IG Publisher Documentation

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Summary

The FHIR team provides an IG Publishing tool that takes the implementation guide content and converts it to a set of 3 different types of files:

  • generated resources ready for inclusion into the published guide (xml, json, ttl formats)
  • a set of fragments ready to include in generated html files, which are then included into a published set of html files as directed by the author
  • Several different zip files: which are used by implementers for various purposes, so should be included in the final published version

Building an IG is a 4 part process:

  1. Installing the publisher
  2. Defining the resources that underpin the Implementation Guide resources (Implementation Guide, Conformance Resources, Knowledge statements, examples) - using either bundles or spreadsheets
  3. Developing the structure and the narrative content that turns the resources into a useful implementation guide
  4. Running the publishing process that will publish it

The outcome of the publishing process is a set of HTML files that represent the implementation guide. These files can be posted to a web server.

Alternatively, you may use the IG publisher to validate and render a set of Profiles, value sets etc without building a formal IG (see command line mode)

Publishing Implementation Guides

Typically, implementation guide publishing works like this:

  • the master source for an implementation guide is in a public GitHub repository
  • editors can run their own local build and share the set of files (full-ig.zip is automatically produced, for convenience) with anyone they want to
  • a CI build is published so everyone can see the output - see [Auto-IG-Publisher Documentation]
  • when formal milestones are achieved, the Implementation Guide is published to the canonical web site for the IG (typically, hl7.org, hl7.org.xx, or fhir.org, but need not be) (See Standard FHIR Publishing Layout Pattern for additional guidance)

For IGs developed on the Simplifier.net infrastructure, see [todo as yet] for publishing details. Non-public Implementation guides can still use the IG build, but cannot use the CI Build infrastructure

Examples

If you want an example of IG source, you can look in one of the following places:

  • FHIR SVN repository, in \build\guides\* - any directory ending in 2 - a variety of styles of implementation guide.
  • Also, there's \build\tests\ig which is used for testing the tooling

Using FHIR IG Publisher

Installing

  1. Get the publisher itself: this is a java jar called org.hl7.fhir.igpublisher.jar. You can get it from the downloads (e.g. http://build.fhir.org/downloads.html) for the version of FHIR you are using (or, if you build locally, from your own publish directory). The jar includes everything from the spec that is required to generate the implementation guide.
  2. Get the publishers helper: you need to install Jekyll in order to publish the said implementation guide. See Windows and Linux instructions.

Make sure you use the correct version of the IG publisher for your guide (check the versions in the log), since the IG publisher only supports the version of FHIR it's been made for.

The publisher can be run as a GUI application, or run from the command line. It can also can be hosted in a server - if you want to host it, talk to Grahame Grieve.

Alternatively, you can use the IG Publisher in web server mode. If you do this, you don't need any installed software.

Using the IG Publisher Web Server

The IG publisher lives at [[1]]. From there, you can upload a ip file containing the contents of the IG. After processing, you can download the output.

Note that it's a little inconvenient to flip between modes (running locally vs using the web publisher) because the standard folder structures include /qa, /temp, and /output - you don't want to upload these - they can be very large (though the IG server will ignore them if you do). Also, the web publisher maintains it's own terminology server cache, and may give different results for expansions etc than if you are using your own txCache in the folder and not keeping it up to date.

You can also use the API to the IG web publisher directly. To do this, POST a zip containing the IG content to http://hapi.fhir.org/igweb/process (Content-Tyepe: application/zip), and after a period of seconds, a zip file containing the generated output will be returned.

Running in GUI mode

Windows: double-click on org.hl7.fhir.igpublisher.jar or right-click and select 'Open'.

Linux: double-click on org.hl7.fhir.igpublisher.jar or right-click and select 'Open With Oracle Java 8 Runtime'.

You can also run it the command line:

 java -jar org.hl7.fhir.igpublisher.jar

Note that this doesn't work in OpenJDK - if you are using openJDK, your only option is to run it from the command prompt, as described below.

This is the IG builder:

Ig-builder.png

To use it, 'Choose' an implementation guide control JSON file, and click 'Execute'. The implementation guide will be built, and then the IG publisher will watch for changes until and do incremental rebuilds until you click 'Stop'.

Running in command line mode

To run in command line mode, run the IG Publisher like this:

 java -jar org.hl7.fhir.igpublisher.jar -ig [source] (-tx [url]) (-watch)

parameters:

  • -ig: a path or a url where the implementation guide JSON control file is found (see control file format documentation)
  • -tx: (optional) address to use for terminology server (default is http://fhir3.healthintersections.com.au - which is currently the only supported option)
  • -watch (optional): if this is present, the publisher will not terminate; instead, it will stay running, and watch for changes to the IG or its contents and re-run when it sees changes. Note that changes the spec or to dependent implementation guides (see below) are not picked up during watch mode

Advanced parameters:

  • -resetTx - clear out the txCache (see comments below about managing the freshness of the txCache)
  • -resetTxErrors - delete any errors from the tcCache, but leave successful operations in the cache

