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

@@ -1,19 +1,54 @@
 interactions:
 - request:
-    body: "--a140cd8d08d737fbd07610f0ad944f32\r\nContent-Disposition: form-data; name=\"workflowSource\";
+    body: "--f947081d17ca51d9ce53dfa7ea9ff40f\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
-      DEFINITION\n\nworkflow HelloDockerHostname {\n  call Hostname {\n  }\n\n  output
-      {\n    File stdout = Hostname.out\n  }\n\n  parameter_meta {\n    stdout: \"hostname
-      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:
+      1.0\n## This is a test workflow that returns the Docker image name and tag\n##
+      and measures execution time of the Hostname task.\n\n#### WORKFLOW DEFINITION\n\nworkflow
+      HelloDockerHostname {\n  input {\n    String docker_image = \"ubuntu:20.04\"
+      \ # Default value but can be overridden\n  }\n\n  call GetStartTime\n\n  call
+      Hostname {\n    input:\n      expected_image = docker_image,\n      start_time
+      = GetStartTime.timestamp  # Add dependency on start time\n  }\n\n  call GetEndTime
+      {\n    input:\n      hostname_done = Hostname.out  # Add dependency on Hostname
+      completion\n  }\n\n  call ValidateExecutionTime {\n    input:\n      start_time
+      = GetStartTime.timestamp,\n      end_time = GetEndTime.timestamp\n  }\n\n  output
+      {\n    File stdout = Hostname.out\n    Float execution_time_seconds = ValidateExecutionTime.duration_seconds\n
+      \   Boolean within_time_limit = ValidateExecutionTime.within_limit\n  }\n\n
+      \ parameter_meta {\n    docker_image: \"Docker image to run the task in (e.g.
+      ubuntu:latest)\"\n  }\n}\n\n#### TASK DEFINITIONS\n\ntask GetStartTime {\n  command
+      <<<\n    date +%s.%N\n  >>>\n\n  output {\n    Float timestamp = read_float(stdout())\n
+      \ }\n\n  runtime {\n    docker: \"ubuntu:20.04\"\n    cpu: 1\n    memory: \"1
+      GB\"\n  }\n}\n\ntask GetEndTime {\n  input {\n    File hostname_done  # Add
+      dependency on Hostname completion\n  }\n\n  command <<<\n    date +%s.%N\n  >>>\n\n
+      \ output {\n    Float timestamp = read_float(stdout())\n  }\n\n  runtime {\n
+      \   docker: \"ubuntu:20.04\"\n    cpu: 1\n    memory: \"1 GB\"\n  }\n}\n\ntask
+      ValidateExecutionTime {\n  input {\n    Float start_time\n    Float end_time\n
+      \ }\n\n  command <<<\n    # Calculate duration using awk for floating point
+      arithmetic\n    duration=$(awk \"BEGIN {print ~{end_time} - ~{start_time}}\")\n
+      \   echo \"$duration\" > duration.txt\n    \n    # Check if duration is less
+      than 120 seconds (2 minutes)\n    awk -v dur=\"$duration\" 'BEGIN {if (dur <
+      120) exit 0; exit 1}'\n    if [ $? -eq 0 ]; then\n      echo \"true\" > within_limit.txt\n
+      \   else\n      echo \"false\" > within_limit.txt\n    fi\n  >>>\n\n  output
+      {\n    Float duration_seconds = read_float(\"duration.txt\")\n    Boolean within_limit
+      = read_boolean(\"within_limit.txt\")\n  }\n\n  runtime {\n    docker: \"ubuntu:20.04\"\n
+      \   cpu: 1\n    memory: \"1 GB\"\n  }\n}\n\ntask Hostname {\n  input {\n    String
+      expected_image\n    Float start_time  # Add start_time as input to create dependency\n
+      \ }\n\n  command <<<\n    # Split expected image into name and tag\n    EXPECTED_IMAGE_NAME=$(echo
+      \"~{expected_image}\" | cut -d':' -f1)\n    EXPECTED_TAG=$(echo \"~{expected_image}\"
+      | cut -d':' -f2)\n\n    # Get current image info\n    CURRENT_IMAGE=$(grep \"ID=\"
