Delete old dataset modelling.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

2 files changed, 0 insertions, 531 deletions

diff --git a/examples/dataset-metadata-git.scm b/examples/dataset-metadata-git.scm
deleted file mode 100755
index c9ea59b..0000000
--- a/examples/dataset-metadata-git.scm
+++ /dev/null
@@ -1,94 +0,0 @@
-#! /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? string-capitalize-first))
- ((transform sql) #:select (call-with-target-database sql-for-each)))
-
-(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 "~a" result))))))
-
-(define (infopages/sql->rtf result)
-  (let* ((get (cut assoc-ref result <>))
-         (get* (compose (lambda (str)
-                          (if (or (string-blank? str)
-                                  (string-ci=?
-                                   (string-trim-both str) "None"))
-                              #f
-                              str))
-                        get))
-         (identifier
-          (string-capitalize-first
-           (regexp-substitute/global
-            #f "[^A-Za-z0-9:]"
-            (get "InfoPageName")
-            'pre "_" 'post)))
-         (dir-name "/export/data/genenetwork/gn-docs/general/datasets/")
-         (file-name (cut string-append dir-name <>))
-         (summary (get* "Summary"))
-         (tissue (get* "AboutTissue"))
-         (specifics (get* "Specifics"))
-         (contributors (get* "Contributors"))
-         (cases (get* "AboutCases"))
-         (platform (get* "AboutPlatform"))
-         (processing (get* "AboutDataProcessing"))
-         (notes (get* "Notes"))
-         (citation (get* "Citation"))
-         (experiment-type (get* "Experiment_Type"))
-         (experiment-design (get* "ExperimentDesign"))
-         (acknowledgment (get* "Acknowledgment")))
-    (for-each (lambda (x)
-                (save-file
-                 (string-append (file-name identifier)
-                                "/"
-                                (car x))
-                 (cdr x)))
-              `(("summary.rtf" . ,summary)
-                ("tissue.rtf" . ,tissue)
-                ("citation.rtf" . ,citation)
-                ("specifics.rtf" . ,specifics)
-                ("cases.rtf" . ,cases)
-                ("platform.rtf" . ,platform)
-                ("processing.rtf" . ,processing)
-                ("notes.rtf" . ,notes)
-                ("experiment-design.rtf" . ,experiment-design)
-                ("experiment-type.rtf" . ,experiment-type)
-                ("contributors.rtf" . ,contributors)
-                ("acknowledgment.rtf" . ,acknowledgment)))))
-
-
-(let* ((option-spec
-        '((settings (single-char #\s) (value #t))))
-       (options (getopt-long (command-line) option-spec))
-       (settings (option-ref options 'settings #f))
-       (query "SELECT InfoPageName, Datasets.Summary, Datasets.AboutTissue, InfoFiles.Specifics,
-Datasets.AboutCases, Datasets.AboutPlatform, Datasets.AboutDataProcessing, InfoFiles.Experiment_Type,
-Datasets.Notes, Datasets.ExperimentDesign, Datasets.Acknowledgment, Datasets.Contributors, Datasets.Citation
-FROM InfoFiles LEFT JOIN Datasets USING (DatasetId)")
-       (%connection-settings
-        (call-with-input-file settings
-          read)))
-  (call-with-target-database
-   %connection-settings
-   (lambda (db)
-     (let ((dir "/export/data/genenetwork/gn-docs/"))
-       (chdir dir)
-       (system "git reset --hard origin")
-       (system "git pull")
-       ;; Clear directory so that we can re-do the dump again from the db.
-       (system "rm -rf general/datasets/*/")
-       (sql-for-each infopages/sql->rtf
-                     db
-                     query)
-       (system "git add general/datasets")
-       (system (format #f "git commit -m ~s" "Update dataset RTF Files."))
