Adding all WDL unit tests to API pytests

WildcardsandConditions/options.json

@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

badRunParseBatchFile/options.json

@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

badValMissingValue/options.json

@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

basicTaskExecution/basicTaskExecution.wdl

@@ -21,8 +21,8 @@ task simpleTask {
   }
 
   command <<<
-    echo "${message}" > output.txt
-    >>>
+    echo "~{message}" > output.txt
+  >>>
 
   output {
     File outputFile = "output.txt"

basicTaskExecution/options.json

@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

testFileoperations/options.json

@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

tests/cromwellapi/cassettes/test-abort/test_abort[helloDockerHostname].yaml

@@ -1,6 +1,6 @@
 interactions:
 - request:
-    body: "--a140cd8d08d737fbd07610f0ad944f32\r\nContent-Disposition: form-data; name=\"workflowSource\";
+    body: "--3a33f97fa4b5785f1d1b22af669d44f6\r\nContent-Disposition: form-data; name=\"workflowSource\";
       filename=\"helloDockerHostname.wdl\"\r\nContent-Type: application/octet-stream\r\n\r\nversion
       1.0\n## This is a test workflow that returns the hostname of the node \n## the
       job is submitted to as a test for Docker functionality on Gizmo.\n\n#### WORKFLOW
@@ -9,11 +9,11 @@ interactions:
       of the node the job was submitted to\"\n  }\n}\n\n#### TASK DEFINITIONS\n\ntask
       Hostname {\n  command <<<\n    echo $(hostname)\n  >>>\n\n  output {\n    File
       out = stdout()\n  }\n\n  runtime {\n    cpu: 1\n    memory: \"1 GB\"\n    docker:
-      \"ubuntu:latest\"\n  }\n\n  parameter_meta {\n    out: \"hostname of the node
-      the job was submitted to\"\n  }\n}\n\r\n--a140cd8d08d737fbd07610f0ad944f32\r\nContent-Disposition:
+      \"ubuntu:20.04\"\n  }\n\n  parameter_meta {\n    out: \"hostname of the node
+      the job was submitted to\"\n  }\n}\n\r\n--3a33f97fa4b5785f1d1b22af669d44f6\r\nContent-Disposition:
       form-data; name=\"workflowOptions\"; filename=\"options.json\"\r\nContent-Type:
       application/json\r\n\r\n{\n    \"workflow_failure_mode\": \"ContinueWhilePossible\",\n
-      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--a140cd8d08d737fbd07610f0ad944f32--\r\n"
+      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--3a33f97fa4b5785f1d1b22af669d44f6--\r\n"
     headers:
       accept:
       - '*/*'
@@ -22,18 +22,18 @@ interactions:
       connection:
       - keep-alive
       content-length:
-      - '1120'
+      - '1119'
       content-type:
-      - multipart/form-data; boundary=a140cd8d08d737fbd07610f0ad944f32
+      - multipart/form-data; boundary=3a33f97fa4b5785f1d1b22af669d44f6
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1
   response:
     body:
-      string: '{"id":"8c838f7b-f771-4cc5-94bc-a509f26dbcf0","status":"Submitted"}'
+      string: '{"id":"6db86d52-d876-4f96-b0f8-ff56df46d15e","status":"Submitted"}'
     headers:
       Connection:
       - keep-alive
@@ -42,7 +42,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status:
@@ -60,14 +60,14 @@ interactions:
       content-length:
       - '0'
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1/8c838f7b-f771-4cc5-94bc-a509f26dbcf0/abort
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1/6db86d52-d876-4f96-b0f8-ff56df46d15e/abort
   response:
     body:
-      string: '{"id":"8c838f7b-f771-4cc5-94bc-a509f26dbcf0","status":"Aborted"}'
+      string: '{"id":"6db86d52-d876-4f96-b0f8-ff56df46d15e","status":"Aborted"}'
     headers:
       Connection:
       - keep-alive
@@ -76,7 +76,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status:

