various

archive_docker_workflow.cwl

@@ -0,0 +1,140 @@
+#!/usr/bin/env cwl-runner
+#
+# Main workflow.  Runs through synthetic data and submits to internal queue
+# Inputs:
+#   submissionId: ID of the Synapse submission to process
+#   adminUploadSynId: ID of a folder accessible only to the submission queue administrator
+#   submitterUploadSynId: ID of a folder accessible to the submitter
+#   workflowSynapseId:  ID of the Synapse entity containing a reference to the workflow file(s)
+#
+cwlVersion: v1.0
+class: Workflow
+
+requirements:
+  - class: StepInputExpressionRequirement
+
+inputs:
+  - id: submissionId
+    type: int
+  - id: adminUploadSynId
+    type: string
+  - id: submitterUploadSynId
+    type: string
+  - id: workflowSynapseId
+    type: string
+  - id: synapseConfig
+    type: File
+
+# there are no output at the workflow engine level.  Everything is uploaded to Synapse
+outputs: []
+
+steps:
+  create_adminsynid_json:
+    run: create_adminsynid_annotation.cwl
+    in:
+      - id: admin_synid
+        source: "#adminUploadSynId"
+    out: [json_out]
+
+  annotate_adminsynid:
+    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.5/annotate_submission.cwl
+    in:
+      - id: submissionid
+        source: "#submissionId"
+      - id: annotation_values
+        source: "#create_adminsynid_json/json_out"
+      - id: to_public
+        default: true
+      - id: force_change_annotation_acl
+        default: true
+      - id: synapse_config
+        source: "#synapseConfig"
+    out: [finished]
+
+  set_permissions:
+    run:  https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.5/set_permissions.cwl
+    in:
+      - id: entityid
+        source: "#submitterUploadSynId"
+      - id: principalid
+        valueFrom: "3407544"
+      - id: permissions
+        valueFrom: "download"
+      - id: synapse_config
+        source: "#synapseConfig"
+    out: []
+
+  get_docker_submission:
+    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.5/get_submission.cwl
+    in:
+      - id: submissionid
+        source: "#submissionId"
+      - id: synapse_config
+        source: "#synapseConfig"
+    out:
+      - id: filepath
+      - id: docker_repository
+      - id: docker_digest
+      - id: entity_id
+      - id: entity_type
+      - id: results
+
+  validate_json:
+    run: validate_main_submission.cwl
+    in:
+      - id: submission
+        source: "#get_docker_submission/filepath"
+      - id: synapse_config
+        source: "#synapseConfig"
+    out:
+      - id: results
+      - id: status
+      - id: invalid_reasons
+      - id: docker_repository
+      - id: docker_digest
+
+  check_status:
+    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.5/check_status.cwl
+    in:
+      - id: status
+        source: "#validate_json/status"
+      - id: previous_annotation_finished
+        source: "#annotate_docker_validation_with_output/finished"
+      - id: previous_email_finished
+        source: "#validate_json_email/finished"
+    out: [finished]
+
+  get_docker_config:
+    run: https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.5/get_docker_config.cwl
+    in:
+      - id: synapse_config
+        source: "#synapseConfig"
+    out: 
+      - id: docker_registry
+      - id: docker_authentication
+
+  archive_docker:
+    run: archive_docker.cwl
+    in:
+      - id: previous_step
+        source: "#check_status/finished"
+      - id: docker_repository
+        source: "#validate_json/docker_repository"
+      - id: docker_digest
+        source: "#validate_json/docker_digest"
+      - id: submissionid
+        source: "#submissionId"
+      - id: docker_registry
+        source: "#get_docker_config/docker_registry"
+      - id: docker_authentication
+        source: "#get_docker_config/docker_authentication"
+      - id: status
+        source: "#validate_json/status"
+      #- id: parentid
+      #  valueFrom: "syn21905730"
+      - id: synapse_config
+        source: "#synapseConfig"
+    out:
+      - id: results
+      - id: archived_docker
+

docker/process_prediction/bin/upload_to_synapse.R

@@ -0,0 +1,86 @@
+synapser::synLogin()
+
+devtools::source_url(
+    "https://raw.githubusercontent.com/Sage-Bionetworks/synapse_tidy_utils/master/utils.R"
+)
+
+"select * from syn21822681 where objectId = 0" %>% 
+    query_synapse_table(row_data = T) %>% 
+    synapser::synDelete()
+
+"select * from syn21822682 where objectId = 0" %>% 
+    query_synapse_table(row_data = T) %>% 
+    synapser::synDelete()
+
+coarse <- "coarse_results.json" %>% 
+    jsonlite::read_json() %>% 
+    purrr::pluck("annotation_string") %>% 
+    stringr::str_split(";") %>% 
+    unlist() %>% 
+    dplyr::tibble("result" = .) %>% 
+    tidyr::separate("result", into = c("result", "metric_value"), sep = ":") %>% 
+    tidyr::separate("result", into = c("dataset", "celltype", "metric"), sep = "_", fill = "left") %>% 
+    dplyr::mutate(
+        "celltype" = dplyr::if_else(
+            is.na(.data$celltype),
+            "Grand mean",
+            .data$celltype
+        ),
+        "dataset" = dplyr::if_else(
+            .data$celltype == "Grand mean",
+            "Grand mean",
+            .data$dataset
+        ),
+        "dataset" = dplyr::if_else(
+            is.na(.data$dataset),
+            "Celltype mean",
+            .data$dataset
+        )
+    ) %>% 
+    dplyr::mutate(
+        "objectId" = 0L,
+        "submitterId" = 3360851L,
+        "repo_name" = "baseline_method7",
+        "submitter" = "andrewelamb",
+        "is_latest" = T,
+        "metric_value" = as.numeric(.data$metric_value)
+    ) %>%
+    synapser::Table("syn21822681", .) %>%
+    synapser::synStore()
+
+fine <- "fine_results.json" %>% 
+    jsonlite::read_json() %>% 
+    purrr::pluck("annotation_string") %>% 
+    stringr::str_split(";") %>% 
+    unlist() %>% 
+    dplyr::tibble("result" = .) %>% 
+    tidyr::separate("result", into = c("result", "metric_value"), sep = ":") %>% 
+    tidyr::separate("result", into = c("dataset", "celltype", "metric"), sep = "_", fill = "left") %>% 
+    dplyr::mutate(
+        "celltype" = dplyr::if_else(
+            is.na(.data$celltype),
+            "Grand mean",
+            .data$celltype
+        ),
+        "dataset" = dplyr::if_else(
+            .data$celltype == "Grand mean",
+            "Grand mean",
+            .data$dataset
+        ),
+        "dataset" = dplyr::if_else(
+            is.na(.data$dataset),
+            "Celltype mean",
+            .data$dataset
+        )
+    ) %>% 
+    dplyr::mutate(
+        "objectId" = 0L,
+        "submitterId" = 3360851L,
+        "repo_name" = "baseline_method7",
+        "submitter" = "andrewelamb",
+        "is_latest" = T,
+        "metric_value" = as.numeric(.data$metric_value)
+    ) %>%
+    synapser::Table("syn21822682", .) %>%
+    synapser::synStore()
+

get_evaluation_parameters.cwl

@@ -143,6 +143,24 @@ expression: |
         cores: 8,
         ram: 30000
        }
+      "9614614": {
+        //Post_Final_Coarse2
+        gold_standard_id: "syn21752552",
+        docker_input_directory: "/home/ubuntu/validation_dir",
+        docker_param_directory: "/home/ubuntu/validation_coarse_param_dir",
+        score_submission: true,
+        cores: 8,
+        ram: 30000
+       },
+      "9614615": {
+        //Post_Final_Fine2
+        gold_standard_id: "syn21752551",
+        docker_input_directory: "/home/ubuntu/validation_dir",
+        docker_param_directory: "/home/ubuntu/validation_fine_param_dir",
+        score_submission: true,
+        cores: 8,
+        ram: 30000
+       }
     };
     return(dict[inputs.evaluationid])
   }