conceptql 0.6.0 → 0.7.0

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data/CHANGELOG.md

@@ -4,6 +4,182 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [0.7.0] - 2026-11-09
+
+### Added
+
+- `ConceptQL::DiagramRenderer`, the diagram renderer of the Jigsaw diagram editor, moved into
+  the gem. It draws a diagram tree (`ConceptQL::Diagram.render`) as a standalone static SVG
+  (`render_static`), a PNG (`png`) or the in-app SVG (`render_app`), with the same drawing as in
+  the editor. Its SVG output differs from the editor's only in the text of the `<style>` element,
+  and its PNG output is byte-identical. The gem ships its assets under `assets/diagram/`: the
+  operator icons, the diagram CSS, and the Roboto fonts with their license (SIL Open Font
+  License 1.1). The gemspec lists both licenses, `MIT` and `OFL-1.1`. The configuration
+  points at them by default, so a host needs no configure call. `require "conceptql"` loads
+  none of the renderer until its first use. `render_static` and `png` run the resvg program,
+  version 0.33.0. `just test-diagram` runs the renderer's tests against the
+  editor's JavaScript references, and `just ci` and GitHub CI run it. The release workflow
+  checks that the built gem contains every file under `assets/diagram/`, and it draws one
+  diagram with the installed gem. See `docs/diagram_renderer.md`.
+  - The renderer's diagram CSS (`assets/diagram/diagram.css`) holds only the rules of the
+    editor's stylesheet that can match an element of a diagram. The editor's page rules (for
+    `html`, `body`, `h1`, `.sidebar` and the like) are left out. In a page, the `<style>` of the
+    in-app SVG applies to the whole page, so a page that used those rules must supply them.
+  - The first `render_static` or `png` call in a process runs `resvg --version`. When resvg
+    reports another version than 0.33.0, the call writes one warning to stderr that names both
+    versions. Then it draws the diagram anyway, and later calls do not check again.
+- An operator class can say `hidden`. A hidden operator still runs, but `ConceptQL.metadata`
+  leaves it out. An operator is not hidden unless it says so, and a subclass does not inherit
+  the mark. `invalid`, `from`, `numeric`, `dedup`, `sum` and `count` are hidden. Before,
+  `ConceptQL.metadata` left out each operator without a category, and these six were the only
+  such operators. Now every operator has a category from `ConceptQL.categories`. The metadata
+  has no `hidden` key, and it publishes the same 119 operators on `gdm` as before.
+- Operator reference documentation in the operator classes. `ConceptQL.metadata` serves two new
+  keys for each operator: `returns`, a text that says which records the operator returns, and
+  `examples`, a list of `{title, statement, help}`. An option or an argument can have a
+  `meaning` key, a text that says what it does. `instructions` stays the hint for typing a
+  value. The `label` option and the `left` and `right` options have a `meaning`. The Metadatable
+  DSL has `returns`, `example` and `option_meaning`, which replaces the meaning of one inherited
+  option. A subclass does not inherit `returns` or the examples. The vocabulary operators serve
+  the `returns` text and the examples of `ConceptQL::Operators::Vocabulary`, each operator
+  only the examples whose statement starts with its own name. All texts are plain text.
+- `ConceptQL.spec_examples_path`, the directory `docs/spec/examples/` in the gem. It holds one
+  file, `<spec_id>.json`, for each spec_id of the operator reference. The file has the
+  examples of that section, each with its `title`, `statement`, `help`, the `columns` and the
+  first 10 `rows` of its result on the test data, and its diagram `tree`
+  (`conceptql-diagram/v1`, with counts). An application can show an operator's help from the
+  file of that operator, without a database. `just spec` writes the files, and
+  `just spec-check` fails when one of them would change.
+- `information_periods` declares its argument, Information Types (a comma-separated list), so
+  an editor can offer the field. The argument is optional: without it, the operator still
+  selects every information period. Each value is a concept ID or a concept code of the
+  `GDM_INFORMATION_TYPE` vocabulary, such as `PARTD`, and a statement can mix both. An unknown
+  code gets the warning `unknown code(s)` and selects no period. Before, every argument went
+  through `to_i`, so a code silently became concept ID 0.
