From 977144775c0c6b19923d27f765503c209157177a Mon Sep 17 00:00:00 2001 From: Matt Jones Date: Fri, 30 Aug 2019 16:20:43 -0800 Subject: [PATCH] Rearrange chapters to have all modules in one chapter. Also, fix the links to the overall schema interactive docs, and suppress warnings on the builds. Images and schemas are now fully complete. --- docs/_bookdown.yml | 2 +- docs/build_book.R | 4 ++-- docs/eml-modules-data-structure.md | 22 +++++++++++----------- docs/eml-modules-discovery-interpret.md | 14 +++++++------- docs/eml-modules-resources.md | 20 ++++++++++---------- docs/eml-modules-utility.md | 6 +++--- docs/eml-schema.md | 4 +--- 7 files changed, 35 insertions(+), 37 deletions(-) diff --git a/docs/_bookdown.yml b/docs/_bookdown.yml index 49ae86aa..3a9ce85a 100644 --- a/docs/_bookdown.yml +++ b/docs/_bookdown.yml @@ -7,11 +7,11 @@ rmd_files: ["index.Rmd", "eml-features.md", "eml-contributors.md", "eml-220info.md", + "eml-schema.md", "eml-modules-resources.md", "eml-modules-data-structure.md", "eml-modules-discovery-interpret.md", "eml-modules-utility.md", - "eml-schema.md", "eml-validation-refs.md", "eml-semantic-annotation-primer.md", "eml-internationalization.md", diff --git a/docs/build_book.R b/docs/build_book.R index 14d837e4..518848c4 100755 --- a/docs/build_book.R +++ b/docs/build_book.R @@ -4,8 +4,8 @@ # of the repo as the index page for the entire book, rather than duplicating # the content or writing new content. -bookdown::render_book("index.Rmd", "bookdown::gitbook") +suppressWarnings(bookdown::render_book("index.Rmd", "bookdown::gitbook")) # Copy the HTML Bookdown produces from the ../README.md file to index.html file.copy("../dist/eml-ecological-metadata-language.html", "../dist/index.html", overwrite = TRUE) -file.copy(dir("../img", full.names = TRUE), "../dist/images", recursive = TRUE) \ No newline at end of file +file.copy(dir("../img", full.names = TRUE), "../dist/images", recursive = TRUE) diff --git a/docs/eml-modules-data-structure.md b/docs/eml-modules-data-structure.md index 30a7fce5..a4d145e1 100644 --- a/docs/eml-modules-data-structure.md +++ b/docs/eml-modules-data-structure.md @@ -1,4 +1,4 @@ -# Data Structure Modules +## Data Structure Modules The following three modules are used to document the logical layout of a dataset. Many datasets are comprised of multiple entities (e.g. a series @@ -16,7 +16,7 @@ eml-entity module is extended for each of these types (dataTable, spatialRaster, spatialVector, etc\...) which are described in the next section. -## The eml-entity module - Entity level information within datasets +### The eml-entity module - Entity level information within datasets Links: @@ -46,7 +46,7 @@ The eml-entity module, like other modules, may be "referenced" via the and then used as a reference in other locations within the EML document via its ID. -## The eml-attribute module - Attribute level information within dataset entities +### The eml-attribute module - Attribute level information within dataset entities Links: @@ -66,7 +66,7 @@ the \ tag. This allows an attribute document to be described once, and then used as a reference in other locations within the EML document via its ID. -### Philosophy of Attribute Units +#### Philosophy of Attribute Units The concept of \"unit\" represents one of the most fundamental categories of metadata. The classic example of data entropy is the case @@ -149,7 +149,7 @@ explicitly label attributes that contain Gregorian date and time values, and allows them to provide the information needed to parse these values into their appropriate components (e.g., days, months, years)./ -## The eml-constraint module - Relationships among and within dataset entities +### The eml-constraint module - Relationships among and within dataset entities Links: @@ -162,7 +162,7 @@ management system. These constraints include primary key constraints, foreign key constraints, unique key constraints, check constraints, and not null constraints, among potential others. -## The eml-dataTable module - Logical information about data table entities +### The eml-dataTable module - Logical information about data table entities Links: @@ -183,7 +183,7 @@ physical distribution of the data table, its overall coverage, the methodology used in creating the data, and other logical structure information such as its orientation, case sensitivity, etc. -## The eml-spatialRaster module - Logical information about regularly gridded geospatial image data +### The eml-spatialRaster module - Logical information about regularly gridded geospatial image data Links: @@ -198,7 +198,7 @@ organization of the raster cells, the cell data values, and if derived via imaging sensors, characteristics about the image and its individual bands. -## The eml-spatialVector module - Logical information about non-gridded geospatial image data +### The eml-spatialVector module - Logical information about non-gridded geospatial image data Links: @@ -212,7 +212,7 @@ relationships among them. Specific attributes of a spatial vector can be documented here including the vector\'s geometry type, count and topology level. -## Schema for validating spatial referencing descriptions +### Schema for validating spatial referencing descriptions This module defines both projected and unprojected coordinate systems for referencing the spatial coordinates of a dataset to the earth. The @@ -222,7 +222,7 @@ coordinate systems that may be referred to by name in the horizCoordSysName element. A custom projection may be defined using this schema for any projection that does not appear in this dictionary. -## The eml-storedProcedure module - Data tables resulting from procedures stored in a database +### The eml-storedProcedure module - Data tables resulting from procedures stored in a database Links: @@ -236,7 +236,7 @@ then invoke them directly from front-end applications. It allows the optional description of any parameters that are expected to be passed to the procedure when it is called. -## The eml-view module - Data tables resulting from a database query +### The eml-view module - Data tables resulting from a database query Links: diff --git a/docs/eml-modules-discovery-interpret.md b/docs/eml-modules-discovery-interpret.md index 2ab1339f..1d1e5868 100644 --- a/docs/eml-modules-discovery-interpret.md +++ b/docs/eml-modules-discovery-interpret.md @@ -1,4 +1,4 @@ -# Discovery and Interpretation Modules +## Discovery and Interpretation Modules The following six modules are used to qualify the resources being described in more detail. They are used to describe access control @@ -11,7 +11,7 @@ in many locations in order to limit the scope of the description. For instance, the eml-coverage module may be used for a particular column of a dataset, rather than the entire dataset as a whole. -## The eml-access module - Access control rules for resources +### The eml-access module - Access control rules for resources Links: @@ -160,7 +160,7 @@ rules can be overridden for particular data entities by adding additional \ elements in the physical/distribution trees of those entities. -## The eml-physical module - Physical file format +### The eml-physical module - Physical file format Links: @@ -188,7 +188,7 @@ the \ tag. This allows a physical document to be described once, and then used as a reference in other locations within the EML document via its ID. -## The eml-party module - People and organization information +### The eml-party module - People and organization information Links: @@ -207,7 +207,7 @@ The eml-party module, like other modules, may be \"referenced\" via the used as a reference in other locations within the EML document via its ID. -## The eml-coverage module - Geographic, temporal, and taxonomic extents of resources +### The eml-coverage module - Geographic, temporal, and taxonomic extents of resources Links: @@ -261,7 +261,7 @@ the \ tag. This allows the coverage extent to be described once, and then used as a reference in other locations within the EML document via its ID. -## The eml-project module - Research context information for resources +### The eml-project module - Research context information for resources Links: @@ -281,7 +281,7 @@ the \ tag. This allows a research project to be described once, and then used as a reference in other locations within the EML document via its ID. -## The eml-methods module - Methodological information for resources +### The eml-methods module - Methodological information for resources Links: diff --git a/docs/eml-modules-resources.md b/docs/eml-modules-resources.md index 84799bc7..f7178466 100644 --- a/docs/eml-modules-resources.md +++ b/docs/eml-modules-resources.md @@ -1,6 +1,6 @@ -# The EML Module and Resources +## The EML Module and Resources -## The eml module - A metadata container +### The eml module - A metadata container Links: @@ -32,7 +32,7 @@ reserved for the inclusion of metadata that may be highly discipline specific and not covered in this version of EML, or it may be used to internally extend fields within the EML standard. -## The eml-resource module - Base information for all resources +### The eml-resource module - Base information for all resources Links: @@ -62,7 +62,7 @@ document in a library of protocols. Likewise, citations are used throughout the top-level resource modules by importing the literature module. -## The eml-dataset module - Dataset specific information +### The eml-dataset module - Dataset specific information Links: @@ -89,7 +89,7 @@ the \ tag. This allows a dataset to be described once, and then used as a reference in other locations within the EML document via its ID. -## The