-       (system "git push origin master")))))
diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
deleted file mode 100755
index 32dba7a..0000000
--- a/examples/dataset-metadata.scm
+++ /dev/null
@@ -1,437 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 getopt-long)
-             (ice-9 match)
-             (ice-9 regex)
-             (transform strings)
-             (transform sql)
-             (transform triples)
-             (transform special-forms))
-
-
-(define-transformer info-files
-  (tables (InfoFiles
-           (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
-           (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
-           (left-join ProbeSetFreeze "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
-           (left-join InbredSet "ON InfoFiles.InbredSetId = InbredSet.InbredSetId")
-           (left-join Species "ON InfoFiles.SpeciesId = Species.SpeciesId")
-           (left-join Datasets "USING (DatasetId)")
-           (left-join DatasetStatus "USING (DatasetStatusId)")
-           (left-join Tissue "USING (TissueId)")
-           (left-join Investigators "USING (InvestigatorId)")
-           (left-join AvgMethod "USING (AvgMethodId)")
-           (left-join Organizations "USING (OrganizationId)")
-           (left-join GeneChip "USING (GeneChipId)"))
-          ;; XXXX: There are datasets that don't have the InbredSetId
-          ;; in the Infofiles table.  This clause allows us to check
-          ;; if they exist in the (Publish/Geno)Freeze tables.
-          "LEFT JOIN InbredSet PublishInbredSet ON PublishFreeze.InbredSetId = PublishInbredSet.InbredSetId LEFT JOIN InbredSet GenoInbredSet ON GenoFreeze.InbredSetId = GenoInbredSet.InbredSetId  WHERE GN_AccesionId IS NOT NULL")
-  (schema-triples
-   (gnt:has_tissue rdfs:domain dcat:Dataset)
-   (gnt:has_tissue a owl:ObjectProperty)
-   (gnt:has_tissue skos:definition "Tissues this resource has")
-   (gnt:uses_normalization rdfs:domain dcat:Dataset)
-   (gnt:uses_normalization a owl:ObjectProperty)
-   (gnt:uses_normalization skos:definition "Normalization techniques this resource has")
-   (gnt:uses_platform rdfs:domain dcat:Dataset)
-   (gnt:uses_platform a owl:ObjectProperty)
-   (gnt:uses_platform skos:definition "The Platform this resource uses")
-   (gnt:has_geo_series_id rdfs:domain dcat:Dataset)
-   (gnt:has_geo_series_id a owl:ObjectProperty)
-   (gnt:has_geo_series_id skos:definition "id of record in NCBI database")
-   (gnt:has_experiment_type rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_type a owl:ObjectProperty)
-   (gnt:has_experiment_type rdfs:label "Experiment Type Metadata")
-   (gnt:has_experiment_type skos:definition "Information about the experiment type")
-   (gnt:has_tissue_info rdfs:domain dcat:Dataset)
-   (gnt:has_tissue_info a owl:ObjectProperty)
-   (gnt:has_tissue_info skos:definition "Metadata about Tissue for this resource")
-   (gnt:has_experiment_design_info rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_design_info rdfs:label "Experiment Design")
-   (gnt:has_experiment_design_info a owl:ObjectProperty)
-   (gnt:has_experiment_design_info skos:definition "Information about how the experiment was designed")
-   (gnt:has_notes rdfs:domain dcat:Dataset)
-   (gnt:has_notes a owl:ObjectProperty)
-   (gnt:has_notes rdfs:label "Notes")
-   (gnt:has_notes skos:definition "Extra Notes about this dataset")
-   (gnt:has_data_processing_info rdfs:domain dcat:Dataset)
-   (gnt:has_data_processing_info rdfs:label "About Data Processing")
-   (gnt:has_data_processing_info a owl:ObjectProperty)
-   (gnt:has_data_processing_info skos:definition "Information about how this dataset was processed")
-   (gnt:has_platform_info rdfs:domain dcat:Dataset)
-   (gnt:has_platform_info a owl:ObjectProperty)
-   (gnt:has_platform_info rdfs:label "About Platform")
-   (gnt:has_platform_info skos:definition "Information about the platform that was used with this dataset")
-   (gnt:has_case_info rdfs:domain dcat:Dataset)
-   (gnt:has_case_info rdfs:label "About Case")
-   (gnt:has_case_info a owl:ObjectProperty)
-   (gnt:has_case_info skos:definition "Information about the cases used in this platform")
-   (gnt:has_summary rdfs:domain dcat:Dataset)
-   (gnt:has_summary rdfs:label "Summary")
-   (gnt:has_summary a owl:ObjectProperty)
-   (gnt:has_summary skos:definition "Summary information about dataset")
-   (gnt:has_citation rdfs:domain dcat:Dataset)
-   (gnt:has_citation rdfs:label "Citation")
-   (gnt:has_citation a owl:ObjectProperty)
