Added note on validation service changing; Added error table #199
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ESapenaVentura
requested review from
dipayan1985,
amnonkhen,
cocathail and
theisuru
amnonkhen
requested changes
Oct 9, 2024
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| | **XML validation (old)** | **BioSamples validation (New)** | | ||
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| | Error at {<sample-name>}. Invalid units "{value-of-units}" for field "{<attribute-name>}". Allowed units are "{<list-of-allowed-values>}" | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must be equal to one of the allowed values:{list-of-allowed-values} | |
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I would add a space after all the colons, in all other error messages and in the app itself. Is there a reason for not using spaces after the colons?
Suggested change
| | Error at {<sample-name>}. Invalid units "{value-of-units}" for field "{<attribute-name>}". Allowed units are "{<list-of-allowed-values>}" | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must be equal to one of the allowed values:{list-of-allowed-values} | | |
| | Error at {<sample-name>}. Invalid units "{value-of-units}" for field "{<attribute-name>}". Allowed units are "{<list-of-allowed-values>}" | sample:{<sample-name>}; attribute: {<path-to-attribute>}; reason: must be equal to one of the allowed values: {list-of-allowed-values} | |
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I left it without spaces to make it more easy to tokenise (one char vs 2), but happy to hear people on this, I don't have a strong preference to be honest
| | Error at {<sample-name>}. The length of field "{<attribute-name>}" value "{<value-provided>}" exceeds the maximum allowed length "{<maximum-length-of-field>}". | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must NOT have more than {<maximum-length-of-field>} characters | | ||
| | Error at {<sample-name>}. The value "{<value-provided>}" for field "{<attribute-name>}" does not match regular expression "{<pattern>}" | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must match pattern {<pattern>} | | ||
| | Missing mandatory field "{<property-name>}". | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must have required property {<property-name>} | | ||
| | Missing recommended field "{<property-name>}". | **DEPRECATED**. Recommended field validation will no longer be supported. | |
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I don't understand. Did missing recommended fields appear as errors in the XML validation?
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In the file I got with the list of errors, it is listed (ERAM.2.1.8=Missing recommended field "{0}".)
| | Error at {<sample-name>}. The value "{<value-provided>}" for field "{<attribute-name>}" does not match regular expression "{<pattern>}" | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must match pattern {<pattern>} | | ||
| | Missing mandatory field "{<property-name>}". | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must have required property {<property-name>} | | ||
| | Missing recommended field "{<property-name>}". | **DEPRECATED**. Recommended field validation will no longer be supported. | | ||
| | Error at {<sample-name>}. Field "{<property-name>}" may only occur once. | sample:{<sample-name>}; attribute:{<path-to-attribute>}; reason:must NOT have more than 1 items | |
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Nope, but that's Biovalidator's error for when maxItems : 1 fails
| | A symonym was used for field "{<property-name>}". Replacing value "{<synonym-property-name>}" with value "{<property-name>}" | **DEPRECATED**. Synonym validation and processing will no longer be supported. | | ||
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| Please note: The new sample validation service may catch more errors that do not have an equivalent on the old service. |
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I don't have an exhaustive list (As I am not sure of all the possible events that may happen validation-wise), but I do have one in mind: If my memory serves me well, XML validation does not validate synonym fields, whereas we added the error on the oneOf to ensure only 1 synonym appears in a document
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Please add link to the ticket. |
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submit/samples.rst:sample_checklist_errors.mdsubmit/samples/sample_checklist/sample_checklist_errors.md:Please let me know if the place/format is correct or not, as I was not entirely sure!
ebi-ait/checklist#107