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* dump.scm (string-blank?): Move to ...
* dump/utils.scm (string-blank?): ... here.
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* dump.scm (dump-investigators): Special case Yohan Bossé's last name.
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The AvgMethod table no longer has duplicate "N/A" records.
* dump.scm (dump-avg-method): Do not deduplicate the AvgMethod table.
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In GeneNetwork, a phenonytpe is currently identified by it's
ID (primary key of the table from MariaDB). The only way to relate it
to a publication is through a publication ID. This is important
because there are some publications with a NULL value for "pubmed ID"
and as such without the publication ID, some data is lost as there's
no way to point to publication with a NULL "pubmed ID."
* dump.scm (dump-publish-xref): Define gn:traitId and
gn:publicationId.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* dump.scm (dump-publication): Delete vertical tab character in
abstracts.
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* dump.scm (dump-groups): New dump.
(main): Call dump-groups.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* dump.scm (dump-case-attributes): New dump.
(main): Call dump-case-attributes.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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A "." at the end of a turtle identifier---for example
"gn:caseAttribute_ethn."---generates an error when trying to validate
the generated RDF.
* dump.scm (string->identifier): Remove trailing "." if it occurs in
the identifier.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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This differentiates it from virtuoso and SPARQL connection parameters.
* dump.scm (call-with-genenetwork-database, dump-data-table): Prefix
SQL connection parameters with sql-.
* README.md (Using): Update documentation of SQL connection
parameters.
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* dump.scm (investigator-attributes->id): Add special case for
investigator "Yohan Bossé".
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* dump.scm (%connection-settings): Use 1th command-line argument.
(%dump-directory): Use 2th command-line argument.
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* dump.scm: Import (rnrs programs).
(%connection-settings): New variable.
(call-with-database): Use %connection-settings.
(%database-name): Delete variable.
(%dump-directory): Set from command-line arguments.
(dump-data-table): Use %connection-settings instead of %database-name.
* README.org (Using): Add command-line arguments to usage
instructions.
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If these macro helper functions are not evaluated at macro expansion
time, the dependent macros will fail to compile.
* dump.scm (string->identifier, field->key, field->assoc-ref,
collect-fields, find-clause, remove-namespace, column-id, dump-id):
Eval at macro expansion time.
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* dump.scm: Do not add to load path.
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* dump.scm (define-dump): Add docstring.
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* dump.scm (syntax-let): New macro.
(define-dump): Use syntax-let.
* .dir-locals.el (scheme-mode): Indent syntax-let correctly.
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* dump.scm (define-dump): Automatically create domain triples for
predicates.
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* dump.scm (remove-namespace, dump-id): New functions.
(define-dump): Dump metadata about the dump itself.
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* dump.scm (dump-schema, column-id): Disambiguate user and User tables
in RDF identifier.
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* dump.scm (column-id): New function.
(dump-schema): Use column-id.
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* dump.scm (%dumped): Delete variable.
(define-dump): Do not register dumped tables and columns to %dumped.
(dumped-table?): Delete function.
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* dump.scm (dump-inbred-set): Set range of gn:inbredSetOfSpecies to
gn:species.
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* dump.scm (dump-info-files): Set range of gn:datasetOfInvestigator to
foaf:Person instead of gn:investigator.
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* dump.scm (dump-species, dump-strain, dump-inbred-set,
dump-phenotype, dump-publication, dump-tissue, dump-investigator,
dump-avg-method, dump-gene-chip, dump-info-files): Add Literal range
triples.
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* dump.scm (dump-phenotype): Remove duplicate predicates
gn:prePublicationDescription and gn:postPublicationDescription.
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gn:authors is a typo.
* dump.scm (dump-publication): Rename gn:authors predicate to
gn:author.
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* dump.scm (triple): Add runtime type checking.
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* dump.scm: Do not import (sxml simple) and (dump string-similarity).
(string-remove-suffix-ci, floor-log1024, human-units,
human-units-color, sxml->xml-string, sxml->graphviz-html, table-label,
table->graphviz-node, column->foreign-table, tables->graphviz-edges):
Move to ...
