| Age | Commit message (Expand) | Author |
|---|
| 2021-12-24 | BUGS: Add bug tracker....* BUGS.org: New file.
| Arun Isaac |
| 2021-12-24 | Visualize RDF schema....* visualize-schema.scm (literal-node-id, rdf-type-nodes,
rdf-literal-nodes, rdf-edges, write-rdf-visualization): New functions.
(main): Call write-rdf-visualization.
| Arun Isaac |
| 2021-12-24 | Wrap SQL visualization code into a function....* visualize-schema.scm (write-sql-visualization, main): New functions.
Invoke main.
| Arun Isaac |
| 2021-12-24 | Import functions from (ccwl graphviz)....* visualize-schema.scm (graph->dot, graph, graph-node, graph-edge,
graph-port, html-string): New functions.
(sxml->graphviz-html): Use html-string.
(foreign-key-graphviz-edges): Use graph-port.
| Arun Isaac |
| 2021-12-24 | Color code dumped tables and columns....* visualize-schema.scm (sxml->graphviz-html): Color code dumped tables
and columns.
| Arun Isaac |
| 2021-12-24 | Fetch entire table schema in single SPARQL query....* visualize-schema.scm (tables): Fetch entire table schema in single
SPARQL query.
| Arun Isaac |
| 2021-12-24 | Add TODO note to prefer JSON query results to CSV....* visualize-schema.scm (sparql-query-records): Add TODO note to prefer
JSON query results to CSV.
| Arun Isaac |
| 2021-12-24 | Document define-dump....* dump.scm (define-dump): Add docstring.
| Arun Isaac |
| 2021-12-24 | Introduce syntax-let abstraction....* dump.scm (syntax-let): New macro.
(define-dump): Use syntax-let.
* .dir-locals.el (scheme-mode): Indent syntax-let correctly.
| Arun Isaac |
| 2021-12-23 | Automatically create domain triples for predicates....* dump.scm (define-dump): Automatically create domain triples for
predicates.
| Arun Isaac |
| 2021-12-23 | Dump metadata about the dump itself....* dump.scm (remove-namespace, dump-id): New functions.
(define-dump): Dump metadata about the dump itself.
| Arun Isaac |
| 2021-12-23 | Disambiguate user and User tables in RDF identifier....* dump.scm (dump-schema, column-id): Disambiguate user and User tables
in RDF identifier.
| Arun Isaac |
| 2021-12-23 | Abstract column id generation to separate function....* dump.scm (column-id): New function.
(dump-schema): Use column-id.
| Arun Isaac |
| 2021-12-23 | Do not register dumped tables and columns to %dumped....* dump.scm (%dumped): Delete variable.
(define-dump): Do not register dumped tables and columns to %dumped.
(dumped-table?): Delete function.
| Arun Isaac |
| 2021-12-23 | Add dumped? field to <column> type....* dump/table.scm (<column>): Add dumped? field. Rename constructor to
column-constructor.
(make-column): Implement as wrapper around column-constructor.
| Arun Isaac |
| 2021-12-23 | Specify range of gn:inbredSetOfSpecies....* dump.scm (dump-inbred-set): Set range of gn:inbredSetOfSpecies to
gn:species.
| Arun Isaac |
| 2021-12-23 | Use foaf:Person instead of gn:investigator....* dump.scm (dump-info-files): Set range of gn:datasetOfInvestigator to
foaf:Person instead of gn:investigator.
| Arun Isaac |
| 2021-12-23 | Add Literal range triples....* 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.
| Arun Isaac |
| 2021-12-23 | Remove duplicate predicates for gn:phenotype....* dump.scm (dump-phenotype): Remove duplicate predicates
gn:prePublicationDescription and gn:postPublicationDescription.
| Arun Isaac |
| 2021-12-23 | Rename gn:authors predicate to gn:author....gn:authors is a typo.
* dump.scm (dump-publication): Rename gn:authors predicate to
gn:author.
| Arun Isaac |
| 2021-12-23 | Add runtime type checking for triple....* dump.scm (triple): Add runtime type checking.
| Arun Isaac |
| 2021-12-20 | Move schema visualization to separate script....* 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.
| Arun Isaac |
| 2021-12-20 | Add guile-sparql to Guix manifest....* guix.scm: Add guile-sparql to manifest.
| Arun Isaac |
| 2021-12-20 | Upgrade ccwl to latest commit....* guix.scm (ccwl): Upgrade to commit
51c12b7e58685b70e7cfd9612dac403cf9ee845c.
| Arun Isaac |
| 2021-12-20 | Capture full column type....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?.
| Arun Isaac |
| 2021-12-20 | Move <table> and <column> types to separate module....* dump.scm (<table>, <column>): Move to ...
