Age | Commit message (Collapse) | Author |
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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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* dump.scm (get-tables-from-comments, dump-table-fields, 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 select-query.
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* dump.scm (camel->lower-camel): Delete function.
(default-metadata-proc): Do not use camel->lower-camel.
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* dump.scm (dump-mapping-method, dump-publication, dump-info-files):
Use string->identifier to build subjects.
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This is slightly more readable.
* dump.scm (string->identifier): Append an underscore to the
identifier prefix.
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* dump.scm (get-tables-from-comments, dump-table-fields): Fix
indentation.
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* dump.scm: Import (dump utils).
(string-blank?): New function.
(scm->triples): Filter out triples with #f or blank string objects.
(process-metadata-alist): Delete function.
(default-metadata-proc): New function.
(dump-species, dump-strain, mapping-method-name->id, dump-inbred-set,
dump-phenotype, dump-publication, dump-publish-xref, dump-tissue,
dump-investigators, dump-avg-method, dump-gene-chip, dump-info-files):
Use map-alist.
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* dump.scm (investigator-email->id): Rename to
investigator-attributes->id. Use first and last names in addition to
the email ID.
(dump-investigators): Use investigator-attributes->id. Include records
that have no email ID.
(dump-info-files): Use investigator-attributes->id. Include records
that have no email ID.
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For the simple task of removing spaces, string-delete is
sufficient. string-replace-substring is overkill.
* dump.scm (fix-email-id): Use string-delete instead of
string-replace-substring.
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Building a turtle identifier from a string after removing illegal
characters and prefixing is an extremely common operation. Abstract
it. Also, mandate identifier prefixes. It is better to play it safe.
* dump.scm (string->identifier): New function.
(binomial-name->species-id, dump-strain, mapping-method-name->id,
inbred-set-name->id, aphenotype-id->id, tissue-short-name->id,
investigator-email->id, avg-method-name->id, gene-chip-name->id): Use
string->identifier.
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* dump.scm (delete-substring): Add docstring.
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* dump.scm (dump-info-files): Deal with AvgMethodId.
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Not all datasets have a non-NULL InfoPageTitle field.
* dump.scm (dump-info-files): Use InfoFileTitle instead of
InfoPageTitle for dataset name.
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* dump.scm (dump-info-files): Extract name of dataset group.
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Not all inbred sets have a mapping method, and the mapping method of
the inbred set has, so far, not been used anywhere.
* dump.scm (mapping-method-name->id, dump-mapping-method): Mark as
unused.
(dump-inbred-set): Do not link inbred-set to mapping-method.
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* dump.scm (dump-avg-method): Allow N/A in name.
(dump-info-files): Allow N/A in avg-method-name.
(avg-method-name->id): Replace / with _.
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* dump.scm (dump-info-files): Remove gn:geoSeries when value starts
with "No Geo Series...".
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* dump.scm: In the gn:prefix, use http instead of https.
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* dump.scm: Remove rdfs: prefix.
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Parentheses became unbalanced due to my careless git use.
* dump.scm: Fix unbalanced parentheses.
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* dump.scm (dump-info-files): New function.
[main]: Call dump-info-files.
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* dump.scm (delete-substrings): New function.
(dump-publication): Replace string-replace-substring with
delete-substrings.
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* dump.scm (dump-publication, dump-tissue): Do not define any property
to be a sub-property of rdfs:label.
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* dump.scm (gene-chip-name->id, dump-gene-chip): New functions.
[main]: Call dump-gene-chip.
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* dump.scm (avg-method-name->id, dump-avg-method): New functions.
[main]: Call dump-avg-method.
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* dump.scm (camel->kebab): Delete function.
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