(dump-schema): Dump schema to RDF.
(main): Call dump-schema without setting schema.dot as the output
file.
* visualize-schema.scm: ... here.
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Capture full column type instead of just whether it is an integer.
* dump.scm (dump-data-table): Capture full column type in <column>
object.
* dump/table.scm (<column>)[int?]: Delete member.
[type]: New member.
Export column-type instead of column-int?.
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* dump.scm (<table>, <column>): Move to ...
* dump/table.scm: ... here.
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* dump.scm (define-dump): Indent better.
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* dump.scm (define-dump): Support schema-triples clause.
(dump-strain, dump-publish-xref, dump-info-files): Add schema-triples
clause.
(main): Output rdfs: prefix.
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* dump.scm (find-clause): New function.
(define-dump): Make order of clauses unspecified.
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* dump.scm (field->key, field->assoc-ref, collect-fields): New
functions.
(define-dump): Redefine with more concise syntax.
* dump.scm (dump-species, dump-strain, dump-mapping-method,
dump-inbred-set, dump-phenotype, dump-publication, dump-publish-xref,
dump-tissue, dump-investigators, dump-avg-method, dump-gene-chip,
dump-info-files): Use new define-dump syntax.
(default-metadata-proc): Delete function.
* .dir-locals.el (scheme-mode): Indent triples form correctly.
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* dump.scm: Use (dump string-similarity).
(trigrams, jaccard-index, jaccard-string-similarity,
jaccard-string-similar?): Move to ...
* dump/string-similarity.scm: ... here.
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* dump.scm (dump-species): Change gn:binomialname to gn:binomialName.
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* dump.scm (table-label): Set port attributes on <td> tag.
(tables->graphviz-edges): Specify ports on edges.
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* dump.scm (table-label): Unset border attribute of <table> tag. Set
cellborder and bgcolor attributes of <table> tag.
(table->graphviz-node): Unset style and fillcolor node attributes. Set
shape node attribute to none.
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* dump.scm (graph->dot): Delete function.
(sxml->graphviz-html): Return a <html-string> object.
(dump-schema): Use graph->dot from (ccwl graphviz).
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* dump.scm (column->foreign-table, tables->graphviz-edges): New
functions.
(dump-schema): Use tables->graphviz-edges.
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* dump.scm (dumped-table?, table-label, table->graphviz-node): New
functions.
(dump-schema): Use table->graphviz-node.
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* dump.scm (human-units-color): New function.
(dump-schema): Use human-units-color.
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This generalizes better and is mathematically cleaner.
* dump.scm (floor-log1024): New function.
(human-units): Use floor-log1024.
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Using sxml allows us to stay in the world of S-expressions.
* dump.scm (sxml->xml-string, sxml->graphviz-html): New function.
(dump-schema): Construct graphviz HTML string using sxml.
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* dump.scm (dump-schema): Highlight tables and columns.
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* dump.scm (replace-substrings): New function.
(graph->dot): Fix HTML string handling.
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* dump.scm (%dumped): New variable.
(define-dump): Append to %dumped when a new table dumping function is
defined.
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* dump.scm (define-dump): New macro.
(dump-species, dump-strain, dump-mapping-method, dump-inbred-set,
dump-phenotype, dump-publication, dump-publish-xref, dump-tissue,
dump-investigators, dump-avg-method, dump-gene-chip, dump-info-files):
Redefine using define-dump.
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* dump.scm (<column>): New type.
(tables): Use <column> objects to represent columns.
(trigrams, jaccard-index, jaccard-string-similarity): New functions.
(dump-schema): Use string similarity and check if foreign key is an
integer.
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* .dir-locals.el (scheme-mode): Indent set-table-columns correctly.
* dump.scm: Import (srfi srfi-9 gnu).
(%database-name): New variable.
(<table>): New type.
(tables, string-remove-suffix-ci, human-units, graph->dot,
dump-schema): New functions.
Invoke dump-schema.
* guix.scm: Import (gnu packages bioinformatics). Add ccwl, graphviz
and guile-libyaml to the manifest.
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