": "repliseq-parta",
+  "output_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput",
+  "workflow_uuid": "4dn-dcic-lab:wf-repliseq-parta-v16",
+  "parameters" :  { "nthreads": 4, "memperthread": "2G" },
+  "input_files" : [
+       {
+           "object_key": "4DNFIZQZ39L9.bwaIndex.tgz",
+           "workflow_argument_name": "bwaIndex",
+           "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+       },
+       {
+           "workflow_argument_name": "fastq",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files",
+           "uuid": "a6ffb820-c600-4c32-9d99-249ed8029022",
+           "object_key": "4DNFI2ZDNVFL.fastq.gz"
+       },
+       {
+           "object_key": "4DNFI823LSII.chrom.sizes",
+           "workflow_argument_name": "chromsizes",
+           "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9",
+           "bucket_name": "elasticbeanstalk-fourfront-webdev-files"
+      }
+  ],
+  "config": {
+    "ebs_type": "io1",
+    "ebs_iops": 500,
+    "shutdown_min": "now",
+    "password": "dragonfly",
+    "log_bucket": "tibanna-output",
+    "key_name": ""
+  }
+}
diff --git a/test_json/unicorn/my_test_tibanna_bucket2.json b/test_json/unicorn/my_test_tibanna_bucket2.json
@@ -1,37 +1,23 @@
 {
   "args": {
     "app_name": "md5",
-    "input_parameters": {},
-    "cwl_child_filenames": [],
-    "cwl_version": "draft-3",
-    "output_target": {
-      "report": "my_outdir/report"
-    },
-    "secondary_output_target": {},
+    "app_version": "0.2.6",
+    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
     "cwl_main_filename": "md5.cwl",
-    "secondary_files": {},
-    "output_S3_bucket": "soo2-tibanna-data",
-    "app_version": "0.0.4",
-    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.0.4/cwl_awsem/",
+    "cwl_version": "v1",
     "input_files": {
       "input_file": {
-        "bucket_name": "soo2-tibanna-data",
-        "object_key": "somefastqfile.fastq.gz"
+        "bucket_name": "soos-4dn-bucket",
+        "object_key": "test.txt"
       }
+    },
+    "output_S3_bucket": "my-tibanna-test-bucket",
+    "output_target": {
+      "report": "my_outdir/report"
     }
   },
   "config": {
-    "ebs_size": 0,
-    "ebs_type": "io1",
-    "json_bucket": "soo2-tibanna-log",
-    "EBS_optimized": "",
-    "ebs_iops": 500,
-    "shutdown_min": 120,
-    "instance_type": "",
-
-
-    "password": "dragonfly",
-    "log_bucket": "soo2-tibanna-log",
-    "key_name": ""
+    "run_name": "md5-public-test",
+    "log_bucket": "my-tibanna-test-bucket"
   }
 }