+- `cpt` and `hcpcs` warn when the data has no record of their vocabulary but has CPT4_HCPCS
+  records, and the lexicon carries CPT4_HCPCS. Production ETL data stores CPT-4 and HCPCS codes
+  only as CPT4_HCPCS, so on that data the two operators select nothing (known issue, bead
+  `conceptql-rpy3`). The warning is "the data has no records of this vocabulary", and it says
+  to use `cpt_or_hcpcs`, which also reads CPT4_HCPCS. `cpt_or_hcpcs` does not give it. The
+  check runs two small existence queries on the data, and it skips a mock database as the
+  other code warnings do.
+
+### Changed
+
+- The `inpatient_length_of_stay` and `outpatient_event_to_return` options of `one_in_two_out`
+  serve their text as `meaning`. Before, it was a `desc` key that the diagram editor did not
+  read.
+- **Breaking:** a code lookup raises `ConceptQL::CodeCaseMismatchError` for a code that its
+  vocabulary stores only in another case. Since 0.6.0 a lookup compares codes case-exactly, so
+  `data_model.concept_ids(db, "GDM_PROV", ["line"])` returned `[]` without a word, because the
+  vocabulary stores `LINE`. t_shank made that call and lost every line row of an export. Now it
+  raises, and the message names the vocabulary, each such code and its stored spellings. The
+  error's `mismatches` attribute holds the same facts. It is an `ArgumentError`. The lookups
+  that take codes raise it: `concept_ids`, `known_codes`, `concepts_to_codes`,
+  `concepts_to_codes_in_class`, `code_meanings`, `concepts` and `concepts_ds`, on the
+  `Lexicon` and on the data model. `concepts` and `concepts_ds` check when they build the
+  dataset. A code that a lookup vocabulary stores in this case is no error, and neither is a
+  code that matches nothing in any case: it still finds no concept. A vocabulary whose
+  vocabulary_formats row declares `(?i:...)` already ignores case, so it never raises. The
+  check reads the concept table without a guard. When the concept table is missing,
+  `known_codes`, `code_meanings` and `concepts_to_codes_in_class` raise
+  `Sequel::DatabaseError`. 0.6.0 returned `[]`, `{}` and `nil`. Each of these lookups takes
+  `check_case: false`, which skips the check and keeps the 0.6.0 answer. A statement does not
+  raise: a vocabulary operator, `provenance` and `place_of_service_filter` pass
+  `check_case: false`. So `["icd10cm", "i16.5"]` still gets the warning
+  `improperly formatted code` and selects no rows. The utilization operators
+  (`hospitalization`, `hospice`, `snf`) look up their own codes with the check.
+- **Breaking:** a positional upstream is a validation error (`has upstreams`) on `after`,
+  `any_overlap`, `before`, `contains`, `during`, `equal`, `except`, `filter`, `match`,
+  `person_filter`, `trim_date_end`, `trim_date_start` and `read`. The first twelve take their
+  operands from the `left` and `right` options, and `read` takes codes. Before, each of them
+  ignored a positional upstream without a word.
+- **Breaking:** `occurrence`, `first` and `last` accept exactly one upstream. A second
+  positional upstream is a validation error (`has multiple upstreams`). Before, they used only
+  the first upstream and dropped the others without a word.
+- **Breaking:** `equal` no longer offers the `within` option, and `first` and `last` no longer
+  offer `group_by_date`. The options had no effect on these operators. A statement that sets
+  one of them fails validation (`unsupported option`). A blank value or `false` passes, so a
+  cleared checkbox in the Jigsaw diagram editor still validates.
+- **Breaking:** `DataModel::Gdm#information_period_where_clause` takes the database as its
+  first argument: `(db, arguments)`. Before, it took only `(arguments)`. It needs the database
+  to look up the concept codes of `information_periods`.
+- The specification moved to `docs/spec/README.md`, and `ConceptQL.spec_path` returns it. Its
+  text comes from the conceptql_spec repository, which held the published spec, and it replaces
+  the copy that was `doc/spec.md`. `just spec` builds it from `docs/spec/README.cql.md` on the
+  DuckDB test data. It draws the diagram images with `ConceptQL::DiagramRenderer`, so it needs
+  resvg 0.33.0, and it needs no checkout of the Jigsaw diagram editor. `just spec-check`
+  draws every image again and fails when a committed image differs from its new drawing, is
+  missing, or is not used. The gem does not ship its diagram images.
+- The `desc` of the published operators changed. The operator classes now hold the reference
+  documentation of the spec, so each `desc` is the summary of its operator's reference section.