Windows example:

Open the command prompt, then paste the following, with the paths adjusted for your computer:

 java -jar "C:\Users\VadimPeretokin\Desktop\fhir-publisher\org.hl7.fhir.igpublisher.jar" -ig "C:\Users\VadimPeretokin\Desktop\fhir-git\tests\ig\test-ig.json" -watch

Linux: Open the terminal (usually Ctrl+Alt+T), then paste the following, with the paths adjusted for your computer:

 java -jar '/home/vadi/Programs/fhir-publisher/org.hl7.fhir.igpublisher.jar' -ig '/home/vadi/Programs/fhir-git/tests/ig/test-ig.json' -watch

Validating without publishing

There is an alternative mode, where you run the IG publisher against a collection of conformance resources (profiles, logical models, value sets etc) without defining an implementation guide. This allows you to validate a set of profiles, and see what they look like. To run the IG publisher in this mode:

 java -jar org.hl7.fhir.igpublisher.jar -source [source] -destination [dest] (-tx [url])

Where source is a directory containing the conformance resources, destination is where to put the generated output (validation.html is the most important). In this case, the IG publisher uses its own internal control file and renders a simple version of the output.

Operation of the IG Publisher

once running, it:

  • reads the control file
  • reads the IG
  • processes any spreadsheets, bundles, and logical models
  • loads all the resources in the IG
  • processes code systems, value sets, structure definitions, structure maps
  • validates the all resources in the IG and produces an HTML QA file with any errors encountered
  • for each resource in the IG, generates a set of files - renderings of the artifact for possible inclusion in the published IG, plus the outputs defined above
  • generates summary output
  • gets the tool (Jekyll) to generate the final output. The Jekyll source is in /pages by default

If you'd like to use another website generation tool, discuss your tool of choice with Grahame Grieve.

IG Publisher Special Output files

The IG Publisher produces (or may produce) several different zip files. The most significant is "validator.pack". This is a zip file that contains all the conformance & example resources, a version marker, and a json file that lists all the pages and urls in the ig itself. This file is used:

  • by the fhir validator - if you refer to the IG directly by it's canonical URL
  • by the IG publisher - if you declare that one IG depends on another
  • by a server - if you add the IG to a server load list

The IG publisher will generate definitions.[fmt].zip (unless instructed not to) - these may be useful for other tools that have format specific requirements, and must have json, xml., or ttl inputs.

In addition, the IG publisher will generate examples.[fmt].zip (unless instructed not to) which contains all the IGs examples

Finally the entire IG output is is provided as full-ig.zip.

Control file

When the IG publisher is executed, it is pointed at a control file. This is a json file that contains all the information that the publisher needs to publish the implementation guide. It has this structure:

 {
   "source": "[ig]", // the name of the ImplementationGuide resource file to load. optional, default = ig.xml
   "version" : "[optional - see below]. default = current build",
   "fixed-business-version" : "[optional - see below]. default = none",
   "logging" : "[optional - see below]  default = none",
   "html-template" : "[optional - see below]. default = none",
   "suppressedWarningFile": "[optional - see below] default = none",
   "suppress-qa" : true | false, // suppress the generation of the QA folder content. default = don't suppress
   "paths" : { // see paths below. optional- defaults apply
     "resources" : [  // optional; default = "resources"
       "[resourcesFolder]" 
      ],
     "pages" : [ // optional; default = "pages"
       "[pagesFolder]"
     ],
     "temp" : "[temp]",  // optional; default = "temp"
     "output" : "[output]",  // optional; default = "output" (and must be output for auto-build)
     "txCache" : "[txCache]",  // optional; default = "no value - txCache not in version control (slower builds)"
     "qa" : "[qa]",  // optional; default = "qc"
     "history" : "[history page]",  // optional; default = no page marked as history page
     "specification" : "[specification]"  // optional; default = "http://hl7.org/fhir"
   },
   "jurisdiction" : "[code]", // see Jurisdiction below. optional
   "language" : "[language]", // see 'Language support' below. optional
   "languages" : [ // optional 
     "[language]"
   ]
   "pre-process" : [{ // optional section see below
      "folder" : "[folder]",
      "transform" : "[xslt file (conditional)]",
      "relativePath" : "[relative path (conditional)]"
   }],
   "sct-edition" : "[uri - see below", // optional - defaults to SCT International
   "no-inactive-codes" : true | false,  // optional; default = false
   "broken-links" : "warning | error", // optional; default to warning, but can be error (stops the build)
   "gen-examples" : "true", // optional, see below (processing options)
   "do-transforms" : "true", // optional, see below (processing options)
   "canonicalBase": "[where this will be published - see above]. Mandatory",
   "dependencyList": [  // optional
     // a list of other implementation guides that this guide depends on
     // e.g. uses profiles, value sets, code systems etc
     // zero or more of this object:
     {
        "name" : "[name of the IG, for logging, and Jekyll variable name for location]",
        "location" : "[http address where the IG lives]",
        "source" : "[folder to get the definitions from if running ahead of publication at location (relative)]"
     }
   ],
   "extension-domains" : [ 
     "[url]" // list of domains from which undeclared extensions are allowed to come from
   ]
   // Templates lists any additional templates beyond "base" and "format" that can be generated for one or more artifact types
   // The list of template names below are examples
   "extraTemplates": ["mapping", "foo", "bar"],
   "defaults": {
     // this object contains the default publishing policy for different types. 
     // Anything not mentioned defaults to true
     "Any": {
       // fragment and template options - see below. example:
       "xml" : false // don't produce xml example
       "template-base" : "sometemplatefile.html"  // use this as the default template for all base pages if not overridden
     },
     "[Type]": {
       // fragment and template options - see below
     }
   },
   "spreadsheets" : [
     "[filename]" // see using spreadsheets
   ], 
   "bundles" : [
     "[id]" // see using bundles below
   ],
   "resources": {
     "[Type]/[id]": {
       "source" : "[optional source file]", 
       "version" : "[optional version]",
       // template and fragment options - see below.  E.g.
       "base": "[overridden name for destination page for things referring to this resource]",
       "template-defns": "[template to use for resource definitions]",
     }
   },
   "special-urls" : [
     // list of special URLs - see below
   ],
   "swagger" : [
     // see swagger section below
   ],
   "tool" : "jekyll" // the tool used for the 3rd step of the build. See tooling below
 }