* dump/table.scm: ... here.
| Arun Isaac |
| 2021-12-17 | Indent define-dump better....* dump.scm (define-dump): Indent better.
| Arun Isaac |
| 2021-12-17 | Document RDF schema during dumping....* dump.scm (define-dump): Support schema-triples clause.
(dump-strain, dump-publish-xref, dump-info-files): Add schema-triples
clause.
(main): Output rdfs: prefix.
| Arun Isaac |
| 2021-12-17 | Make order of clauses in define-dump unspecified....* dump.scm (find-clause): New function.
(define-dump): Make order of clauses unspecified.
| Arun Isaac |
| 2021-12-16 | Make define-dump syntax more concise....* 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.
| Arun Isaac |
| 2021-12-16 | Add tests....* tests.scm: New file.
| Arun Isaac |
| 2021-12-16 | Specify map-alist behaviour for multiple set verbs....* dump/utils.scm (map-alist): Specify behaviour for multiple set
verbs.
| Arun Isaac |
| 2021-12-16 | Generalize collect-keys and key->assoc-ref....The generalized versions---collect forms and translate-forms---will be
required by other macros.
* dump/utils.scm (collect-forms, translate forms): New public
functions.
(collect-keys): Rewrite in terms of collect-forms.
(key->assoc-ref): Rewrite in terms of translate-forms.
| Arun Isaac |
| 2021-12-16 | Rename away delete from (srfi srfi-1)....delete from (srfi srfi-1) somehow interferes with the delete verb of
map-alist. It is not clear why.
* dump/utils.scm (dump): Rename delete to srfi:delete while importing.
| Arun Isaac |
| 2021-12-15 | Move string similarity functions to separate module....* dump.scm: Use (dump string-similarity).
(trigrams, jaccard-index, jaccard-string-similarity,
jaccard-string-similar?): Move to ...
* dump/string-similarity.scm: ... here.
| Arun Isaac |
| 2021-12-14 | Camel case gn:binomialName....* dump.scm (dump-species): Change gn:binomialname to gn:binomialName.
| Arun Isaac |
| 2021-12-14 | Use node ports to indicate foreign key relations precisely....* dump.scm (table-label): Set port attributes on <td> tag.
(tables->graphviz-edges): Specify ports on edges.
| Arun Isaac |
| 2021-12-14 | Specify appearance using HTML table....* 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.
| Arun Isaac |
| 2021-12-14 | Take advantage of bug fixes in bleeding edge (ccwl graphviz)....* dump.scm (graph->dot): Delete function.
(sxml->graphviz-html): Return a <html-string> object.
(dump-schema): Use graph->dot from (ccwl graphviz).
| Arun Isaac |
| 2021-12-13 | Upgrade to bleeding edge (ccwl graphviz)....This fixes a few bugs and brings in new features from (ccwl graphviz).
* guix.scm: Import (gnu packages autotools), (guix git-download)
and (guix packages). Prefix (gnu packages bioinformatics) imports with
guix:.
(ccwl): New variable.
| Arun Isaac |
| 2021-12-13 | Abstract out table to graphviz edge conversion....* dump.scm (column->foreign-table, tables->graphviz-edges): New
functions.
(dump-schema): Use tables->graphviz-edges.
| Arun Isaac |
| 2021-12-13 | Abstract out table to graphviz node conversion....* dump.scm (dumped-table?, table-label, table->graphviz-node): New
functions.
(dump-schema): Use table->graphviz-node.
| Arun Isaac |
| 2021-12-13 | Color table headers by size....* dump.scm (human-units-color): New function.
(dump-schema): Use human-units-color.
| Arun Isaac |
| 2021-12-13 | Implement human units conversion in terms of log1024....This generalizes better and is mathematically cleaner.
* dump.scm (floor-log1024): New function.
(human-units): Use floor-log1024.
| Arun Isaac |
| 2021-12-13 | Use sxml to construct graphviz HTML strings....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.
| Arun Isaac |
| 2021-12-11 | Highlight dumped tables and columns....* dump.scm (dump-schema): Highlight tables and columns.
| Arun Isaac |
| 2021-12-11 | Fix HTML string handling in dot output....* dump.scm (replace-substrings): New function.
(graph->dot): Fix HTML string handling.
| Arun Isaac |
| 2021-12-11 | Log dumped tables and columns....* dump.scm (%dumped): New variable.
(define-dump): Append to %dumped when a new table dumping function is
defined.
| Arun Isaac |
| 2021-12-11 | Abstract out definition of table dumping functions....* 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.
| Arun Isaac |
| 2021-12-11 | Use string similarity and check if foreign key is an integer....* 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.
| Arun Isaac |