+  `ConceptQL.metadata` serves the new texts, so a system that keeps a copy of the metadata,
+  such as the Jigsaw diagram editor, sees a different payload.
+- The spec build writes the reference section of each published `spec_id` and the quick
+  reference of Appendix E from `ConceptQL.metadata` of `Database.new(nil, data_model: :gdm)`.
+  A section has the operator's `desc`, its upstream operators or its `left` and `right`
+  operands, its arguments and options with their `meaning`, its `returns` text and its examples
+  with their results and diagrams. `docs/spec/README.cql.md` marks the place of each generated
+  block with a directive, `<!-- conceptql-spec: operator <spec_id> -->`, and the spec's
+  Appendix D describes the directives. The hand-written copies of these texts are removed from
+  the spec.
+- The spec lists every vocabulary operator with the full name of its vocabulary and its
+  domain, in a table that the build writes from `ConceptQL.metadata` at the new directive
+  `<!-- conceptql-spec: vocabulary-operators -->`. It marks a deprecated operator, such as
+  `drg`. The `Vocabulary` Operator section is now a `##` section of its own, so that it stays
+  under the 40,000-byte limit of a spec section. The other selection operators moved under a
+  new heading, Other Selection Operators. The anchors of the operator sections did not change.
+- `ConceptQL.metadata` gives `read` and the multiple vocabulary operators, such as
+  `cpt_or_hcpcs`, a `long_name`. Before, it was empty. `read` has the long name of the Read
+  vocabulary in the OHDSI vocabulary table, "NHS UK Read Codes Version 2 (HSCIC)". A multiple
+  vocabulary operator names its vocabularies, for example "CPT4, HCPCS and CPT4_HCPCS". The
+  metadata of `read` also has `predominant_domains`, `["condition_occurrence"]`. Before, it was
+  empty.
+
+### Removed
+
+- The `hidden` column of `config/vocabularies.csv`, with `Vocabularies::Entry#hidden?` and
+  `Vocabularies::Entry#visible?`. No code used them. The column did not hide any operator, and
+  it is not connected to the new `hidden` mark of an operator.
+- **Breaking:** `Vocabularies::Entry#vocabulary_long_name`.
+  `Vocabularies::Entry#vocabulary_full_name` replaces it and reads the `vocabulary_full_name`
+  column. An `Entry` built from a hash takes the key `vocabulary_full_name`, not
+  `vocabulary_long_name`. `Entry#long_name` stays.
+
+### Fixed
+
+- `min_upstreams` and `max_upstreams` in `ConceptQL.metadata` say how many positional
+  upstreams pass validation (99 means no limit). Before, `min_upstreams` always equalled
+  `max_upstreams`. `union` and `co_reported` served 99/99 and now serve 1/99. `first`, `last`
+  and `occurrence` served 99/99 and now serve 1/1. `person` and `death` served 1/1 and now
+  serve 0/1. `trim_date_end` and `trim_date_start` served 1/1 and now serve 0/0.
+
+- The `long_name` in a vocabulary operator's metadata is the vocabulary's full name, read from
+  the `vocabulary_full_name` column of `config/vocabularies.csv` and the lexicons. Before, it
+  fell back to the short name (`atc` served "WHO ATC", not "WHO Anatomic Therapeutic Chemical
+  Classification") or was nil. The `short_name` does not change.
+
+- `race`: an Unknown argument selected no patients. It now selects the patients with no race or
+  race concept ID 0. A race concept ID argument now also selects the more detailed races of
+  `config/race.yml`, as a race name does. Before, that was missed, which showed only with the
+  GDM vocabularies.
+
+- `ethnicity`: Unknown now also selects the patients with no ethnicity, not only ethnicity
+  concept ID 0.
+
+- Operator help texts that disagreed with the code: the input hints of `within` and `at_least`
+  (the temporal operators and `occurrence`), of `time_window`'s `start` and `end`, and of
+  `episode`'s `gap_of`; the old `desc` of the `TrimDate` base class; and the summary `desc` of
+  the vocabulary operators.
+
+- A vocabulary whose domain is blank has no domain, so its operators select
+  `condition_occurrence` records. The GDM vocabulary table (`gdm_vocabs.vocabularies` in the
+  test data) gives all but one of its vocabularies the domain `''`, and the last one a NULL
+  domain. Before, the operators of the `''` vocabularies, such as
+  `cms_place_of_service`, got `criterion_domain` `''`, their predominant domain in the
+  metadata was `''`, and their annotation counts were keyed by `''`. The OHDSI vocabulary
+  tables give no domain, so they were not affected.
+
 ## [0.6.0] - 2026-11-02
 
