Eelectron Client : "fastq file does not exist" error message appears, even if fastq exists

[KuzminaAnna]

Describe the problem/error: Error message "fastq file does not exist" appears after uploading csv file which contains invalid control or invalid collection_date values. It happens even when fastq file is valid and exist.

Expected behaviour: "fastq file does not exist" error shouldn’t appears if fastq file exist and valid.

Steps to Reproduce:

• Upload sample with invalid control (like "-'" or "+'") or with invalid collection_date. (NOTE: don't forget to add .fastq.gz files.)
• Verify error message
• Actual response:

{ "validation":{ "status":"failure", "errors": [{ "sample_name": "sample31", "error": "None in the control field is not valid; field must be either empty or contain the one of the keywords negative, positive" }, { "sample_name": "sample32", "error": "-' in the control field is not valid; field must be either empty or contain the one of the keywords negative, positive" }, { "sample_name": "sample33", "error": "+' in the control field is not valid; field must be either empty or contain the one of the keywords negative, positive" }, { "sample_name": "sample34", "error": "Positive in the control field is not valid; field must be either empty or contain the one of the keywords negative, positive" }, {"sample_name": "sample34", "error": "fastq1 file does not exist"}, { "sample_name": "sample34", "error": "fastq2 file does not exist" }, { "sample_name": "sample35", "error": "Negative in the control field is not valid; field must be either empty or contain the one of the keywords negative, positive" }, {"sample_name": "sample35", "error": "fastq1 file does not exist"}, { "sample_name": "sample35", "error": "fastq2 file does not exist" }] } } System Identification: DEV, STAGE Reproducible? Yes If multiple areas are impacted list areas: Electron client all platforms. If compatibility/interoperability is impacted list products (e.g.): Gpas Portals. illumina-fastq-upload_collection_date_invalid4_time_stamp.csv illumina-fastq-upload_control_invalid5_none.csv

[KuzminaAnna]

Internal EC ticket ID: https://gbujira.us.oracle.com/browse/HCELEC-535 Deepak was going to submit a ticket to the shared Oxford Jira

[bede]

Given that the title of this ticket includes "fastq file does not exist", it would have been useful if the fastq files had been provided. In their absence, I created my own fastqs and was unable to replicate this issue in either gpas-cli 0.6.0, 0.7.1 or the current master branch.

Please could Deepak provide a complete MWE, including said FASTQs, or else I will close.

Also, please could future issues be replicated in gpas-cli before reporting them?