-   (gnt:has_citation skos:definition "Citation for this dataset")
-   (gnt:has_contributors rdfs:domain dcat:Dataset)
-   (gnt:has_contributors rdfs:label "Contributors")
-   (gnt:has_contributors a owl:ObjectProperty)
-   (gnt:has_contributors skos:definition "Contributors of this resource")
-   (gnt:has_experiment_design rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_design rdfs:label "Experiment Design")
-   (gnt:has_experiment_design a owl:ObjectProperty)
-   (gnt:has_experiment_design skos:definition "Experiment Design for this resource")
-   (gnt:has_tissue_info rdfs:domain dcat:Dataset)
-   (gnt:has_tissue_info rdfs:label "Tissue Information")
-   (gnt:has_tissue_info a owl:ObjectProperty)
-   (gnt:has_tissue_info skos:definition "Tissue information about dataset")
-   (gnt:has_experiment_type skos:definition "Information about the experiment type")
-   (gnt:has_acknowledgement rdfs:domain dcat:Dataset)
-   (gnt:has_acknowledgement rdfs:label "Acknowledgement")
-   (gnt:has_acknowledgement a owl:ObjectProperty)
-   (gnt:has_acknowledgement skos:definition "People to acknowledge"))
-  (triples
-      (string->identifier
-       "" (let ((info-page-name (field InfoFiles InfoPageName))
-                (info-title (field InfoFiles Title)))
-            (format #f "~a"
-                    (if (and (string? info-page-name)
-                             (string=? (string-downcase (string-trim-both info-page-name))
-                                       "none"))
-                        info-title info-page-name))))
-    (set rdf:type 'dcat:Dataset)
-    (set xkos:classifiedUnder
-         (let ([dataset-type
-                (string-trim-both
-                 (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotype', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotype', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:probeset', '')))"
-                         DatasetType)))])
-           (if (not (string-null? dataset-type))
-               (string->symbol
-                dataset-type)
-               "")))
-    (set rdfs:label (normalize-string-field (field InfoFiles InfoPageName)))
-    (set skos:prefLabel
-         (normalize-string-field
-          (field ("IFNULL(GenoFreeze.FullName, IFNULL(PublishFreeze.FullName, ''))"
-                  DatasetFullName))))
-    (set skos:altLabel (field Datasets DatasetName DatasetGroup))
-    (set dct:title (normalize-string-field (field Datasets PublicationTitle)))
-    (set dct:created
-         (normalize-string-field
-          (field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
-                  createTimeGenoFreeze))))
-    (set dcat:contactPoint
-         (investigator-attributes->id (field Investigators FirstName)
-                                      (field Investigators LastName)
-                                      ""))
-    (set foaf:Organization
-         (field Organizations OrganizationName))
-    (set dct:identifier (format #f "GN~a" (field InfoFiles GN_AccesionId)))
-    (set dct:accessRights (string-downcase
-                           (field DatasetStatus DatasetStatusName)))
-    (set gnt:has_strain
-         (string->identifier
-          "set"
-          (field ("IFNULL(InbredSet.Name, IFNULL(PublishInbredSet.Name, GenoInbredSet.Name))"
-                  InbredSetName))
-          #:separator "_"))
-    (set gnt:has_tissue (string->identifier "tissue"
-                                            (field Tissue Short_Name)
-                                            #:separator "_"))
-    (set gnt:uses_normalization
-         (let ((avg-method (normalize-string-field (field AvgMethod Name AvgMethodName))))
-           (if (not (string-blank? avg-method))
-               (string->identifier "avg_method" avg-method #:separator "_")
-               "")))
-    (set gnt:has_summary
-         (let* ((summary-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/summary.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (summary
-                 (field InfoFiles Summary)))
-           (if (or (null? summary) (string-blank? summary))
-               "" (string->symbol summary-link))))
-    (set gnt:has_tissue_info
-         (let* ((tissue-info-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/tissue.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (tissue-info
-                 (field Datasets AboutTissue)))
-           (if (or (null? tissue-info) (string-blank? tissue-info))
-               "" (string->symbol tissue-info-link))))
