Add datasets.scm

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

2 files changed, 167 insertions, 112 deletions

diff --git a/examples/datasets.scm b/examples/datasets.scm
new file mode 100755
index 0000000..d8b3a00
--- /dev/null
+++ b/examples/datasets.scm
@@ -0,0 +1,163 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (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 gn:dataset->metadata
+  (tables (Datasets
+           (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId"))
+          ;; Skip monkey datasets
+          "WHERE InfoFiles.InfoPageName NOT LIKE 'INIA_MacFas_%'"
+          "GROUP BY Datasets.DatasetId")
+  (schema-triples
+    (gnt:has_case_info a owl:ObjectProperty)
+    (gnt:has_case_info rdfs:comment "Information about the cases used in this platform")
+    (gnt:has_case_info rdfs:domain dcat:Dataset)
+    (gnt:has_case_info rdfs:label "About Case")
+    (gnt:has_citation a owl:ObjectProperty)
+    (gnt:has_citation rdfs:comment "Citation for this dataset")
+    (gnt:has_citation rdfs:domain dcat:Dataset)
+    (gnt:has_citation rdfs:label "Citation")
+    (gnt:has_contributors a owl:ObjectProperty)
+    (gnt:has_contributors rdfs:comment "Contributors of this resource")
+    (gnt:has_contributors rdfs:comment "Contributors of this resource")
+    (gnt:has_contributors rdfs:domain dcat:Dataset)
+    (gnt:has_contributors rdfs:label "Contributors")
+    (gnt:has_data_processing_info a owl:ObjectProperty)
+    (gnt:has_data_processing_info rdfs:comment "Information about how this dataset was processed")
+    (gnt:has_data_processing_info rdfs:domain dcat:Dataset)
+    (gnt:has_data_processing_info rdfs:label "About Data Processing")
+    (gnt:has_experiment_design a owl:ObjectProperty)
+    (gnt:has_experiment_design rdfs:comment "Experiment Design for this resource")
+    (gnt:has_experiment_design rdfs:domain dcat:Dataset)
+    (gnt:has_experiment_design rdfs:label "Experiment Design")
+    (gnt:has_experiment_design_info a owl:ObjectProperty)
+    (gnt:has_experiment_design_info rdfs:comment "Information about how the experiment was designed")
+    (gnt:has_experiment_design_info rdfs:domain dcat:Dataset)
+    (gnt:has_experiment_design_info rdfs:label "Experiment Design")
+    (gnt:has_experiment_type a owl:ObjectProperty)
+    (gnt:has_experiment_type rdfs:comment "Information about the experiment type")
+    (gnt:has_experiment_type rdfs:domain dcat:Dataset)
+    (gnt:has_experiment_type rdfs:label "Experiment Type Metadata")
+    (gnt:has_platform_info a owl:ObjectProperty)
+    (gnt:has_platform_info rdfs:comment "Information about the platform that was used with this dataset")
+    (gnt:has_platform_info rdfs:domain dcat:Dataset)
+    (gnt:has_platform_info rdfs:label "About Platform")
+    (gnt:has_samples a owl:ObjectProperty)
+    (gnt:has_samples rdfs:domain dcat:Dataset)
+    (gnt:has_samples rdfs:label "Samples")
+    (gnt:has_specifics a owl:ObjectProperty)
+    (gnt:has_specifics rdfs:comment "Has specifics")
+    (gnt:has_specifics rdfs:domain dcat:Dataset)
+    (gnt:has_specifics rdfs:label "Specifics")
+    (gnt:has_summary a owl:ObjectProperty)
+    (gnt:has_summary rdfs:comment "Summary information about dataset")
+    (gnt:has_summary rdfs:domain dcat:Dataset)
+    (gnt:has_summary rdfs:label "Summary")
+    (gnt:has_tissue_info a owl:ObjectProperty)
+    (gnt:has_tissue_info rdfs:domain dcat:Dataset)
+    (gnt:has_tissue_info rdfs:label "Metadata about Tissue for this resource"))
+  (triples (string->identifier "dataset" (field InfoFiles InfoPageName) #:separator "_")
+    (set rdf:type 'dcat:Dataset)
+    (set dct:title (normalize-string-field (field InfoFiles InfoPageName)))
+    (set dct:identifier (format #f "GN~a" (field InfoFiles GN_AccesionId)))
+    (set gnt:has_experiment_type
+         (let ((experiment-type
+                (field InfoFiles Experiment_Type)))
+           (if (or (null? experiment-type) (string-blank? experiment-type))
+               "" (sanitize-rdf-string experiment-type))))
+    (set gnt:has_tissue_info
+         (let ((tissue-info
+                (field Datasets AboutTissue)))
+           (if (or (null? tissue-info) (string-blank? tissue-info))
+               "" (sanitize-rdf-string tissue-info))))
+    (set gnt:has_summary
+         (let* ((summary
+                 (field Datasets Summary)))
+           (if (or (null? summary) (string-blank? summary))
+               "" (sanitize-rdf-string summary))))
+    (set gnt:has_citation
+         (let ((citation
+                (field Datasets Citation)))
+           (if (or (null? citation) (string-blank? citation))
+               "" (sanitize-rdf-string citation))))
+    (set gnt:has_samples
+         (let ((samples
+                (field InfoFiles samples)))
+           (if (or (null? samples) (string-blank? samples))
+               "" (sanitize-rdf-string samples))))
+    (set gnt:has_specifics
+         (let* ((specifics
+                 (field InfoFiles Specifics)))