The control file must be maintained by the editor of the implementation guide.

Version

The IG publisher lives in the current build (http://build.fhir.org), where it is maintained in an ongoing fashion. The IG publisher knows how to publish IGs for the following versions:

  • 1.0.2: DSTU2
  • 1.4.0: May 2016 draft release (supported for some stakeholders who use it, and make that possible)
  • 3.0.0: DSTU3
  • [current] - the current build.

The IG publisher may work with other versions (e.g. forks of R4 candidate versions) but this is not guaranteed.

If you are using a version other than the current build, you need to specify the version in the control file:

 "version" : "1.0.2"

Business Version

You can impose a fixed business version on all the conformance resources using

 "fixed-business-version" : "1.2"

If you use this, then the version element in the source for all the conformance resources in the IG must be either the same as the nominated business version, or empty.

This approach to profile versioning means that profiles do not need to have their cannonical URLs changed when substantive changes are made (nor do references to those profiles need to be updated). Instead, all profile references within an IG simply use a consistent canonical URL. When instances declare the profile in an instance, they combine the canonical URL with the profile/IG version as follows:

[someurl]|[someVersion]

E.g. <profile value="http://example.org/fhir/StructureDefinition/someProfileId%7C1.2"/>

This tells the validator which version of the profile must be used when validating the instance.

Paths

The IG publisher defines the following paths that can be configured in the control file:

  • [resources]: the directory or set of directories where all the input FHIR resources are found (usually conformance resources and examples). Multiple directories can be used to allow source files to be grouped - e.g. separate folders for examples, vocabulary-related files and 'other' files.
  • [pages]: the directory or set of directories that contain the jekyll source (not process, just passed to Jekyll for processing). Multiple directories can be used if it makes implementation guide maintenance easier to separate certain files. (Also see pre-process.)
  • [temp]: a scratch directory that is used for the temporary source for jekyll processing (do not use this directory for anything else)
  • [output]: where the final output from the tool (the complete IG) will be placed
  • [qa]: a folder where the validation output (validation.html) will be produced, along with a page for each fragment (for css style checking)
  • [txCache]: where the terminology service cache goes. see below.
  • [history page]: the page that lists the history of the implementation guide. This page is manually managed when the IG is published formally, so it is not produced (and cannot be produced) but is not listed as a broken link

All these folders are file paths that are relative to the control file. They are usually sub-folders, for version control/build convenience, but do not need to be. There is one more path:

  • [specification]

This is an HTTP page (http:// or file:// that points to the version of the specification on which this IG is based (use a version specific reference, not http://hl7.org/fhir itself, unless the IG is synced to the current build). It should also be the version on which the IG itself is based.

DependencyList

As stated above this is a list of other implementation guides that this guide depends on. For example building a profile upon a another profile or referencing another profile's structuredefinitions, value sets, code systems etc.

an example of this would be:

  "dependencyList": [
   
    {
       "name" : "uscore",
       "location" : "http://hl7.org/fhir/us/core",
       "source" : "definitions.json.zip"
    }

Note that a source file is generated by the IG publisher. This definitions folder 'lives' in the resources folder specified in the "[resources]" path defined above.

In theory, all extensions that are referred to should be from Implementation Guides explicitly listed in the dependencyList. However, for a variety of reasons, that's not always possible. So particular domains that are explicitly allowed as unregistered extensions can be added using the allowed-domains list - an array of strings:

 "allowed-domains" : [
   "http://my.server.url"
 ]

Terminology Service Cache

The IG Publisher uses a terminology server to support it's operations (presently, this is fhir3.healthintersections.com/au, but is planned to move to tx.fhir.org soon). In order to improve operational performance, the IG publisher caches the outcome of all interactions with the terminology server. This makes a substantial difference to the performance of the publication, but also means that there's a risk of the terminology content becoming stale.

