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2022-05-04Special case investigator ID for "Yohan Bossé".Arun Isaac
* dump.scm (investigator-attributes->id): Add special case for investigator "Yohan Bossé".
2022-04-15pre-inst-env: Rename prepend-path-env! to prepend-path-environment!.Arun Isaac
* pre-inst-env (prepend-path-env!): Rename to prepend-path-environment!. Adjust invocations of prepend-path-env!.
2022-03-10Ignore 0th command-line argument.Arun Isaac
* dump.scm (%connection-settings): Use 1th command-line argument. (%dump-directory): Use 2th command-line argument.
2022-03-10Accept connection parameters and dump directory as arguments.Arun Isaac
* 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.
2022-03-10Rename the delete verb of map-alist to remove.Arun Isaac
The delete verb of map-alist somehow interacts with the delete function from (srfi srfi-1), and I'm not able to figure out how. It is simpler to just rename the delete verb to remove. * dump/utils.scm: Do not rename the delete function from (srfi srfi-1). (map-alist): Rename the delete verb to remove. * tests.scm ("map-alist docstring example"): Update test.
2022-03-10Work around broken upstream guile-sparql package.Arun Isaac
* manifest.scm: Import guile-sparql with guix: prefix. (guile-sparql): New variable.
2022-03-10Remove guix: prefix from guile-libyaml.Arun Isaac
This reverses an accidental commit of work in progress code. * manifest.scm: Remove guix: prefix from guile-libyaml.
2022-03-10Use run64 to run tests.Arun Isaac
* manifest.scm: Import (guix build-system gnu) and (guix licenses). (run64): New variable. Add run64 to manifest. * Makefile (GUILE): Delete variable. (RUN64): New variable. (check): Use run64 instead of guile to run tests.
2022-03-10Add Makefile.Arun Isaac
* Makefile: New file.
2022-03-10Allow tabs in Makefiles.Arun Isaac
* .dir-locals.el (makefile-gmake-mode): Set indent-tabs-mode to t.
2022-03-09Rename guix.scm to manifest.scm.Arun Isaac
We only have a manifest, not a package definition. So, rename it as such, making `guix shell' invocations briefer. * guix.scm: Rename to manifest.scm. In documentation comments, make `guix shell' implicitly pick up the manifest file. * README.org (Using): Make `guix shell' implicitly pick up the manifest file.
2022-01-04Eval macro helper functions at macro expansion time.Arun Isaac
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.
2021-12-27BUGS: Add "Dump table and field annotations to RDF" bug.Arun Isaac
* BUGS.org (Dump table and field annotations to RDF): New bug.
2021-12-24Make visualize-schema executable.Arun Isaac
* visualize-schema.scm: Add shebang and grant execution permissions.
2021-12-24README: Execute dump.scm directly without invoking guile.Arun Isaac
* README.org (Using): Execute dump.scm directly without explicitly invoking guile.
2021-12-24Add pre-inst-env.Arun Isaac
* pre-inst-env: New file.
2021-12-24Do not add to load path in script.Arun Isaac
* dump.scm: Do not add to load path.
2021-12-24README: Add Using section.Arun Isaac
* README.org (Using): New section.
2021-12-24README: Add Contributing section.Arun Isaac
* README.org (Contributing): New section.
2021-12-24BUGS: Add table size estimates bug.Arun Isaac
* BUGS.org (Fix table size estimates): New bug.
2021-12-24BUGS: Add bug tracker.Arun Isaac
* BUGS.org: New file.
2021-12-24Visualize RDF schema.Arun Isaac
* visualize-schema.scm (literal-node-id, rdf-type-nodes, rdf-literal-nodes, rdf-edges, write-rdf-visualization): New functions. (main): Call write-rdf-visualization.
2021-12-24Wrap SQL visualization code into a function.Arun Isaac
* visualize-schema.scm (write-sql-visualization, main): New functions. Invoke main.
2021-12-24Import functions from (ccwl graphviz).Arun Isaac
* 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.