eml-literature module - Citation-specific information +### The eml-literature module - Citation-specific information Links: @@ -105,7 +105,7 @@ Similar to other eml modules, each of the CitationType elements may be reference As of EML 2.2.0, each CitationType element can use the \ element as an alternative to encoding citations in the EML XML structures. BibTeX entries generally play well inside of XML structures, but XML escaping is still needed for special characters so consider embedding BibTeX entries in CDATA blocks if XML escaping is cumbersome. -### eml-literature module - literature cited +#### eml-literature module - literature cited Citations to articles or other resources that are referenced in the data set or its associated metadata should be included in a \ element. \ is a CitationListType cataloging one or more citations that represent a bibliography of works related to the data set for reference, comparison, or other purposes. These citations can be a series of \ elements, a \ element featuring one or more BibTeX-style citations, or a mix of the two types. @@ -180,7 +180,7 @@ Citations to articles or other resources that are referenced in the data set or ``` -### eml-literature module - usage citation +#### eml-literature module - usage citation A citation to an article or other resource in which the data set is used or referenced should be included in a \ element, a CitationType detailing a literature resource that has used or references this data set. It is not expected that one or more usage citations will necessarily be an exhaustive list of resources that employ the data set, but rather will serve as a example(s) and pointer(s) to scholarly works in which this data set has been used. The \ element can be a \ or \ element. @@ -227,7 +227,7 @@ A citation to an article or other resource in which the data set is used or refe ``` -### eml-literature module - reference publication +#### eml-literature module - reference publication A citation to an article or other resource that serves as an important reference for a data set should be documented in a \ element. Anyone using the data set should generally cite the data set itself (using the creator, pubDate, title, publisher, and packageId fields), and consider providing an additional citation to the reference publication. The \ element will typically be used when the data set and a companion or associated paper are published near concurrently. Common cases where a reference publication may be useful include when a data paper is published that describes the dataset, or when a paper is intended to be the canonical or exemplar reference to the dataset – these are features that distinguish the \ CitationType from the \ CitationType. @@ -257,7 +257,7 @@ A citation to an article or other resource that serves as an important reference ``` -## The eml-software module - Software specific information +### The eml-software module - Software specific information Links: @@ -276,7 +276,7 @@ the \ tag. This allows a software resource to be described once, and then used as a reference in other locations within the EML document via its ID. -## The eml-protocol module - Research protocol specific information +### The eml-protocol module - Research protocol specific information Links: diff --git a/docs/eml-modules-utility.md b/docs/eml-modules-utility.md index 854be63e..1e36a160 100644 --- a/docs/eml-modules-utility.md +++ b/docs/eml-modules-utility.md @@ -1,4 +1,4 @@ -# Utility Modules +## Utility Modules The following modules are used to highlight the information being documented in each of the above modules where prose may be needed to @@ -6,7 +6,7 @@ convey the critical metadata. The eml-text module provides a number of text-based constructs to enhance a document (including sections, paragraphs, lists, subscript, superscript, emphasis, etc.) -## The eml-text module - Text field formatting +### The eml-text module - Text field formatting Links: @@ -29,7 +29,7 @@ text blocks. Combinations of plain text, docbook sections, and markdown sections can be interleaved in any order, but most people will likely find the markdown syntax the easiest to use. -## The eml-semantics module - Semantic annotations for formalized statements about EML components +### The eml-semantics module - Semantic annotations for formalized statements about EML components Links: diff --git a/docs/eml-schema.md b/docs/eml-schema.md index 6f322097..6ce71401 100644 --- a/docs/eml-schema.md +++ b/docs/eml-schema.md @@ -5,6 +5,4 @@ of a valid EML document. In this chapter, all of the elements and types defined within those EML schemas are displayed using diagrams illustrating the relationships among these components. -```{r echo=FALSE} -knitr::include_url("./schema/index.html", height="1200px") -``` +Browse EML Schema Documentation