+      /etc/os-release | head -n1 | cut -d'=' -f2)\n    CURRENT_VERSION=$(grep \"VERSION_ID=\"
+      /etc/os-release | cut -d'\"' -f2)\n\n    # Compare image name\n    if [[ \"$CURRENT_IMAGE\"
+      != \"$EXPECTED_IMAGE_NAME\" ]]; then\n      echo \"Error: Expected Docker image
+      $EXPECTED_IMAGE_NAME but got: $CURRENT_IMAGE\"\n      exit 1\n    fi\n\n    #
+      Compare version/tag\n    if [[ \"$CURRENT_VERSION\" != \"$EXPECTED_TAG\" ]];
+      then\n      echo \"Error: Expected version $EXPECTED_TAG but got: $CURRENT_VERSION\"\n
+      \     exit 1\n    fi\n\n    echo \"Verified Docker Image: $CURRENT_IMAGE:$CURRENT_VERSION\"\n
+      \   echo \"Expected Image: ~{expected_image}\"\n    echo \"Hostname: $(hostname)\"\n
+      \ >>>\n\n  output {\n    File out = stdout()\n  }\n\n  runtime {\n    cpu: 1\n
+      \   memory: \"1 GB\"\n    docker: \"~{expected_image}\"\n  }\n\n  parameter_meta
+      {\n    expected_image: \"Docker image that should be running this task\"\n  }\n}\n\r\n--f947081d17ca51d9ce53dfa7ea9ff40f\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--f947081d17ca51d9ce53dfa7ea9ff40f--\r\n"
     headers:
       accept:
       - '*/*'
@@ -22,18 +57,18 @@ interactions:
       connection:
       - keep-alive
       content-length:
-      - '1120'
+      - '3904'
       content-type:
-      - multipart/form-data; boundary=a140cd8d08d737fbd07610f0ad944f32
+      - multipart/form-data; boundary=f947081d17ca51d9ce53dfa7ea9ff40f
       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":"bd701a72-0f44-4305-a287-a4f389b79608","status":"Submitted"}'
     headers:
       Connection:
       - keep-alive
@@ -42,7 +77,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Tue, 11 Feb 2025 07:38:44 GMT
       Server:
       - nginx/1.25.3
     status:
@@ -60,14 +95,14 @@ 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/bd701a72-0f44-4305-a287-a4f389b79608/abort
   response:
     body:
-      string: '{"id":"8c838f7b-f771-4cc5-94bc-a509f26dbcf0","status":"Aborted"}'
+      string: '{"id":"bd701a72-0f44-4305-a287-a4f389b79608","status":"Aborted"}'
     headers:
       Connection:
       - keep-alive
@@ -76,7 +111,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Tue, 11 Feb 2025 07:38:44 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: "--eba35b3a333a10d4292171ad0ec20510\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--eba35b3a333a10d4292171ad0ec20510\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--eba35b3a333a10d4292171ad0ec20510--\r\n"
     headers:
       accept:
       - '*/*'
@@ -23,16 +23,16 @@ interactions:
       content-length:
       - '1071'
       content-type:
-      - multipart/form-data; boundary=35d29ba0213e6a30bee8707a58c65735
+      - multipart/form-data; boundary=eba35b3a333a10d4292171ad0ec20510
       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":"5b7becef-b90a-4286-8901-068785a631db","status":"Submitted"}'
     headers:
       Connection:
       - keep-alive
@@ -41,7 +41,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Tue, 11 Feb 2025 07:38:44 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/v1/5b7becef-b90a-4286-8901-068785a631db/abort
   response:
     body:
-      string: '{"id":"ec04a1f3-7ae5-4ab9-9b96-44ccd289d02e","status":"Aborted"}'
+      string: '{"id":"5b7becef-b90a-4286-8901-068785a631db","status":"Aborted"}'
     headers:
       Connection:
       - keep-alive
@@ -75,7 +75,7 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Tue, 28 Jan 2025 19:20:42 GMT
+      - Tue, 11 Feb 2025 07:38:44 GMT
       Server:
       - nginx/1.25.3
     status: