diff --git a/automate/minimus_mdf_flow.py b/automate/minimus_mdf_flow.py index 0673408..cfa8614 100644 --- a/automate/minimus_mdf_flow.py +++ b/automate/minimus_mdf_flow.py @@ -45,10 +45,9 @@ def email_submission_to_admin(sender_email, admin_email): "__Private_Parameters": ["send_credentials"], }, "ResultPath": "$.EmailSubmissionResult", - "Next": "Check Metadata Only" - }, - } - + "Next": "Check Metadata Only", + }, + } def check_update_metadata_only(): @@ -63,7 +62,7 @@ def check_update_metadata_only(): "Next": "ChooseCuration", } ], - "Default": "CreateDestinationDir", + "Default": "CreateDatasetDir", } } @@ -77,11 +76,23 @@ def file_transfer_steps(): * Remove the temporary write permission """ return { - "CreateDestinationDir": { - "Comment": "Create a destination directory for the transfered data", + "CreateDatasetDir": { + "Comment": "Insure the dataset directory exists before attempting to create the version subdirectory", "Type": "Action", "ActionUrl": "https://actions.globus.org/transfer/mkdir", "ExceptionOnActionFailure": False, + "Parameters": { + "endpoint_id.$": "$.user_transfer_inputs.destination_endpoint_id", + "path.$": "$.user_transfer_inputs.dataset_path", + }, + "ResultPath": "$.CreateDatasetDirResult", + "Next": "CreateDestinationDir", + }, + "CreateDestinationDir": { + "Comment": "Create a destination directory for the transferred data", + "Type": "Action", + "ActionUrl": "https://actions.globus.org/transfer/mkdir", + "ExceptionOnActionFailure": True, "Parameters": { "endpoint_id.$": "$.user_transfer_inputs.destination_endpoint_id", "path.$": "$.user_transfer_inputs.transfer_items[0].destination_path", @@ -89,8 +100,13 @@ def file_transfer_steps(): "ResultPath": "$.CreateDestinationDirResult", "Catch": [ { - "ErrorEquals": ["ActionFailedException", "States.Runtime"], - "Next": "FailUserPermission", + "ErrorEquals": [ + "ActionFailedException", + "States.Runtime", + "EndpointError", + ], + "ResultPath": "$.CreateDestinationDirResult", + "Next": "ExceptionState", } ], "Next": "UserPermissions", @@ -111,8 +127,13 @@ def file_transfer_steps(): "ResultPath": "$.UserPermissionResult", "Catch": [ { - "ErrorEquals": ["ActionFailedException", "States.Runtime"], - "Next": "FailUserPermission", + "ErrorEquals": [ + "ActionFailedException", + "States.Runtime", + "EndpointError", + ], + "ResultPath": "$.UserPermissionResult", + "Next": "ExceptionState", } ], "Next": "UserTransfer", @@ -145,8 +166,13 @@ def file_transfer_steps(): "ResultPath": "$.UndoUserPermissionResult", "Catch": [ { - "ErrorEquals": ["ActionFailedException", "States.Runtime"], - "Next": "FailUserPermission", + "ErrorEquals": [ + "ActionFailedException", + "States.Runtime", + "EndpointError", + ], + "ResultPath": "$.UndoUserPermissionResult", + "Next": "ExceptionState", } ], "Next": "CheckUserTransfer", @@ -160,25 +186,7 @@ def file_transfer_steps(): "Next": "ChooseCuration", } ], - "Default": "FailUserTransfer", - }, - "FailUserTransfer": { - "Type": "ExpressionEval", - "Parameters": { - "title": "MDF Submission Failed", - "message.=": "'Your MDF submission ' + `$.source_id` + ' failed during transfer, please try again or contact materialsdatafacility@uchicago.edu:\n' + `$.UserTransferResult.details`", - }, - "ResultPath": "$.FinalState", - "Next": "NotifyUserEnd", - }, - "FailUserPermission": { - "Type": "ExpressionEval", - "Parameters": { - "title": "MDF Permission Settings Failed", - "message.=": "'Your MDF submission ' + `$.source_id` + ' failed to transfer, please try again or contact materialsdatafacility@uchicago.edu:\n' + `$.UserPermissionResult.details`", - }, - "ResultPath": "$.FinalState", - "Next": "NotifyUserEnd", + "Default": "ExceptionState", }, } @@ -283,10 +291,10 @@ def curation_steps(sender_email, admin_email): "Type": "ExpressionEval", "Parameters": { "title": "MDF Submission Rejected", - "message.=": "'Your submission (' + `$.source_id` + ') was rejected by a curator and did not complete the publication process. The curator gave the following reason: '+ `$.CurateResult.details.output.CurationResult.details.parameters.user_input`", + "message.=": "'Your submission (' + `$.dataset_mdata.mdf.versioned_source_id` + ') was rejected by a curator and did not complete the publication process. The curator gave the following reason: '+ `$.CurateResult.details.output.CurationResult.details.parameters.user_input`", }, "ResultPath": "$.FinalState", - "Next": "NotifyUserEnd", + "Next": "ExceptionState", }, } @@ -363,7 +371,7 @@ def search_ingest_steps(): } -def notify_user_steps(sender_email): +def notify_user_steps(sender_email, email_template): """ Check on the final status of the submission and notify the submitting user as appropriate @@ -383,10 +391,18 @@ def notify_user_steps(sender_email): "ActionUrl": action_providers.notify, "ExceptionOnActionFailure": True, "Parameters": { - "body_template.$": "$.FinalState.message", + "body_mimetype": "text/html", + "body_template": email_template, + "body_variables": { + "greeting.$": "$.dataset_mdata.dc.creators[0].givenName", + "contributors.$": "$.creators_list", + "title.$": "$.dataset_mdata.dc.titles[0].title", + "year.$": "$.dataset_mdata.dc.publicationYear", + "doi.$": "$.dataset_mdata.dc.identifier.identifier" + }, "destination.$": "$.submitting_user_email", "sender": sender_email, - "subject.$": "$.FinalState.title", + "subject": "Dataset Accepted for Publication in the Materials Data Facility", "send_credentials": [ { "credential_method": "email", @@ -417,7 +433,16 @@ def exception_state(sender_email): "sender": sender_email, "destination.$": "$.submitting_user_email", "subject": "Submission Failed to Ingest", - "body_template.=": "'Submission ' + `$.source_id` + ' fatally errored processing in Flow '+ `$._context.action_id` + '. Please review the Flow log for details about this exception.'", + "body_template": """ +

Submission Failed to Ingest

+ "Submission: $source_id received a fatal error while processing flow. + Please review the Flow log for details about this exception. + + """, + "body_variables": { + "source_id.$": "$.dataset_mdata.mdf.source_id", + "flow_log_link.$": "$._context.run_id", + }, "notification_method": "any", "notification_priority": "high", "send_credentials": [ @@ -431,7 +456,7 @@ def exception_state(sender_email): }, "ResultPath": "$.ExceptionNotifyResult", "WaitTime": 86400, - "Next": "NotifyUserEnd", + "Next": "EndSubmission", }, } @@ -443,6 +468,11 @@ def flow_def( administered_by, description="", ): + # The success email is a nicely formatted html message. Read that from this file to make format testing easier + with open("success_email_template.html", "r") as f: + email_template = f.read() + + return GlobusAutomateFlowDef( title="MDF Ingest Flow", subtitle="Ingest Materials Data Facility Submissions", @@ -461,7 +491,7 @@ def flow_def( **curation_steps(sender_email, admin_email), **mint_doi_steps(), **search_ingest_steps(), - **notify_user_steps(sender_email), + **notify_user_steps(sender_email, email_template), **exception_state(sender_email), "EndSubmission": {"Type": "Pass", "End": True}, }, diff --git a/automate/success_email_template.html b/automate/success_email_template.html new file mode 100644 index 0000000..972903d --- /dev/null +++ b/automate/success_email_template.html @@ -0,0 +1,163 @@ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+

+ $greeting,

+ Thank you for your contribution to the Materials Data Facility, + and towards open science. Your dataset has been published with + the + following information.

+

+ best,

+

+ Ben +

+
+ + + + + + + + + + + + +
+

+ Your Dataset Citation Information

+
+

+
+

+ + $contributors. "$title." Materials Data Facility, $year. + + https://doi.org/$doi +
+ +
+
+

+ Citing MDF

+

+ You can help us build support for MDF by citing + the papers below. 

+
+ + + + + + +
+
    +
  • +

    + Blaiszik, B., K. Chard, J. Pruyne, R. + Ananthakrishnan, S. Tuecke, and I. + Foster. + "The Materials Data Facility: Data + Services to + Advance Materials Science Research." JOM + 68, no. + 8 (July 6, 2016): + 2045-2052. + doi:10.1007/s11837-016-2001-3.

    +
    • +
  • +

    + Blaiszik, Ben, Logan Ward, Marcus + Schwarting, + Jonathon Gaff, Ryan Chard, Daniel Pike, + Kyle + Chard, and + Ian Foster. "A Data Ecosystem to Support + Machine + Learning in + Materials Science." MRS Communications + (October + 10, 2019): 1-9. + doi:10.1557/mrc.2019.118.

    +
    • +
+
+
+ + + + + + + + + + + + + +
+ + + Publish More Data
+

+ Questions? Contact  + + materialsdatafacility@uchicago.edu + +

+
+
+