2021-12-24Color code dumped tables and columns.Arun Isaac
* visualize-schema.scm (sxml->graphviz-html): Color code dumped tables and columns.
2021-12-24Fetch entire table schema in single SPARQL query.Arun Isaac
* visualize-schema.scm (tables): Fetch entire table schema in single SPARQL query.
2021-12-24Add TODO note to prefer JSON query results to CSV.Arun Isaac
* visualize-schema.scm (sparql-query-records): Add TODO note to prefer JSON query results to CSV.
2021-12-24Document define-dump.Arun Isaac
* dump.scm (define-dump): Add docstring.
2021-12-24Introduce syntax-let abstraction.Arun Isaac
* dump.scm (syntax-let): New macro. (define-dump): Use syntax-let. * .dir-locals.el (scheme-mode): Indent syntax-let correctly.
2021-12-23Automatically create domain triples for predicates.Arun Isaac
* dump.scm (define-dump): Automatically create domain triples for predicates.
2021-12-23Dump metadata about the dump itself.Arun Isaac
* dump.scm (remove-namespace, dump-id): New functions. (define-dump): Dump metadata about the dump itself.
2021-12-23Disambiguate user and User tables in RDF identifier.Arun Isaac
* dump.scm (dump-schema, column-id): Disambiguate user and User tables in RDF identifier.
2021-12-23Abstract column id generation to separate function.Arun Isaac
* dump.scm (column-id): New function. (dump-schema): Use column-id.
2021-12-23Do not register dumped tables and columns to %dumped.Arun Isaac
* dump.scm (%dumped): Delete variable. (define-dump): Do not register dumped tables and columns to %dumped. (dumped-table?): Delete function.
2021-12-23Add dumped? field to <column> type.Arun Isaac
* dump/table.scm (<column>): Add dumped? field. Rename constructor to column-constructor. (make-column): Implement as wrapper around column-constructor.
2021-12-23Specify range of gn:inbredSetOfSpecies.Arun Isaac
* dump.scm (dump-inbred-set): Set range of gn:inbredSetOfSpecies to gn:species.
2021-12-23Use foaf:Person instead of gn:investigator.Arun Isaac
* dump.scm (dump-info-files): Set range of gn:datasetOfInvestigator to foaf:Person instead of gn:investigator.
2021-12-23Add Literal range triples.Arun Isaac
* 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.
2021-12-23Remove duplicate predicates for gn:phenotype.Arun Isaac
* dump.scm (dump-phenotype): Remove duplicate predicates gn:prePublicationDescription and gn:postPublicationDescription.
2021-12-23Rename gn:authors predicate to gn:author.Arun Isaac
gn:authors is a typo. * dump.scm (dump-publication): Rename gn:authors predicate to gn:author.
2021-12-23Add runtime type checking for triple.Arun Isaac
* dump.scm (triple): Add runtime type checking.
2021-12-20Move schema visualization to separate script.Arun Isaac
* 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.
2021-12-20Add guile-sparql to Guix manifest.Arun Isaac
* guix.scm: Add guile-sparql to manifest.
2021-12-20Upgrade ccwl to latest commit.Arun Isaac
* guix.scm (ccwl): Upgrade to commit 51c12b7e58685b70e7cfd9612dac403cf9ee845c.
2021-12-20Capture full column type.Arun Isaac
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?.
2021-12-20Move <table> and <column> types to separate module.Arun Isaac
* dump.scm (<table>, <column>): Move to ... * dump/table.scm: ... here.
2021-12-17Indent define-dump better.Arun Isaac
* dump.scm (define-dump): Indent better.
2021-12-17Document RDF schema during dumping.Arun Isaac
* dump.scm (define-dump): Support schema-triples clause. (dump-strain, dump-publish-xref, dump-info-files): Add schema-triples clause. (main): Output rdfs: prefix.
2021-12-17Make order of clauses in define-dump unspecified.Arun Isaac
* dump.scm (find-clause): New function. (define-dump): Make order of clauses unspecified.
2021-12-16Make define-dump syntax more concise.Arun Isaac
* 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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