Documentation

Welcome to the bio.tools linter documentation.

API

This website uses an API exposed by the server, that is publicly available. To see the automatically generated documentation of the API, see this link.

Monitoring

This server runs an instance of Monitoror for status monitoring. Is it available publicly at this link.

Error types

EDAM INPUT DISCREPANCY

see source code

This error is returned when a tool is annotated with an EDAM operation which has a has_input restriction, however the value (operation input) of that restriction in not present in the tool's annotation.

For example, the Visualisation operation has a has_input restriction of an Image data type. This error is returned when the Image input data type is not present in the tools annotations.

EDAM INVALID

see source code

This error is returned when a tool is clasified with an EDAM term which could not be found in the EDAM ontology. Such a case is rare as the bio.tools website checks for invalid classification, but may happen in aggregated data.

see source code

This error is returned when a tool is clasified with an EDAM term which is marked as not recommended for annotation.

EDAM OBSOLETE

see source code

This error is returned when a tool is clasified with an EDAM term which is marked as obsolete.

EDAM OUTPUT DISCREPANCY

see source code

This error is returned when a tool is annotated with an EDAM operation which has a has_output restriction, however the value (operation output) of that restriction in not present in the tool's annotation.

For example, the Visualisation operation has a has_output restriction of an Image data type. This error is returned when the Image output data type is not present in the tools annotations.

EDAM TOPIC DISCREPANCY

see source code

This error is returned when a tool is annotated with an EDAM term which has a has_topic restriction, however the value (topic) of that restriction in not present in the tool's annotation.

For example, the Structure analysis operation has a has_topic restriction of the Structure analysis topic. This error is returned when the Structure analysis topic is not present in the tools annotations.

PMID, PMCID and DOI conversion

see source code

These errors occur when an article has more digital identifiers than it is assigned. For example, if a paper has both a DOI and a PMID, but only a DOI is assigned, the linter will show a DOI_BUT_NOT_PMID error. This is checked using the NCBI AnyID Converter API.

PMID, PMCID and DOI discrepancy

see source code

These errors occur when a tool has a publication but the publications IDs (PMID, PMCID and DOI) lead to different publication.

URL BAD STATUS

see source code

This error occurs when a website doesn't return a status code that signifies success, such as a 404 or 403.

URL TIMEOUT

see source code

This error occurs when the linter tries to connect to a website but is unsuccessful. This signifies a server failure.

URL INVALID

see source code

This error occurs when a URL could not be parsed, for example because it contains invisible Unicode characters. For more information, look up a Unicode invisible character checker, such as this.

URL LINTER

see source code

This error is returned when the linter encounters an error it was not programmed to handle. Such cases are rare and should be fixed.

URL NO SSL

see source code

This error occurs when a website does not use the Transport Layer Security for secure communications. Such an error can only be fixed by the website administrator.

URL PERMANENT REDIRECT

see source code

This error is returned when a website returned a redirection, that tells the browser to go somewhere else.

URL TIMEOUT

see source code

This error occurs when a website does use the Transport Layer Security however the certificate is invalid or expired.

URL TIMEOUT

see source code

This error occurs when a website takes over 30 seconds to respond. This signifies a server failure.

URL TOO MANY REDIRECTS

see source code

This error is returned when a website returns an infinite redirection loop. Such an error may be an improperly configured server or DDoS mitigation flagging the linter as malicious.

URL UNUSED SSL

see source code

This error occurs when a website does use the Transport Layer Security for secure communications, but the URL link does not signify it does by starting with https://.