IG authors can choose to put the terminology cache into version control. This means that all builds (either by authors or by CI builds) get the same content, and reduces the load on the terminology server. Also, all authors get fully efficient publication. This also means that flushing the terminology cache is under the control of the editors process. It also means that editors have to commit the contents of the txCache when committing. Note that there is never any reason not to simply commit whatever changes have happened, and no user review is needed on this.

Note that the CI build does not maintain it's own persistent cache; if the terminology cache is not in version control, it will not have a terminology cache.

There are several ways to delete the terminology service cache:

  • find the directory and manually delete content from it (e.g. all files). This is can be done safely at any time
  • run the IG Publisher with the parameter -resetTx - this clears the folder
  • run the IG Publisher with the parameter -resetTxErrors - this clears the folder of any errors from the terminology server but keeps successful operations
  • the terminology cache will be flushed completely when the terminology server is upgraded

Terminology Options

If you use SNOMED CT, you must specify a SNOMED CT Edition to use:

 "sct-edition" : "http://snomed.info/sct/[module]",

where [module] comes from this list:

  • International: 900000000000207008
  • us: 731000124108
  • AU: 32506021000036107
  • Spanish: 449081005
  • Danish: 554471000005108
  • Dutch: 11000146104
  • Swedish: 45991000052106
  • UK: 999000041000000102
  • CA: 20611000087101

Note that you can only specify a version supported by the infrastructure (currently: International, US, AU, CA). You can specify a version if you want (but it will fail if this is a different version to the infrastructure). You will have to delete the terminology cache if you change this value.

In addition to this, you can specify whether to include inactive codes or not:

   "activeOnly" : "true",

By default, inactive codes are included

Pre-processing Pages

The IG publisher can pre-process pages. If you specify a pre-process option, then the IG publisher will copy the content from the pre-process directory and will then do one or more of two things:

  • rather than putting it directly in the "pages" folder, will place it in the designated subfolder of pages. This allows pointing to a folder that contains content intended to map to _data, _includes or some other sub-folder without needing to create a directory hierarcy in the implementation guide's source files
  • executing the specified transform on it as it copies the content. Directory structure will be preserved. Note: changes to the transform are not picked up when running in -watch mode.

The transform engine uses XSLT1 not XSLT2 (e.g. the standard java transform engine).

Processing Options

These are global flags that control FHIR specific pre-processing associated of profiles. All the flags default to false.

Fragment & Template Options

When deciding whether to produce a particular kind of fragment, the IG Publisher will look for a property of type boolean with the name given below. Similarly, when deciding to produce a particular type of web page, it will look for a template file (also described below).

In either case, it will look in the following places, in order:

  • on the resource entry for the resource in question
  • on the defaults entry for the resource type in question
  • on the defaults entry for "ANY"

For fragment codes, if the IG tool doesn't find anything, it will produce the fragment. For templates, if no template is found, it will NOT produce an output page.

Fragment Codes

There will be one each of these fragments for each resource type that is found:

  • xml: XML version of the resource (all resource types)
  • json: JSON version of the resource (all resource types)
  • ttl: Turtle version of the resource (all resource types)
  • xml-html: html representation of XML version of the resource (all resource types)
  • json-html: html representation of JSON version of the resource (all resource types)
  • ttl-html: html representation of Turtle version of the resource (all resource types)
  • html: narrative of resource as html
  • summary: An html summary for the resource (all conformance resources)
  • content: An HTML representation of the content in resource (code system, concept map, structure map)
  • xref: A list of all the places where the resource is used (all conformance resources)
  • cld: An HTML representation of the content in resource (value set)
  • expansion: The expansion of the value set (Value set)
  • shex: ShEx statement for the structure (Structure Definition)
  • sch: schematron statement for the structure (Structure Definition)
  • json-schema: JSON Schema statement for the structure (Structure Definition)
  • header: Description of the identification of the structure (Structure Definition)
  • diff: Logical Table of the diff (Structure Definition)
  • snapshot: Logical Table of the snapshot (Structure Definition)
  • pseudo-xml: XML template for the snapshot (Structure Definition);
  • pseudo-json: JSON template for the snapshot (Structure Definition)
  • pseudo-ttl: Turtle template for the snapshot (Structure Definition)
  • uml: UML diagram for the structure (Structure Definition)
  • tx: Terminology Notes for the structure (Structure Definition)
  • inv: invariant summary for the structure (Structure Definition)
  • dict: Detailed Element Definitions (Structure Definition)
  • dict-active: Detailed Element Definitions (Structure Definition), but only including elements with max cardinality > 0
  • maps: Presentation of the mappings (Structure Definition)
  • span: Presentation of all profiles a profile refers to (StructureDefinition where derivation = constraint)
  • spanall: Presentation of all profiles & base resources a profile refers to (StructureDefinition where derivation = constraint)
  • script: Script language rendition of a StructureMap (StructureMap)
  • profiles: List of Profiles generated from a StructureMap (StructureMap)

In addition, the publisher produces the following set of fragments for listing all the content:

  • list-[type].xhtml
  • table-[type].xhtml

If there are any structure definitions of the right type, the publisher will also produce the following:

  • table-profiles.xhtml & list-profiles.xhtml
  • table-extensions.xhtml & list-extensions.xhtml
  • table-logicals.xhtml & list-logicals.xhtml

Page templates

The IG tooling can automatically generate 0 or more HTML pages for each type of resource included in the IG. To generate files for resources, a template file must be declared that provides the base structure for what the resource file should look like. The template file will be a jekyll source file (e.g. html or markdown etc.) containing imports, variable references and other embedded control tags used by the static generation tool to produce the fully populated resource-specific pages.

The template can be declared in the default section for ANY or a specific type or for a specific artifact id. There are three standard templates available:

  • template-base defines the base page that acts as the home page when references are encountered to that resource. Each resource should have one of these
  • template-defns defines the base that provides the data dictionary with anchors for each data element in a structure definition. (In the future, this may be applicable to other resources too - let us know)
  • template-fmt defines the page format for pretty-printed views of the JSON, XML and TTL representations of the resource.

The file names of these generated pages will default to the following:

  • base: [ResourceType]-[id].html
  • defns: [ResourceType]-[id]-definitions.html
  • fmt: [ResourceType]-[id].[fmt].html where [fmt] is xml, json and ttl

In addition to these, additional template types can be declared (e.g. for mappings, lists of referenced elements, etc.) To provide support for additional template types, the name of each template type must be included in the extraTemplates list. This name is appended to "template-" to create the name of the template tag. (For example, "template-mapping", "template-foo" and "template-bar" in the example above.) The default file name is [ResourceType]-[id]-[templateName].html, for example [ResourceType]-[id]-mapping.html.

These file names can be overridden on a per-resource instance basis by declaring an alternate name in the resource declaration. For example,

 "StructureDefinition/123": {
   "base": "my123.html",
   "defns": "my123-defs.html"
 }

When the template files are used, they are pre-processed and then copied to the correct place for the xml/json/ttl wrapper for each resource. When copied, the following strings will be replaced:

  • {{[title]}} - a description of the content of the resource (typical use: <h2>{{[title]}}</h2>)
  • {{[name]}} - the path for the source fragment to include (proper use: {% include {{[name]}}.xhtml %})
  • {{[id]}} - the id of the resource
  • [[[type]}} - the type of the resource
  • [[[uid]}} - type-id (combination)

HTML Template

In addition to the pages generated from artifacts, implementation guides will typically have non-generated HTML pages that provide navigation, background and other supporting information. In most IGs, these pages will follow a typical pattern in terms of header and footer, with only the "body" of the page changing. To allow this content to be edited in pure XHTML (with schema validation support), the IG publisher allows identifying a Jekyll template file that is to be used for some or all such files. The tool will look for HTML pages that are referenced in the implementation guide file but are not present in the pages folder. For each one found, it will look for a corresponding XML file and apply the templates specified with the html-template property.

Suppressed Warnings

Warnings and information messages will occasionally be generated that are "known" and unavoidable based on the design of a particular implementation guide. When there are a large number of these, it can be difficult for someone reviewing the qa page to distinguish which warnings they need to pay attention to and which are new/important. This option allows the IG configuration file to identify a text file containing a list of warnings to suppress from the QA reports. Each line of the file should contain either the full text of the warning to suppress (as shown in qa.txt) or just the display message to suppress (if the message should be suppressed regardless of which file or location triggers the issue). This mechanism can suppress information messages, warning messages and errors related to broken links (e.g. if a link is created to a file produced during post-processing or that otherwise isn't resolvable during the IG publication process).

For example to suppress a couple of informational messages for any artifact and a error message related to a specific artifact in the QA report create a text file 'mySuppressedWarnings.txt' (or whatever name you like) which contains the following three lines:

Instance includes element that is not marked as 'mustSupport' and was validated against profiles declaring mustSupport=true
Unable to check minimum required (1) due to lack of slicing validation
Communication/rr-example-3: Communication.definition: Unable to resolve resource 'PlanDefinition/authoringagency-1'

and add the following line to the configuration file. :

 "suppressedWarningFile": "[path]mySuppressedWarnings.txt"

Loading Resources

Resources are loaded as follows:

  • The IG resource is loaded (by literal filename)
  • any spreadsheets are loaded (by literal filename) and converted to resources (for editor support, all the identities of the generated resources are noted in the validation output)
  • any bundles are loaded (by Type/id)
  • any resources referenced in the IG resource are loaded (by Type/Id)

Note: The IG resource must use sourceReference references by id. e.g.

 <sourceReference>
   <reference value="ValueSet/my-value-set"/>
 </sourceReference>

A Type/Id reference is resolved to a to a local file by the control file, using the object /resources/"[Type]/[id]". If this object does not exist, the IG publication will fail. If this object exists, and has no "source" property, then the source property specifies the location of the file source relative to the IG file. If there is no "source" property, the IG publisher will look for [resources]/[Type]-[id].xml/json or [Type]-[id].xml/json (it's at editor discretion whether to store files using the simpler form, since this can cause conflicts between different resources with the same id (e.g. both Patient and Practitioner with the id of 'example')

By default, the version of the input resource is assumed to be the same version is the IG Publisher itself. However the IG publisher can also load resources from Forge. in order to load resources from forge, specify the version "1.0.1" for each forge resource. Note: this is only known to work reliably for StructureDefinition resources

Using Bundles

There's 2 different ways to use Bundles. The first way is examples of type Bundle. These are treated like any other resource. The second is where the bundle is a collection that contains a set of resources that need to be processed individually by the IG Publisher. To specify one of these bundles, use the "bundles" property:

   "bundles" : [
     "[id]"
   ]

The bundles property is an array of strings, where each entry is the id of a bundle. The bundle will be located using the standard resource location process, but once loaded, the bundle itself will be ignored, and the individual resources processed directly. Each resource in the bundle must have an entry in the resources section, and should be entered in the implementation guide.

Using Spreadsheets

For legacy reasons, it's possible to author profiles using spreadsheets. This approach is deprecated. To get the IG publisher to process a spreadsheet:

   "spreadsheets" : [
     "[filename]"
   ]

This is an array of strings, which each entry is the filename of the spreadsheet, relative to the control file. Each resource represented in the spreadsheet (profiles, value sets, search parameters) must have an entry in the resources section, and should be entered in the implementation guide. Note that the loading is order dependent - the author must ensure dependent profiles are listed and loaded after the ones they depend on.

There's some differences between the spreadsheets used in the build directly, and the spreadsheets used by the IG Publisher, and these are changes that must be made manually:

  • Value Set references - use either
    • ValueSet/xxx a reference to a value set defined in the IG, and registered directly in the implemnentation guide resource
    • http(s)://... a reference to a value set from outside the IG, or in the IG
    • valueset-xxx where:
      • valueset-xxx is the name of a file found in the same directory as the spreadsheet
      • The filename must not have .xml or .json on it, but a file with either .xml or .json appended to it must exist
      • The file must be a ValueSet resource, with an id of xxx and the appropriate canonical URL
  • Search Parameters
    • You have to provide a fluent path expression directly ("Expression")
    • you have to provide a description directly
    • you have to specify the target types directly
  • Types
    • the build tool allows for the use of "SimpleQuantity" and other data type profiles (not that the build tool uses any other) as types, but they have to be invoked as profiles in the IG spreadsheets
    • You can specify ElementDefinition.type.versioning by appending a ~ then the versioning code to the type
  • Note that IG publisher enforces the use of correct ids and canonical URLs against the base stated in the control file

Special URLs

For MetadataResources - CodeSystem, ValueSet, etc (anything with a canonical URL) - the IG publisher expects that their Canonical URL is equal to [canonical]/[type]/[id] where [canonical is the IG canonical URL. The IG publisher will ensure that the IG itself is an valid FHIR implementation guide and responds correctly to requests for the resources by their canonical URL.

However in some cases, it's not possible or appropriate for a metadata resource to use the same canonical URL as where the IG is publishing it. In these cases, the URLs that are exempt from this rules need to listed explicitly in the special-urls property, which is array of strings that are the exempt URLs.

Notes:

  • URLs have to be explicitly listed because it's too easy for an author to make a mistake and get the canonical URL wrong
  • one case for using this facility is where the IG includes a resource that is also published elsewhere. Author's should think hard before doing this - referring to a resource by it's canonical URL rather than copying into the IG is generally a much better approach in terms of ongoing maintenance.

Jurisdiction

The IG publisher can be configured to automatically fill out the Jurisdication on any Metadata Resources it encounters ([Resource].jurisdiction). Provide one or mode codes separated by commas, where the code is taken from http://build.fhir.org/valueset-jurisdiction.html (countries or regions only, no US states. System is not needed). Use code 001 for international specifications.

Language Support

Note: this section is draft - the functionality described here is not yet implemented.

By default, the IG publisher is semi-language agnostic. Content from resources or pages is published in whatever language is expressed in the resources and the pages, but text injected by the IG publisher itself (some sprinkled text scattered through the include files) is in English. The intent of this mode is to support English language publishing.

It's possible to publish Implementation Guides in other languages, or to publish them in multiple languages. Note, though, that there is always a single master language that the IG Publisher uses when publishing.

Specifying an Alternate Master Language

To change the language from English, specify a language using the "language" property in the json control file:

 "language" : "es-AR"

(The language tag is a standard xml:lang .e.g. BCP 47 tag. It must have a language, and may have a country (as shown above). Other sub-tags are not allowed)

When an alternative language is specified, the IG publisher changes how it works in the following ways:

  • When reading any text from a resource definition, the IG publisher will first look at any [translation extensions] on the element for a matching language tag (full match including country first, then partial match). If there's no matching extension, it will just use the element value. This applies to any elements of type 'string' or 'markdown'
  • When looking up codes on the terminology server, the IG publisher will ask for the specified language. tx.fhir.org uses the same approach as immediately above in this case. Note: to get code system displays in additional languages defined on tx.fhir.org, talk to Grahame Grieve
  • Any text that is used by the IG publisher that is not in the specified language will be pass to an internal translation module that can translate the text to the target language. This is driven by a configuration file that has a list of mappings from language to language. The input file to configure this is languages.json in the same directory as the config file. There will be a file produced in the qa directory, also called languages.txt, which is the same file with any untranslated texts added (to help editors build the language file)
  • Any content in the pages is left untouched.

Using multiple languages

In addition, the IG publisher can produce fragments in multiple languages. To do this, specify additional languages using the language property;

 "languages" : [ "du", "es", "ru"]

Note that you must specify a primary language if you specify additional languages.

When you specify additional languages, for each output file that the IG publisher creates, it will also create additional fragments with same base file name, with -[lang] appended, in the specified language. This way, authors can build IGs in multiple languages. In this case, the language file will contain additional langauge codes but work as otherwise described above.

Sharing Language Translations Across IGs

Todo. Not sure about this yet

Build Tools

Jekyll

Installation: https://jekyllrb.com/ (see [Jekyll on Windows] for windows users)

in config file:

  "tool":"jekyll"


For Jekyll, some data files are also generated. The data from these is available when generating pages. e.g.

 { { site.data.fhir.version } } 

inserts the version of the FHIR specification used by the build (without spaces between the {, which can't be done properly on this wiki). The following data is available:

  • path : path to the main FHIR specification
  • canonical : canonical path to this specification
  • errorCount : number of errors in the build file (not including HTML validation errors)
  • version : version of FHIR
  • revision : revision of FHIR
  • versionFull : version-revision
  • totalFiles : total number of files found by the build
  • processedFiles : number of files genrated by the build
  • genDate : date of generation (so date stamps in the pages can match those in the conformance resources)

Also, a file generated for the structure definitions. Each structure definition is listed by it's id, along with the following data for each id. For example this is some Jekyll liquid syntax to access the Resource type from an example instance using the type parameter from the list below.

   include list-{{ site.data.structuredefinitions.{{[id]}}.type | slugify }}.xhtml
  • url : full canonical url for the structure
  • name : the name given for it
  • path : the path to it in the built html
  • kind : the kind (complex data type, resource, logical model)
  • type : the base type
  • base : the url for structure definition from which it derives
  • basename : the name of the structure definition from which it derives
  • basepath : the url to the structure definition from which it derives
  • status : the status (draft, active, retired)
  • date : the date in the resource
  • publisher : the stated publisher
  • copyright : the stated copyright for the resource
  • description : the description for the resource
  • contextType : the type of context associated with an extension structure definition
  • contexts : an array of paths for each allowed context path for an extension

Rules for Implementation Guides

Format Support

The Implementation Guide supports 3 formats, as defined in the FHIR specification:

  • XML
  • JSON
  • Turtle (RDF)

Note: in this documentation, [fmt] is one of 'xml', 'json', and 'ttl'.

By default, the IG publisher will produce all 3 of these formats. It is recommended to produce all 3, though specific formats can be turned off - but you must produce at least one.

Layout

The Implementation Guide author is free to lay out the content in what form they choose. However there are some rules about the arrangement of the implementation guide that must be followed:

  • the home page should be 'index.html' (this is not a technical requirement, but is a human convenience)
  • for each resource in the implementation guide, whether a conformance resource or an example, the IG Publisher will produce
    • [Type]-[id].html - the home page for the resource (note: you can rename this page using the control file)
    • [Type]-[id].[fmt] - the resource for the specified format (pretty printed)
    •  !! [Type]-[id].canonical.[fmt] - the resource for the specified format in canonical format (not produced for ttl) (not currently produced)
    • redirects from /[Type]/[id] to one of the pages above (depending on request format)
    • [Type]-[id].[fmt].html - An HTML wrapper around the specified format, with a link to the native form
  • the IG publisher will produce the files definitions.[fmt].zip. The community will expect that these are published along with the guide as these enable the conformance tooling to work with the guide. These should be referenced somewhere from the guide, but the tooling will just expect that they exist at [canonical]/definitions.[fmt].zip, irrespective of whether they are linked from the narrative

URLs

Canonical URL

The Implementation Guide must nominate a canonical URL, which we'll refer to as [canonical]. This canonical URL is used throughout all the resources (this is enforced by the publisher). The canonical URL should point to the current version of the IG that you're publishing, so if someone enters the canonical URL into their browser, they will get the IG home page (for example, http://example.com/fhir/mypatientprofile).

If possible, this should also be a FHIR server hosting resources - so a GET of [canonical]/[Type]/[id] should return a FHIR resource. For example, http://example.com/fhir/Patient/mysamplepatient would give you a sample Patient resource used throughout the specification.

