| Age | Commit message (Expand) | Author |
|---|
| 2022-03-10 | Accept connection parameters and dump directory as arguments....* 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.
| Arun Isaac |
| 2022-03-10 | Rename the delete verb of map-alist to remove....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.
| Arun Isaac |
| 2022-03-10 | Work around broken upstream guile-sparql package....* manifest.scm: Import guile-sparql with guix: prefix.
(guile-sparql): New variable.
| Arun Isaac |
| 2022-03-10 | Remove guix: prefix from guile-libyaml....This reverses an accidental commit of work in progress code.
* manifest.scm: Remove guix: prefix from guile-libyaml.
| Arun Isaac |
| 2022-03-10 | Use run64 to run tests....* 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.
| Arun Isaac |
| 2022-03-10 | Add Makefile....* Makefile: New file.
| Arun Isaac |
| 2022-03-10 | Allow tabs in Makefiles....* .dir-locals.el (makefile-gmake-mode): Set indent-tabs-mode to t.
| Arun Isaac |
| 2022-03-09 | Rename guix.scm to manifest.scm....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.
| Arun Isaac |
| 2022-01-04 | Eval macro helper functions at macro expansion time....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.
| Arun Isaac |
| 2021-12-27 | BUGS: Add "Dump table and field annotations to RDF" bug....* BUGS.org (Dump table and field annotations to RDF): New bug.
| Arun Isaac |
| 2021-12-24 | Make visualize-schema executable....* visualize-schema.scm: Add shebang and grant execution permissions.
| Arun Isaac |
| 2021-12-24 | README: Execute dump.scm directly without invoking guile....* README.org (Using): Execute dump.scm directly without explicitly
invoking guile.
| Arun Isaac |
| 2021-12-24 | Add pre-inst-env....* pre-inst-env: New file.
| Arun Isaac |
| 2021-12-24 | Do not add to load path in script....* dump.scm: Do not add to load path.
| Arun Isaac |
| 2021-12-24 | README: Add Using section....* README.org (Using): New section.
| Arun Isaac |
| 2021-12-24 | README: Add Contributing section....* README.org (Contributing): New section.
| Arun Isaac |
| 2021-12-24 | BUGS: Add table size estimates bug....* BUGS.org (Fix table size estimates): New bug.
| Arun Isaac |
| 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 |
