| Age | Commit message (Expand) | Author |
|---|
| 2021-12-11 | Remove rdflib python code....* rdf.py: Delete file.
| Arun Isaac |
| 2021-12-11 | Visualize schema....* .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.
| Arun Isaac |
| 2021-12-11 | Use select-query....* 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.
| Arun Isaac |
| 2021-12-11 | Implement S-expression like SQL select query....* dump/sql.scm: Import (srfi srfi-1). Export select-query.
(select-query): New macro.
| Arun Isaac |
| 2021-12-04 | Add emacs directory local variables....* .dir-locals.el: New file.
| Arun Isaac |
| 2021-12-04 | Remove redundant camel->lower-camel function....* dump.scm (camel->lower-camel): Delete function.
(default-metadata-proc): Do not use camel->lower-camel.
| Arun Isaac |
| 2021-12-04 | Build subjects exclusively with string->identifier....* dump.scm (dump-mapping-method, dump-publication, dump-info-files):
Use string->identifier to build subjects.
| Arun Isaac |
| 2021-12-04 | Append an underscore to the identifier prefix....This is slightly more readable.
* dump.scm (string->identifier): Append an underscore to the
identifier prefix.
| Arun Isaac |
| 2021-12-04 | Fix indentation....* dump.scm (get-tables-from-comments, dump-table-fields): Fix
indentation.
| Arun Isaac |
| 2021-12-04 | Use the map-alist DSL....* 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.
| Arun Isaac |
| 2021-12-04 | Implement the map-alist DSL....map-alist is a DSL to transform one association list into
another. These transformations are frequently required when dumping
tables, especially metadata tables.
* dump/utils.scm: New file.
| Arun Isaac |
| 2021-12-02 | Construct investigator ID using first and last names too....* 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.
| Arun Isaac |
| 2021-12-02 | Use string-delete instead of string-replace-substring....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.
| Arun Isaac |
| 2021-12-02 | Abstract out string->identifier....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.
| Arun Isaac |
| 2021-12-02 | Document delete-substrings....* dump.scm (delete-substring): Add docstring.
| Arun Isaac |
| 2021-12-01 | Deal with AvgMethodId = 0....* dump.scm (dump-info-files): Deal with AvgMethodId.
| Arun Isaac |
| 2021-12-01 | Use InfoFileTitle instead of InfoPageTitle for dataset name....Not all datasets have a non-NULL InfoPageTitle field.
* dump.scm (dump-info-files): Use InfoFileTitle instead of
InfoPageTitle for dataset name.
| Arun Isaac |
| 2021-12-01 | Extract name of dataset group....* dump.scm (dump-info-files): Extract name of dataset group.
| Arun Isaac |
| 2021-12-01 | Do not link inbred-set to mapping-method....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.
| Arun Isaac |
| 2021-12-01 | Allow N/A avg method....* 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 _.
| Arun Isaac |
| 2021-12-01 | Remove gn:geoSeries when value starts with "No Geo Series..."....* dump.scm (dump-info-files): Remove gn:geoSeries when value starts
with "No Geo Series...".
| Arun Isaac |
| 2021-12-01 | In the gn: prefix, use http instead of https....* dump.scm: In the gn:prefix, use http instead of https.
| Arun Isaac |
| 2021-12-01 | Remove dependency on python-rdflib....* guix.scm: Remove python-rdflib.
(python-berkeleydb, python-rdflib-6): Delete variables.
| Arun Isaac |
| 2021-12-01 | Replace guix environment with guix shell....guix environment is deprecated.
* guix.scm: Replace guix environment with guix shell.
| Arun Isaac |
| 2021-12-01 | Remove unrequired rdfs: prefix....* dump.scm: Remove rdfs: prefix.
| Arun Isaac |
| 2021-11-11 | Fix unbalanced parentheses....Parentheses became unbalanced due to my careless git use.
* dump.scm: Fix unbalanced parentheses.
| Arun Isaac |
| 2021-11-09 | Use upstream guile-dbi and guile-dbd-mysql....* guix.scm: Do not prefix guix: in importing (gnu packages guile-xyz).
(guile-dbi, guile-dbi-bootstrap, guile-dbd-mysql): Delete variables.
| Arun Isaac |
| 2021-09-14 | Dump InfoFiles....* dump.scm (dump-info-files): New function.
[main]: Call dump-info-files.
| Arun Isaac |
| 2021-09-14 | Abstract out deleting substrings....* dump.scm (delete-substrings): New function.
(dump-publication): Replace string-replace-substring with
delete-substrings.
| Arun Isaac |
| 2021-09-14 | Update python-rdflib package....* guix.scm: Import (gnu packages dbm), (guix build-system python)
and (guix download).
(python-berkeleydb, python-rdflib-6): New variables.
[mainfest]: Replace python-rdflib with python-rdflib-6. Remove
python-urrlib3.
| Arun Isaac |
| 2021-09-14 | Update guile-dbi package....* guix.scm (guile-dbi): Update to 2.1.8.
(guile-dbi-bootstrap): Inherit from guile-dbi instead of
guix:guile-dbi.
Update comments about contributing upstream.
| Arun Isaac |
| 2021-09-14 | Do not define sub-properties of rdfs:label....* dump.scm (dump-publication, dump-tissue): Do not define any property
to be a sub-property of rdfs:label.
| Arun Isaac |
| 2021-09-14 | Dump GeneChip....* dump.scm (gene-chip-name->id, dump-gene-chip): New functions.
[main]: Call dump-gene-chip.
| Arun Isaac |
| 2021-09-14 | Dump AvgMethod....* dump.scm (avg-method-name->id, dump-avg-method): New functions.
[main]: Call dump-avg-method.
| Arun Isaac |
| 2021-09-14 | Delete unused camel->kebab function....* dump.scm (camel->kebab): Delete function.
| Arun Isaac |
| 2021-09-09 | Dump Investigators....* dump.scm (fix-email-id, investigator-email->id, dump-investigators):
New functions.
Invoke dump-investigators.
| Arun Isaac |
| 2021-09-09 | Dump Tissue....* dump.scm (tissue-short-name->id, dump-tissue): New functions.
Invoke dump-tissue.
| Arun Isaac |
| 2021-09-09 | Add foaf prefix....* dump.scm: Add foaf prefix.
| Arun Isaac |
| 2021-09-09 | Abstract out prefix entries....* dump.scm (prefix): New function.
Use prefix.
| Arun Isaac |
| 2021-08-27 | Initial commit | Arun Isaac |