ImplementationGuide.url

The ImplementationGuide.url element in your ImplementationGuide resource should be set to [canonical]/ImplementationGuide/[id], and that should redirect you to the base URL when entered into the browser - for example, entering ImplementationGuide.url of http://example.com/fhir/mypatientprofile/ImplementationGuide/mypatientprofile in the browser should take you to http://example.com/fhir/mypatientprofile.

History

Each Implementation Guide is also responsible for maintaining it's own published history. The standard way that this works for FHIR should be followed by the implementation guides:

  • The current copy of the specification lives at [canonical]
  • the published version history lives at [canonical]/directory.html (or similar name) and is manually maintained. It lists the current version, maybe the dev version location, and a history of past milestones
  • the past milestones live at [canonical]/[id] where id is either a milestone name like "stu1" or a date (recommended format = YYYY)
  • at least the home page of all the versions (current or historical) references the published version history in a prominent location

The IG publisher is only able to produce a single snapshot of the IG at a time - so in order to create your history, you'll need to manually move old versions to [canonical]/[id] and update the [canonical]/directory.html with a link to it.

Styles

All the generated fragments are generated assuming that the standard FHIR styles in fhir.css apply to the specified classes in the generated content. To keep the content valid, the simplest way is to include fhir.css in all your html pages as a style reference. But you don't have to do this; if you have some other styling system, you can make arrangements for the correct css definitions - which are deliberately very static - to be made available in some other form. You can even replace the styles completely and use your own.

Note, however this warning: The FHIR team does not provide support for replacing any CSS styles. In order to assist with this, for every generated fragment, there is a matching .html file created in the qa directory. The FHIR team will respond to any issue relating to incorrect display of the content of the qa html files. If the content does not appear correctly in the IG, but does appear correctly in the qa files, then this is assumed to be a problem with the IG styling, and not the problem of the IG Publisher authors.

Implementation Guide Layouts

Generally, there are 3 different approaches to organizing an implementation guide

  • let the IG build generate an html file for each conformance resource (don't need to fill the instances out in the json control file, just use the templates to make them look like you want). Write some introduction pages stringing them altogether
  • hand write a page for each conformance resource, bringing in pieces of html into the pages, and choosing the page names for the resources (in the control file). And writing narrative to string all the pages together
  • write a set of pages, and include the bits of html into the page where appropriate. Each conformance resource has a notional home somewhere in one of the pages (again, in the control file, using [page]#[fragment]

All 3 approaches are valid, with different advantages and disadvantages. You can mix'n'match all 3 approaches - it's driven by how you create the pages, and configure the IG output. The key thing is to have a very clear idea how the pages are strung together, and how the resource identification / page naming strategy works for your implementation guide.

Swagger

Note: this section is draft - the functionality described here is not yet implemented.

The IG publisher can produce swagger definitions for the API defined by the implementation guide. The following object goes into the JSON control file (described above):

 "swagger" : [{
   "mode" : "single | split",
   "capabilities" : "[id]",
 }]

The IG publisher will produce one set of swagger definitions for each entry in the list.

Mode

Whether to generate a single swagger file for all resources (single), or a file for each resource (split).

Capabilities

The id of the capabilities statement to use as the base for generating the swagger file.

Troubleshooting

Notes about troubleshooting:

  1. before doing any trouble shooting, make sure you are running the latest IG publisher for the version of FHIR you are using
  2. Jekyll may not run if you have spaces your file path. Move to root directory, or eliminate spaces.
  3. if the Jekyll part of the build fails, it fails completely, and the old output is left in place
  4. if the build completes, and there's problems in the output, first, work through all the errors in the validation output before you ask for help
  5. Jekyll error "Permission denied @unlink_internal" - you have a file locked in the temp or output directory. Close any files in editors, and ensure you are only running one publisher
  6. If you're going to ask Grahame for help send the file fhir-ig-publishing.log in your temp directory to grahame@hl7.org along with a detailed description of what the problem is. (Alternatively, run the GUI version click, wait for the end ofthe run, and the click on the 'Debug Summary' button which puts the log on the clipboard so you can send pate it into your email)

Before you ask about any terminology or dependency related issues, delete the content of your txCache directory, and run the IG publisher again

Logging

The IG publisher performs 3 sorts of logging:

  • basic progress logging to stdout (what you see)
  • A full log to [tmp]/fhir-ig-publishing-tmp.log
  • in case of build failure, a debugging report to fhir-ig-publishing.log

You can change to amount of logging that goes to stdout using this option in the json file:

 "logging" : ["option1", "option2"]

where the options are any of these words:

  • init: log extra details about the IG publisher initialization sequence
  • progress: log extra details about the sequence of actions taken by the IG publisher
  • context: log each time a resource is added to the context (e.g. support validation)
  • html: log HTML link checking details
  • tx: detailed messages from the terminology sub-system

This is particularly useful when debugging the auto-build when all you get is the stdout.

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