+           (if (or (null? specifics) (string-blank? specifics))
+               "" (sanitize-rdf-string specifics))))
+    (set gnt:has_case_info
+         (let ((cases
+                (field Datasets AboutCases)))
+           (if (or (null? cases) (string-blank? cases))
+               "" (sanitize-rdf-string cases))))
+    (set gnt:has_platform_info
+         (let* ((platform
+                 (field Datasets AboutPlatform)))
+           (if (or (null? platform) (string-blank? platform))
+               "" (sanitize-rdf-string platform))))
+    (set gnt:has_data_processing_info
+         (let* ((processing
+                 (field Datasets AboutDataProcessing)))
+           (if (or (null? processing) (string-blank? processing))
+               "" (sanitize-rdf-string processing))))
+    (set gnt:has_experiment_design
+         (let ((experiment-design
+                (field Datasets ExperimentDesign)))
+           (if (or (null? experiment-design) (string-blank? experiment-design))
+               "" (sanitize-rdf-string experiment-design))))
+    (set gnt:has_contributors
+         (let ((contributors
+                (field Datasets Contributors)))
+           (if (or (null? contributors) (string-blank? contributors))
+               "" (sanitize-rdf-string contributors))))))
+
+
+(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 "Datasets Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("dct:" "<http://purl.org/dc/terms/>")
+      ("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
+      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
+   (inputs
+    (list gn:dataset->metadata))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm
index da33950..f338693 100755
--- a/examples/molecular-traits.scm
+++ b/examples/molecular-traits.scm
@@ -83,66 +83,14 @@
            (left-join GeneChip "ON GeneChip.Id =  InfoFiles.GeneChipId"))
           "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
   (schema-triples
-   (gnt:has_case_info a owl:ObjectProperty)
-   (gnt:has_case_info rdfs:comment "Information about the cases used in this platform")
-   (gnt:has_case_info rdfs:domain dcat:Dataset)
-   (gnt:has_case_info rdfs:label "About Case")
-   (gnt:has_citation a owl:ObjectProperty)
-   (gnt:has_citation rdfs:comment "Citation for this dataset")
-   (gnt:has_citation rdfs:domain dcat:Dataset)
-   (gnt:has_citation rdfs:label "Citation")
-   (gnt:has_contributors a owl:ObjectProperty)
-   (gnt:has_contributors rdfs:comment "Contributors of this resource")
-   (gnt:has_contributors rdfs:comment "Contributors of this resource")
-   (gnt:has_contributors rdfs:domain dcat:Dataset)
-   (gnt:has_contributors rdfs:label "Contributors")
-   (gnt:has_data_processing_info a owl:ObjectProperty)
-   (gnt:has_data_processing_info rdfs:comment "Information about how this dataset was processed")
-   (gnt:has_data_processing_info rdfs:domain dcat:Dataset)
-   (gnt:has_data_processing_info rdfs:label "About Data Processing")
-   (gnt:has_experiment_design a owl:ObjectProperty)
-   (gnt:has_experiment_design rdfs:comment "Experiment Design for this resource")
-   (gnt:has_experiment_design rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_design rdfs:label "Experiment Design")
-   (gnt:has_experiment_design_info a owl:ObjectProperty)
-   (gnt:has_experiment_design_info rdfs:comment "Information about how the experiment was designed")
-   (gnt:has_experiment_design_info rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_design_info rdfs:label "Experiment Design")
-   (gnt:has_experiment_type a owl:ObjectProperty)
-   (gnt:has_experiment_type rdfs:comment "Information about the experiment type")
-   (gnt:has_experiment_type rdfs:domain dcat:Dataset)
-   (gnt:has_experiment_type rdfs:label "Experiment Type Metadata")
-   (gnt:has_platform_info a owl:ObjectProperty)
-   (gnt:has_platform_info rdfs:comment "Information about the platform that was used with this dataset")
-   (gnt:has_platform_info rdfs:domain dcat:Dataset)
-   (gnt:has_platform_info rdfs:label "About Platform")
-   (gnt:has_samples a owl:ObjectProperty)
-   (gnt:has_samples rdfs:domain dcat:Dataset)
-   (gnt:has_samples rdfs:label "Samples")
-   (gnt:has_specifics a owl:ObjectProperty)
-   (gnt:has_specifics rdfs:comment "Has specifics")
-   (gnt:has_specifics rdfs:domain dcat:Dataset)
-   (gnt:has_specifics rdfs:label "Specifics")
-   (gnt:has_summary a owl:ObjectProperty)
-   (gnt:has_summary rdfs:comment "Summary information about dataset")
-   (gnt:has_summary rdfs:domain dcat:Dataset)
-   (gnt:has_summary rdfs:label "Summary")
-   (gnt:has_tissue_info a owl:ObjectProperty)
-   (gnt:has_tissue_info rdfs:domain dcat:Dataset)
-   (gnt:has_tissue_info rdfs:label "Metadata about Tissue for this resource")
    (gnt:uses_genechip a owl:ObjectProperty)
    (gnt:uses_genechip rdfs:domain dcat:Dataset)
-   (gnt:uses_genechip skos:definition "The Platform this resource uses")
-   (gnt:uses_normalization_method rdfs:comment "The method used to map genetic or experimental data for this resource.")
+   (gnt:uses_genechip skos:definition "The Platform this resource uses for it's molecular traits.")
+   (gnt:uses_normalization_method rdfs:comment "The normalization method used for the molecular traits in this dataset")
    (gnt:uses_normalization_method rdfs:domain dcat:Dataset)
-   (gnt:uses_normalization_method rdfs:label "Averaging method")
+   (gnt:uses_normalization_method rdfs:label "Averaging method used for the molecular traits in this dataset.")
    (gnt:uses_normalization_method rdfs:range gnc:avg_method))
- (gnt:uses_normalization_method a owl:ObjectProperty)
   (triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_")
-    (set rdf:type 'dcat:Dataset)
-    (set skos:prefLabel (field ProbeSetFreeze Name))
-    (set dct:title (normalize-string-field (field InfoFiles InfoPageName)))
-    (set rdfs:label (normalize-string-field (field InfoFiles InfoPageName)))
     (set dct:created (annotate-field (field ProbeSetFreeze CreateTime) '^^xsd:datetime))
     (set gnt:uses_normalization_method
          (string->identifier "avg_method" (field AvgMethod Name AvgMethodName) #:separator "_"))
@@ -153,63 +101,7 @@
     (set gnt:has_molecular_trait
          (string->identifier "trait" (field Tissue Short_Name) #:separator "_"))
     (set gnt:uses_genechip
-         (string->identifier "platform" (field GeneChip Name) #:separator "_"))
-    (set dct:identifier (format #f "GN~a" (field InfoFiles GN_AccesionId)))
-    (set gnt:has_experiment_type
-         (let ((experiment-type
-                (field InfoFiles Experiment_Type)))
-           (if (or (null? experiment-type) (string-blank? experiment-type))
-               "" (sanitize-rdf-string experiment-type))))
-    (set gnt:has_tissue_info
-         (let ((tissue-info
-                (field Datasets AboutTissue)))
-           (if (or (null? tissue-info) (string-blank? tissue-info))
-               "" (sanitize-rdf-string tissue-info))))
-    (set gnt:has_summary
-         (let* ((summary
-                 (field Datasets Summary)))
-           (if (or (null? summary) (string-blank? summary))
-               "" (sanitize-rdf-string summary))))
-    (set gnt:has_citation
-         (let ((citation
-                (field Datasets Citation)))
-           (if (or (null? citation) (string-blank? citation))
-               "" (sanitize-rdf-string citation))))
-    (set gnt:has_samples
-         (let ((samples
-                (field InfoFiles samples)))
-           (if (or (null? samples) (string-blank? samples))
-               "" (sanitize-rdf-string samples))))
-    (set gnt:has_specifics
-         (let* ((specifics
-                 (field InfoFiles Specifics)))
-           (if (or (null? specifics) (string-blank? specifics))
-               "" (sanitize-rdf-string specifics))))
-    (set gnt:has_case_info
-         (let ((cases
-                (field Datasets AboutCases)))
-           (if (or (null? cases) (string-blank? cases))
-               "" (sanitize-rdf-string cases))))
-    (set gnt:has_platform_info
-         (let* ((platform
-                 (field Datasets AboutPlatform)))
-           (if (or (null? platform) (string-blank? platform))
-               "" (sanitize-rdf-string platform))))
-    (set gnt:has_data_processing_info
-         (let* ((processing
-                 (field Datasets AboutDataProcessing)))
-           (if (or (null? processing) (string-blank? processing))
-               "" (sanitize-rdf-string processing))))
-    (set gnt:has_experiment_design
-         (let ((experiment-design
-                (field Datasets ExperimentDesign)))
-           (if (or (null? experiment-design) (string-blank? experiment-design))
-               "" (sanitize-rdf-string experiment-design))))
-    (set gnt:has_contributors
-         (let ((contributors
-                (field Datasets Contributors)))
-           (if (or (null? contributors) (string-blank? contributors))
-               "" (sanitize-rdf-string contributors))))))
+         (string->identifier "platform" (field GeneChip Name) #:separator "_"))))
 
 
 (let* ((option-spec