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Merge pull request #93 from bio-tools/fix_biotoolsID_pattern
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bio.tools ID to be a subset of xs:NCName (fixes #79)
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@joncison
joncison authored Nov 15, 2017
2 parents d254fb1 + 1933691 commit b7edbbe
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6 changes: 3 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -7,7 +7,6 @@ Description of changes are grouped as follows:
* **Fixed:** a bug fix
* **Misc:** some miscellaneous other change

# November 17, 2016 biotoolsSchema-2.0.0.xsd released

## Added
1. Added "Unpublished" to patterns for 'doiType' (simple type) and 'pmid' and 'pmcid' (elements) to support the specification that a publication is not available for a tool (as required by the bio.tools information standard (https://github.com/bio-tools/biotoolsSchemaDocs/blob/master/information_requirement.rst).
Expand Down Expand Up @@ -35,7 +34,7 @@ Description of changes are grouped as follows:
** 9. 'biotoolsCURIE' added
** 9.1 0...1 cardinality
** 9.2 type of xs:anyURI
** 9.2 regex is biotools:[A-Za-z0-9_\-_~.]+
** 9.2 regex is `biotools:[_a-zA-Z][_\-.0-9a-zA-Z]*`

## Added / changed / removed
1. 'publication->type' enum, mulitple modifications:
Expand Down Expand Up @@ -79,9 +78,10 @@ Description of changes are grouped as follows:
7.6 'credit->typeRole' cardinality changed from 0...many from 0...1
7.7 'credit->typeRole' enum extended with "Primary contact" to indicate this credit is a primary contact for the software.
** 8. 'summary->description' 'maxlen' facet reduced to 500 from 1000.
9. 'biotoolsIdType' (as used now only by 'relation->biotoolsId') refactored:
9. 'biotoolsIdType' refactored and used in multiple places:
10.0 'minLen' facet is 1
10.1 'maxLen' facet removed
Pattern `[_a-zA-Z][_\-.0-9a-zA-Z]*` added (used in `biotoolsIdType`, `biotoolsCURIE`, and `biotoolsUrlType`).
**10. 'relation->biotoolsId' type changed from `biotoolsUrlType` to `biotoolsIdType` simple type.
11. 'linkType->comment' type set to textType (consistent with other free-text comments) ('linkType' is complex type used by 'link->comment' and 'documentation->comment' elements)
12. 'credit->orcidId' changed to 'credit->orcidid'
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30 changes: 13 additions & 17 deletions biotools_dev.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<!-- edited with XMLSpy v2012 rel. 2 sp1 (x64) (http://www.altova.com) by Jon Ison (private) -->
<!-- edited at GitHub (https://github.com) by Matus Kalas -->
<xs:schema xmlns="http://bio.tools" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:altova="http://www.altova.com/xml-schema-extensions" targetNamespace="http://bio.tools" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:element name="tools">
<xs:annotation>
Expand Down Expand Up @@ -132,8 +133,7 @@
</xs:element>
<xs:element name="biotoolsID" minOccurs="0">
<xs:annotation>
<xs:documentation>Unique ID of the tool that is assigned upon registration of the software in bio.tools, normally identical to tool name.</xs:documentation>
<xs:documentation>The ID is a URL-safe derivative of (often identical to) the tool name restricted to 12 characters maximum. Unreserved characters (uppercase and lowercase letters, decimal digits, hyphen, period, underscore, and tilde) are allowed. All other characters including reserved characters and other characters deemed unsafe are not allowed. Spaces can be preserved as underscore ("_").</xs:documentation>
<xs:documentation>Unique ID (case insensitive) of the tool that is assigned upon registration of the software in bio.tools, normally identical or similar to tool name.</xs:documentation>
<xs:appinfo>
<uiTip>Unique ID of the tool that is assigned upon registration of the software in bio.tools.</uiTip>
<biotoolsUsage>Optional</biotoolsUsage>
Expand Down Expand Up @@ -162,7 +162,7 @@
<xs:restriction base="xs:anyURI">
<xs:minLength value="1"/>
<xs:whiteSpace value="collapse"/>
<xs:pattern value="biotools:[A-Za-z0-9_\-_~.]+"/>
<xs:pattern value="biotools:[_a-zA-Z][_\-.0-9a-zA-Z]*"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
Expand Down Expand Up @@ -209,15 +209,10 @@
<xs:element name="type" minOccurs="0">
<xs:annotation>
<xs:documentation>Type of tool identifier.</xs:documentation>
<xs:documentation>bio.tools toolIDs are a URL-safe derivative of (often identical to) the tool name. Unreserved characters (uppercase and lowercase letters, decimal digits, hyphen, period, underscore, and tilde) are allowed. All other characters including reserved characters and other characters deemed unsafe are not allowed. Spaces can be preserved as underscore ("_").</xs:documentation>
<xs:appinfo>
<uiTip>Type of identifier.</uiTip>
<biotoolsUsage>Optional</biotoolsUsage>
<enum>
<enumItem>
<term>toolID</term>
<uiTip>Unique ID of the tool that is assigned upon registration of the software in bio.tools, normally identical to tool name.</uiTip>
</enumItem>
<enumItem>
<term>DOI</term>
<uiTip>Digital Object Identifier of the software assigned (typically) by the software developer or service provider.</uiTip>
Expand Down Expand Up @@ -1226,8 +1221,8 @@
<xs:sequence>
<xs:element name="biotoolsId">
<xs:annotation>
<xs:documentation>bio.tools ID (URL) of an existing bio.tools entry which this software is related to.</xs:documentation>
<xs:documentation>Relations may only be defined between registered software. The ID is a URL in the bio.tools namespace and reflects (normally exactly) the tool name and version: see http://biotools.readthedocs.io/.</xs:documentation>
<xs:documentation>bio.tools ID (URL) of an existing bio.tools entry which this software is related to.</xs:documentation>
<xs:documentation>Relations may only be defined between registered software. The ID is a URL in the bio.tools namespace and reflects (normally exactly) the tool name and version: see http://biotools.readthedocs.io/.</xs:documentation>
<xs:appinfo>
<uiTip>bio.tools ID (URL) of an existing bio.tools entry which this software is related to.</uiTip>
<biotoolsUsage>Optional</biotoolsUsage>
Expand Down Expand Up @@ -1365,7 +1360,7 @@
<xs:documentation>The value is text adhering to a strict syntax, see https://github.com/bio-tools/biotoolsschema.</xs:documentation>
<xs:appinfo>
<altova:exampleValues>
<altova:example value="/tool/{toolID}"/>
<altova:example value="/{toolID}"/>
</altova:exampleValues>
</xs:appinfo>
</xs:annotation>
Expand Down Expand Up @@ -2427,7 +2422,7 @@
<xs:documentation>URL supporting FTP.</xs:documentation>
<xs:appinfo>
<altova:exampleValues>
<altova:example value="http://someURL.org"/>
<altova:example value="http://someurl.org"/>
</altova:exampleValues>
</xs:appinfo>
</xs:annotation>
Expand All @@ -2439,10 +2434,10 @@
</xs:simpleType>
<xs:simpleType name="urlType">
<xs:annotation>
<xs:documentation>URL.</xs:documentation>
<xs:documentation>An HTTP or HTTPS URL.</xs:documentation>
<xs:appinfo>
<altova:exampleValues>
<altova:example value="http://someURL.org"/>
<altova:example value="http://someurl.org"/>
</altova:exampleValues>
</xs:appinfo>
</xs:annotation>
Expand All @@ -2452,15 +2447,15 @@
</xs:simpleType>
<xs:simpleType name="biotoolsUrlType">
<xs:annotation>
<xs:documentation>URL in the bio.tools tool namespace (bio.tools/tool/{version} or bio.tools/t{v}).</xs:documentation>
<xs:documentation>URL in the bio.tools namespace, in form of http(s)://bio.tools/{toolID}.</xs:documentation>
<xs:appinfo>
<altova:exampleValues>
<altova:example value="https://bio.tools/signalp"/>
</altova:exampleValues>
</xs:appinfo>
</xs:annotation>
<xs:restriction base="xs:anyURI">
<xs:pattern value="https?://bio.tools/[A-Za-z0-9_\- _ ~]+"/>
<xs:pattern value="https?://bio.tools/[_a-zA-Z][_\-.0-9a-zA-Z]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="biotoolsCollectionIdType">
Expand Down Expand Up @@ -2661,6 +2656,7 @@
<xs:simpleType name="biotoolsIdType">
<xs:annotation>
<xs:documentation>bio.tools tool ID.</xs:documentation>
<xs:documentation>bio.tools tool IDs are a URL-safe and Linked-Data-safe derivative of (often identical to) the tool name. Allowed characters are uppercase and lowercase English letters (case insensitive!), decimal digits, hyphen, period, and underscore. The tool ID must start with a letter or an underscore. Spaces can be preserved as underscore ("_").</xs:documentation>
<xs:appinfo>
<altova:exampleValues>
<altova:example value="signalp"/>
Expand All @@ -2670,7 +2666,7 @@
</xs:annotation>
<xs:restriction base="xs:anyURI">
<xs:minLength value="1"/>
<xs:pattern value="[A-Za-z0-9_\-_~.]+"/>
<xs:pattern value="[_a-zA-Z][_\-.0-9a-zA-Z]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="versionType">
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