-    (set gnt:has_citation
-         (let* ((citation-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/citation.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (citation
-                 (field Datasets Citation)))
-           (if (or (null? citation) (string-blank? citation))
-               "" (string->symbol citation-link))))
-    (set gnt:hasSpecifics
-         (let* ((specifics-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/specifics.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (specifics
-                 (field InfoFiles Specifics)))
-           (if (or (null? specifics) (string-blank? specifics))
-               "" (string->symbol specifics-link))))
-    (set gnt:has_case_info
-         (let* ((cases-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/cases.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (cases
-                 (field Datasets AboutCases)))
-           (if (or (null? cases) (string-blank? cases))
-               "" (string->symbol cases-link))))
-    (set gnt:has_platform_info
-         (let* ((platform-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/platform.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (platform
-                 (field Datasets AboutPlatform)))
-           (if (or (null? platform) (string-blank? platform))
-               "" (string->symbol platform-link))))
-    (set gnt:has_data_processing_info
-         (let* ((processing-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/processing.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (processing
-                 (field Datasets AboutDataProcessing)))
-           (if (or (null? processing) (string-blank? processing))
-               "" (string->symbol processing-link))))
-    (set gnt:has_notes
-         (let* ((notes-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/notes.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (notes
-                 (field Datasets Notes)))
-           (if (or (null? notes) (string-blank? notes))
-               "" (string->symbol notes-link))))
-    (set gnt:has_experiment_type
-         (let* ((experiment-type-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/experiment-type.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (experiment-type
-                 (field InfoFiles Experiment_Type)))
-           (if (or (null? experiment-type) (string-blank? experiment-type))
-               "" (string->symbol experiment-type-link))))
-    (set gnt:has_experiment_design
-         (let* ((experiment-design-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/experiment-design.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (experiment-design
-                 (field Datasets ExperimentDesign)))
-           (if (or (null? experiment-design) (string-blank? experiment-design))
-               "" (string->symbol experiment-design-link))))
-    (set gnt:has_contributors
-         (let* ((contributors-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/contributors.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (contributors
-                 (field Datasets Contributors)))
-           (if (or (null? contributors) (string-blank? contributors))
-               "" (string->symbol contributors-link))))
-    (set gnt:has_acknowledgement
-         (let* ((acknowledgment-link
-                 (format
-                  #f "<https://git.genenetwork.org/gn-docs/tree/general/datasets/~a/acknowledgment.rtf>"
-                  (string-capitalize-first
-                   (regexp-substitute/global
-                    #f "[^A-Za-z0-9:]"
-                    (field InfoFiles InfoPageName)
-                    'pre "_" 'post))))
-                (acknowledgment
-                 (field Datasets Acknowledgment)))
-           (if (or (null? acknowledgment) (string-blank? acknowledgment))
-               "" (string->symbol acknowledgment-link))))
-    (set gnt:uses_platform
-         (string->identifier "platform"
-                             (field GeneChip Name GeneChip)
-                             #:separator "_"))
-    (set gnt:has_geo_series_id
-         (let ((s
-                (string-match "GSE[0-9]*"
-                              (field ("IFNULL(Datasets.GeoSeries, '')" GeoSeries)))))
-           (if s (ontology
-                  'geoSeries: (match:substring s))
-               "")))))
-
-;; These are phenotype datasets that don't have Infofile metadata
-(define-transformer publishfreeze
-  (tables (PublishFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
-           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL")
-  (triples
-      (string->identifier "" (field PublishFreeze Name))
-    (set rdf:type 'dcat:Dataset)
-    (set xkos:classifiedUnder 'gnc:phenotype)
-    (set dct:title (field PublishFreeze FullName))
-    (set rdfs:label (field PublishFreeze Name))
-    (set skos:altLabel (field PublishFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field PublishFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:has_strain
-         (string->identifier
-          "set" (field InbredSet Name InbredSetName)
-          #:separator "_"))))
-
-(define-transformer genofreeze
-  (tables (GenoFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
-           (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
-  (triples
-      (string->identifier "" (field GenoFreeze Name))
-    (set rdf:type 'dcat:Dataset)
-    (set xkos:classifiedUnder 'gnc:genotype)
-    (set rdfs:label (field GenoFreeze Name))
-    (set dct:title (field GenoFreeze FullName))
-    (set skos:altLabel (field GenoFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field GenoFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:has_strain
-         (string->identifier
-          "set" (field InbredSet Name InbredSetName)
-          #:separator "_"
-          #:proc (lambda (x) x)))))
-
-(define-transformer probesetfreeze
-  (tables (ProbeSetFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
-           (left-join ProbeFreeze "USING (ProbeFreezeId)")
-           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
-           (left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
-           (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
-          "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
-  (schema-triples
-   (gnt:uses_normalization rdfs:domain gnc:probeset)
-   (gnt:uses_data_scale rdfs:domain gnc:probeset)
-   (gnt:uses_data_scale a owl:ObjectProperty)
-   (gnt:uses_data_scale skos:definition "Thi data scale this resource uses"))
-  (triples
-      (string->identifier "" (field ProbeSetFreeze Name))
-    (set rdf:type 'dcat:Dataset)
-    (set xkos:classifiedUnder 'gnc:probeset)
-    (set gnt:uses_normalization
-         (let ((avg-method (field AvgMethod Name AvgMethodName)))
-           (if (string-blank? avg-method)
-               #f
-               avg-method)))
-    (set dct:title (field ProbeSetFreeze FullName))
-    (set rdfs:label (field ProbeSetFreeze ShortName))
-    (set skos:prefLabel (field ProbeSetFreeze Name))
-    (set skos:altLabel (field ProbeSetFreeze Name2))
-    (set dct:created (annotate-field
-                      (field ProbeSetFreeze CreateTime)
-                      '^^xsd:datetime))
-    (set gnt:uses_data_scale (field ProbeSetFreeze DataScale))
-    (set gnt:has_tissue (string->identifier "tissue" (field Tissue Short_Name) #:separator "_"))
-    (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
-
-
-
-(let* ((option-spec
-        '((settings (single-char #\s) (value #t))
-          (output (single-char #\o) (value #t))
-          (documentation (single-char #\d) (value #t))))
-       (options (getopt-long (command-line) option-spec))
-       (settings (option-ref options 'settings #f))
-       (output (option-ref options 'output #f))
-       (documentation (option-ref options 'documentation #f))
-       (%connection-settings
-        (call-with-input-file settings
-          read)))
-  (with-documentation
-   (name "Info files / Investigators Metadata")
-   (connection %connection-settings)
-   (table-metadata? #f)
-   (prefixes
-    '(("v:" "<http://www.w3.org/2006/vcard/ns#>")
-      ("foaf:" "<http://xmlns.com/foaf/0.1/#term_>")
-      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-      ("dcat:" "<http://www.w3.org/ns/dcat#>")
-      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
-      ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
-      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
-      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
-      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
-      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-      ("owl:" "<http://www.w3.org/2002/07/owl#>")
-      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
-      ("dct:" "<http://purl.org/dc/terms/>")))
-   (inputs
-    (list info-files
-          publishfreeze
-          genofreeze
-          probesetfreeze
-          gene-chip))
-   (outputs
-    `(#:documentation ,documentation
-      #:rdf ,output))))
-
-