tests/cromwellapi/cassettes/test-abort/test_abort[helloHostname].yaml

@@ -1,6 +1,6 @@
 interactions:
 - request:
-    body: "--35d29ba0213e6a30bee8707a58c65735\r\nContent-Disposition: form-data; name=\"workflowSource\";
+    body: "--ce533472646b2abdc3163de323107ea1\r\nContent-Disposition: form-data; name=\"workflowSource\";
       filename=\"helloHostname.wdl\"\r\nContent-Type: application/octet-stream\r\n\r\nversion
       1.0\n## This is a test workflow that returns the hostname of the node \n## the
       job is submitted to as a test for the Gizmo backend. \n\n#### WORKFLOW DEFINITION\n\nworkflow
@@ -9,10 +9,10 @@ interactions:
       to\"\n  }\n}\n\n#### TASK DEFINITIONS\n\ntask Hostname {\n  command <<<\n    echo
       $(hostname)\n  >>>\n\n  output {\n    File out = stdout()\n  }\n  \n  runtime
       {\n    cpu: 1\n    memory: \"1 GB\"\n  }\n\n  parameter_meta {\n    out: \"hostname
-      of the node the job was submitted to\"\n  }\n}\n\r\n--35d29ba0213e6a30bee8707a58c65735\r\nContent-Disposition:
+      of the node the job was submitted to\"\n  }\n}\n\r\n--ce533472646b2abdc3163de323107ea1\r\nContent-Disposition:
       form-data; name=\"workflowOptions\"; filename=\"options.json\"\r\nContent-Type:
       application/json\r\n\r\n{\n    \"workflow_failure_mode\": \"ContinueWhilePossible\",\n
-      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--35d29ba0213e6a30bee8707a58c65735--\r\n"
+      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--ce533472646b2abdc3163de323107ea1--\r\n"
     headers:
       accept:
       - '*/*'
@@ -23,16 +23,16 @@ interactions:
       content-length:
       - '1071'
       content-type:
-      - multipart/form-data; boundary=35d29ba0213e6a30bee8707a58c65735
+      - multipart/form-data; boundary=ce533472646b2abdc3163de323107ea1
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1
   response:
     body:
-      string: '{"id":"ec04a1f3-7ae5-4ab9-9b96-44ccd289d02e","status":"Submitted"}'
+      string: '{"id":"6ebad157-22f0-4767-b1ce-30093f315f32","status":"Submitted"}'
     headers:
       Connection:
       - keep-alive
@@ -41,7 +41,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status:
@@ -59,14 +59,14 @@ interactions:
       content-length:
       - '0'
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1/ec04a1f3-7ae5-4ab9-9b96-44ccd289d02e/abort
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1/6ebad157-22f0-4767-b1ce-30093f315f32/abort
   response:
     body:
-      string: '{"id":"ec04a1f3-7ae5-4ab9-9b96-44ccd289d02e","status":"Aborted"}'
+      string: '{"id":"6ebad157-22f0-4767-b1ce-30093f315f32","status":"Aborted"}'
     headers:
       Connection:
       - keep-alive
@@ -75,7 +75,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status:

tests/cromwellapi/cassettes/test-abort/test_abort[helloModuleHostname].yaml

@@ -1,6 +1,6 @@
 interactions:
 - request:
-    body: "--02624d37f2fd65af51a47311135684b2\r\nContent-Disposition: form-data; name=\"workflowSource\";
+    body: "--6db9b6995fd0324a84bdf128cd23787a\r\nContent-Disposition: form-data; name=\"workflowSource\";
       filename=\"helloModuleHostname.wdl\"\r\nContent-Type: application/octet-stream\r\n\r\nversion
       1.0\n## This is a test workflow that returns the hostname of the node \n## the
       job is submitted to as a test for module functionality on Gizmo.\n\n#### WORKFLOW
@@ -10,10 +10,10 @@ interactions:
       Hostname {\n  command <<<\n    echo $(hostname)\n  >>>\n\n  output {\n    File
       out = stdout()\n  }\n\n  runtime {\n    cpu: 1\n    memory: \"1 GB\"\n    modules:
       \"Python/3.7.4-foss-2019b-fh1\"\n  }\n\n  parameter_meta {\n    out: \"hostname
-      of the node the job was submitted to\"\n  }\n}\n\r\n--02624d37f2fd65af51a47311135684b2\r\nContent-Disposition:
+      of the node the job was submitted to\"\n  }\n}\n\r\n--6db9b6995fd0324a84bdf128cd23787a\r\nContent-Disposition:
       form-data; name=\"workflowOptions\"; filename=\"options.json\"\r\nContent-Type:
       application/json\r\n\r\n{\n    \"workflow_failure_mode\": \"ContinueWhilePossible\",\n
-      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--02624d37f2fd65af51a47311135684b2--\r\n"
+      \   \"write_to_cache\": false,\n    \"read_from_cache\": false\n}\n\r\n--6db9b6995fd0324a84bdf128cd23787a--\r\n"
     headers:
       accept:
       - '*/*'
@@ -24,16 +24,16 @@ interactions:
       content-length:
       - '1135'
       content-type:
-      - multipart/form-data; boundary=02624d37f2fd65af51a47311135684b2
+      - multipart/form-data; boundary=6db9b6995fd0324a84bdf128cd23787a
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1
   response:
     body:
-      string: '{"id":"8761261f-03aa-4409-b913-8933c5215f1b","status":"Submitted"}'
+      string: '{"id":"652e4441-abb3-413f-b861-c354d5c3ba4f","status":"Submitted"}'
     headers:
       Connection:
       - keep-alive
@@ -42,7 +42,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status:
@@ -60,14 +60,14 @@ interactions:
       content-length:
       - '0'
       host:
-      - gizmok96.fhcrc.org:38031
+      - gizmoj32.fhcrc.org:35541
       user-agent:
       - python-httpx/0.28.1
     method: POST
-    uri: https://gizmok96.fhcrc.org:38031/api/workflows/v1/8761261f-03aa-4409-b913-8933c5215f1b/abort
+    uri: https://gizmoj32.fhcrc.org:35541/api/workflows/v1/652e4441-abb3-413f-b861-c354d5c3ba4f/abort
   response:
     body:
-      string: '{"id":"8761261f-03aa-4409-b913-8933c5215f1b","status":"Aborted"}'
+      string: '{"id":"652e4441-abb3-413f-b861-c354d5c3ba4f","status":"Aborted"}'
     headers:
       Connection:
       - keep-alive
@@ -76,7 +76,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Thu, 06 Feb 2025 05:26:59 GMT
       Server:
       - nginx/1.25.3
     status: