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Add a command line argument to specify the base uri #349

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Add a command line argument to specify the base uri #349

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b89723a
Add a command line argument to specify the base uri
stevorobs3 Dec 4, 2023
4ff340a
Remove unused binding
stevorobs3 Dec 4, 2023
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4 changes: 2 additions & 2 deletions src/csv2rdf/csvw.clj
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Expand Up @@ -58,9 +58,9 @@
like `:minimal`, but it also includes RDF data from the CSVW metadata
json file."
([tabular-source metadata-source] (csv->rdf tabular-source metadata-source {}))
([tabular-source metadata-source {:keys [mode] :as options}]
([tabular-source metadata-source {:keys [mode base-uri]}]
(let [mode (or mode :standard)
{:keys [tables] :as metadata} (processing/get-metadata tabular-source metadata-source)
{:keys [tables] :as metadata} (processing/get-metadata tabular-source metadata-source base-uri)
table-group-dialect (:dialect metadata)
output-tables (remove properties/suppress-output? tables)
{:keys [statements] :as ctx} (table-group-context mode metadata)
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11 changes: 7 additions & 4 deletions src/csv2rdf/main.clj
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Expand Up @@ -15,6 +15,7 @@
[["-t" "--tabular TABULAR" "Location of the tabular file"]
["-u" "--user-metadata METADATA" "Location of the metadata file"]
["-o" "--output-file OUTPUT" "Output file to write to"]
["-b" "--base-uri URI" "The base uri to use"]
["-m" "--mode MODE" "CSVW mode to run"
:validate [#(contains? #{:minimal :standard :annotated} %)]
:default :standard
Expand Down Expand Up @@ -51,9 +52,10 @@
:summary summary}))
options)))

(defn- write-output [writer {:keys [rdf-format tabular-source metadata-source mode]}]
(defn- write-output [writer {:keys [rdf-format tabular-source metadata-source mode base-uri]}]
(let [dest (gio/rdf-writer writer :format rdf-format :prefixes nil)]
(csvw/csv->rdf->destination tabular-source metadata-source dest {:mode mode})))
(csvw/csv->rdf->destination tabular-source metadata-source dest {:mode mode
:base-uri base-uri})))

(defmulti display-error
"Displays an exception in the UI"
Expand All @@ -71,11 +73,12 @@

(defn- inner-main [args]
(let [options (parse-cli-options args)
{:keys [mode tabular user-metadata output-file]} options
{:keys [mode tabular user-metadata output-file base-uri]} options
opts {:tabular-source (some-> tabular parse-source)
:metadata-source (some-> user-metadata parse-source)
:rdf-format (or (some-> output-file formats/->rdf-format) RDFFormat/TURTLE)
:mode mode}
:mode mode
:base-uri (some-> base-uri (URI.))}
output-file (some-> output-file io/file)]
(if output-file
(with-open [w (io/writer output-file)]
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7 changes: 2 additions & 5 deletions src/csv2rdf/metadata.clj
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Expand Up @@ -18,12 +18,9 @@

:else (make-error context "Expected top-level of metadata document to describe a table or table group"))))

(defn parse-table-group-from-source [source]
(defn parse-table-group-from-source [source base-uri]
(let [json (source/get-json source)]
(parse-metadata-json (source/->uri source) json)))

(s/fdef parse-table-group-from-source
:args (s/cat :source (s/and ::source/uriable ::source/json-source)))
(parse-metadata-json (or base-uri (source/->uri source)) json)))

(defn ^{:tabular-spec "5.1"} overriding-metadata
"Construct an 'overriding metadata' document if the user provides both tabular and
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11 changes: 6 additions & 5 deletions src/csv2rdf/tabular/processing.clj
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Expand Up @@ -17,23 +17,24 @@
(table/validate-compatible validating? user-table table-metadata)
(table/compatibility-merge user-table table-metadata)))

(defn- from-metadata-source [metadata-source]
(let [{:keys [tables] :as user-table-group} (meta/parse-table-group-from-source metadata-source)
(defn- from-metadata-source [metadata-source base-uri]
(let [{:keys [tables] :as user-table-group} (meta/parse-table-group-from-source metadata-source base-uri)
validating? false
merged-tables (mapv (fn [table] (validate-merge-table validating? table)) tables)
merged-table-group (assoc user-table-group :tables merged-tables)]
(set-table-group-parents merged-table-group)))

(defn ^{:tabular-spec "6.1"} get-metadata

"Retrieves and resolves the metadata given either a tabular data source or metadata source. If user metadata
is provided, each referenced table definition is validated against the corresponding tabular data file."
[tabular-source metadata-source]
[tabular-source metadata-source base-uri]
(cond
(and (some? tabular-source) (some? metadata-source))
(from-metadata-source (meta/overriding-metadata tabular-source metadata-source))
(from-metadata-source (meta/overriding-metadata tabular-source metadata-source) base-uri)

(some? metadata-source)
(from-metadata-source metadata-source)
(from-metadata-source metadata-source base-uri)

(some? tabular-source)
(from-tabular-source tabular-source)
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