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Update user docs #364

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merged 2 commits into from
Oct 26, 2023
Merged

Update user docs #364

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87f00a3
Update docs
anngvu Oct 26, 2023
19091db
Build jsonld
nfosi-service Oct 26, 2023
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15 changes: 13 additions & 2 deletions NF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -2061,7 +2061,7 @@
"@id" : "bts:centimeter"
} ],
"rdfs:label" : "workingDistanceUnit",
"rdfs:comment" : "TBD",
"rdfs:comment" : "Unit for working distance.",
"@type" : "rdfs:Class",
"sms:displayName" : "workingDistanceUnit"
}, {
Expand Down Expand Up @@ -2187,6 +2187,17 @@
"rdfs:comment" : "Technology used to perturb gene",
"@type" : "rdfs:Class",
"sms:displayName" : "genePerturbationTechnology"
}, {
"@id" : "bts:relatedResource",
"@type" : "rdfs:Class",
"rdfs:comment" : "A related resource.",
"rdfs:label" : "relatedResource",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
"@id" : "http://schema.biothings.io/"
},
"sms:displayName" : "relatedResource",
"sms:required" : "sms:false"
}, {
"@id" : "bts:specimenID",
"@type" : "rdfs:Class",
Expand Down Expand Up @@ -5029,7 +5040,7 @@
}, {
"@id" : "bts:relatedStudies",
"@type" : "rdfs:Class",
"rdfs:comment" : "Studies similar to the current study.",
"rdfs:comment" : "Studies similar to the current study. Subproperty of `relatedResource`.",
"rdfs:label" : "relatedStudies",
"rdfs:subClassOf" : [ ],
"schema:isPartOf" : {
Expand Down
83 changes: 55 additions & 28 deletions docs/docTemplate.R
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Original file line number Diff line number Diff line change
@@ -1,3 +1,55 @@
read_properties <- function(file = "../modules/props.yaml") {
props <- yaml::read_yaml(file)$slots
# props <- rbindlist(props, fill = TRUE, idcol = "Property")
props
}

# The range of prop `assay` is anything of class `Assay` --
# However, the json-ld does not make this so conceptually concise for props, instead listing all possible values
# In the docs, we don't want to enumerate all values and instead want to create a _link_ to a class that defines the range
# To do this, we can infer class by look up the class of the first listed enum for that prop
# The range could also be inferred to be a boolean or string/integer rather than a class
summarize_range <- function(prop_id, schema, return_labels = FALSE) {

enums <- nfportalutils::get_by_prop_from_json_schema(id = prop_id,
prop = "schema:rangeIncludes",
schema = schema,
return_labels = FALSE)

# handle how enums are presented
if(is.null(enums)) return("")
if(length(enums) < 5) return(paste(gsub("bts:", "", enums), collapse = ","))
if("bts:Yes" %in% enums) return("Y/N")

enum1 <- enums[1]

# additional lookup class
class <- nfportalutils::get_by_prop_from_json_schema(enum1,
prop = "rdfs:subClassOf",
schema = schema,
return_labels = FALSE)[[1]]
if(length(class) > 1) warning(enum1, " has multiple parent classes")
class <- sub("bts:", "", class[1]) # use first but warn
class <- paste0("#", class)
class
}

#' @param prop_id Namespaced id, e.g. "bts:tumorType"
summarize_range_linkml <- function(prop_id, props) {
prop_id <- sub("^bts:", "", prop_id)

# union ranges
if(!is.null(props[[prop_id]]$any_of)) {
paste0("#", unlist(props[[prop_id]]$any_of, use.names = F), collapse = "|")

} else {
class <- props[[prop_id]]$range
if(is.null(range)) class <- ""
paste0("#", class)
}
}


#' Generate template documentation
#'
#' Basically tries to present a template in a conventional format similar to:
Expand Down Expand Up @@ -38,40 +90,15 @@ docTemplate <- function(templates,
schema = schema,
return_labels = FALSE)

# The range of prop `assay` is anything of class `Assay` --
# However, the json-ld does not make this so conceptually concise for props, instead listing all possible values
# In the docs, we don't want to enumerate all values and instead want to create a _link_ to a class that defines the range
# To do this, we can infer class by look up the class of the first listed enum for that prop
# The range could also be inferred to be a boolean or string/integer rather than a class
summarize_range <- function(prop_id, schema, return_labels = FALSE) {

enums <- nfportalutils::get_by_prop_from_json_schema(id = prop_id,
prop = "schema:rangeIncludes",
schema = schema,
return_labels = FALSE)
if(is.null(enums)) return("")
if(length(enums) < 5) return(paste(gsub("bts:", "", enums), collapse = ","))
if("bts:Yes" %in% enums) return("Y/N")
enum1 <- enums[1]
# additional lookup class
class <- nfportalutils::get_by_prop_from_json_schema(enum1,
prop = "rdfs:subClassOf",
schema = schema,
return_labels = FALSE)[[1]]
if(length(class) > 1) warning(enum1, " has multiple parent classes")
class <- sub("bts:", "", class[1]) # use first but warn
class <- paste0("#", class)
class
}

prop_ref <- read_properties()

# because of the way schematic imports biothings without us having much control over it some ids can be duplicated (!)
schema <- schema[!duplicated(sapply(schema, function(x) x$`@id`))]
sms <- Filter(function(x) x$`@id` %in% prop_ids, schema)
sms <- lapply(sms, function(x) {
list(Field = x$`sms:displayName`,
Description = if(!is.null(x$`rdfs:comment`)) x$`rdfs:comment` else " ",
Required = if(!is.null(x$`sms:required`)) sub("sms:", "", x$`sms:required`) else "?",
ValidRange = summarize_range(x$`@id`, schema))
ValidRange = summarize_range_linkml(prop_id = x$`@id`, props = prop_ref))
})
tt <- rbindlist(sms)

Expand Down
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