diff options
| -rwxr-xr-x | examples/dataset-metadata-git.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/examples/dataset-metadata-git.scm b/examples/dataset-metadata-git.scm new file mode 100755 index 0000000..f2bde48 --- /dev/null +++ b/examples/dataset-metadata-git.scm @@ -0,0 +1,76 @@ +#! /usr/bin/env guile + +!# +(use-modules + (ice-9 getopt-long) + (srfi srfi-26) + ((ice-9 regex) #:select (regexp-substitute/global)) + ((transform strings) #:select (string-blank?)) + ((transform sql) #:select (call-with-target-database sql-for-each)) + ((transform triples) #:select (string->identifier))) + +(define (save-file file result) + (when result + (let ((dir-name (dirname file))) + (unless (file-exists? dir-name) + (mkdir dir-name)) + (with-output-to-file file + (lambda () + (format #t result)))))) + +(define (infopages/sql->rtf result) + (let* ((get (cut assoc-ref result <>)) + (get* (compose (lambda (str) + (if (string-blank? str) + #f + str)) + get)) + (identifier (string->identifier + "" + (regexp-substitute/global #f "[^A-Za-z0-9:]" + (get "InfoPageName") + 'pre "_" 'post))) + (dir-name (string-append "/export/data/genenetwork/data/")) + (file-name (cut string-append dir-name <>)) + (summary (get* "Summary")) + (tissue (get* "AboutTissue")) + (specifics (get* "Specifics")) + (cases (get* "AboutCases")) + (platform (get* "AboutPlatform")) + (processing (get* "AboutDataProcessing")) + (notes (get* "Notes")) + (experiment-design (get* "ExperimentDesign")) + (acknowledgment (get* "Acknowledgment"))) + (for-each (lambda (x) + (save-file (file-name (string-append dir-name (car x))) + (cdr x))) + `(("summary.rtf" . ,summary) + ("tissue.rtf" . ,tissue) + ("specifics.rtf" . ,specifics) + ("cases.rtf" . ,cases) + ("platform.rtf" . ,platform) + ("processing.rtf" . ,processing) + ("notes.rtf" . ,notes) + ("experiment-design.rtf" . ,experiment-design) + ("acknowledgement.rtf" . ,acknowledgement))))) + +(let* ((option-spec + '((settings (single-char #\s) (value #t)) + (output (single-char #\o) (value #t)))) + (options (getopt-long (command-line) option-spec)) + (settings (option-ref options 'settings #f)) + (output (option-ref options 'output #f)) + (query "SELECT InfoPageName, Datasets.Summary, Datasets.AboutTissue, InfoFiles.Specifics, +Datasets.AboutCases, Datasets.AboutPlatform, Datasets.AboutDataProcessing, +Datasets.Notes, Datasets.ExperimentDesign, Datasets.Acknowledgment +FROM InfoFiles LEFT JOIN Datasets USING (DatasetId) LIMIT 2") + (%connection-settings + (call-with-input-file settings + read))) + ;; TODO + (call-with-target-database + %connection-settings + (lambda (db) + (sql-for-each infopages/sql->rtf + db + query)))) |