 ### Added

data/README.md

@@ -6,7 +6,9 @@ This gem interprets the ConceptQL language and translates it into SQL queries co
 
 ## Further Reading
 
-If you're interested in reading up on ConceptQL, a the specifications document is [available in markdown format](https://github.com/outcomesinsights/conceptql_spec).
+The ConceptQL specification is [docs/spec/README.md](docs/spec/README.md).
+
+`ConceptQL::DiagramRenderer` draws a statement's diagram as an SVG or a PNG. See [docs/diagram_renderer.md](docs/diagram_renderer.md).
 
 ## Motivation for ConceptQL
 
@@ -31,7 +33,7 @@ For instance, using ConceptQL we can take a statement that looks like this:
 
 And generate a diagram that looks like this:
 
-![](doc/diagram_0.png)
+![](docs/spec/images/511539320d6cfd34954d3b092148bda1cb870caadc44211e3f189262d160f89f.svg)
 
 And generate SQL that looks like this:
 

data/assets/diagram/diagram.css

@@ -0,0 +1,331 @@
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+
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+ * Hide the overflow in IE.
+ */
+/* line 240, frontend/app/styles/mvcss/modules/../_01_reset.scss */
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+/* line 141, frontend/app/styles/mvcss/modules/../_04_base.sass */
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+  display: block;
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+/* line 17, frontend/app/styles/mvcss/modules/_vis.sass */
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+  animation: vis 0.5s cubic-bezier(0.215, 0.61, 0.355, 1) 0.2s backwards;
+  background: #f4f2f3;
+  cursor: move;
+}
+
+/* line 30, frontend/app/styles/mvcss/modules/_vis.sass */
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+/* line 52, frontend/app/styles/mvcss/modules/_vis.sass */
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+/* line 133, frontend/app/styles/mvcss/modules/_vis.sass */
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+/* line 140, frontend/app/styles/mvcss/modules/_vis.sass */
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+/* line 142, frontend/app/styles/mvcss/modules/_vis.sass */
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+  stroke: #f4f2f3;
+  stroke-width: 3px;
+  transition: all 0.4s cubic-bezier(0.215, 0.61, 0.355, 1);
+}
+
+/* line 237, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-icon {
+  color: white;
+}
+
+/* line 242, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-label {
+  color: #afa8ad;
+  opacity: 0;
+  transition: all 0.4s cubic-bezier(0.215, 0.61, 0.355, 1);
+  visibility: hidden;
+}
+
+/* line 249, frontend/app/styles/mvcss/modules/_vis.sass */
+.is-label .vis-node-label {
+  opacity: 1;
+  visibility: visible;
+}
+
+/* line 255, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point {
+  color: #959294;
+  transition: all 0.4s cubic-bezier(0.215, 0.61, 0.355, 1);
+}
+
+/* line 259, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="condition_occurrence"] {
+  color: #ad4a5b;
+}
+
+/* line 261, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="death"] {
+  color: #704a4a;
+}
+
+/* line 263, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="drug_exposure"] {
+  color: #9f57a5;
+}
+
+/* line 265, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="observation_period"] {
+  color: #6fbbba;
+}
+
+/* line 267, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="person"] {
+  color: #7193cd;
+}
+
+/* line 269, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="placeholder"] {
+  color: #f6f3f5;
+}
+
+/* line 271, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="procedure_occurrence"] {
+  color: #90d796;
+}
+
+/* line 273, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point[data-color="visit_occurrence"] {
+  color: #d1a776;
+}
+
+/* line 276, frontend/app/styles/mvcss/modules/_vis.sass */
+.vis-node-point-base {
+  stroke: #f4f2f3;
+  stroke-width: 3px;
+}

data/assets/diagram/fonts/OFL.txt

@@ -0,0 +1,93 @@
+Copyright 2011 The Roboto Project Authors (https://github.com/googlefonts/roboto-classic)
+
+This Font Software is licensed under the SIL Open Font License, Version 1.1.
+This license is copied below, and is also available with a FAQ at:
+https://openfontlicense.org
+
+
+-----------------------------------------------------------
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+-----------------------------------------------------------
+
+PREAMBLE
+The goals of the Open Font License (OFL) are to stimulate worldwide
+development of collaborative font projects, to support the font creation
+efforts of academic and linguistic communities, and to provide a free and
+open framework in which fonts may be shared and improved in partnership
+with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves. The
+fonts, including any derivative works, can be bundled, embedded, 
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works. The fonts and derivatives,
+however, cannot be released under any other type of license. The
+requirement for fonts to remain under this license does not apply
+to any document created using the fonts or their derivatives.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components as
+distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to a
+new environment.
+
+"Author" refers to any designer, engineer, programmer, technical
+writer or other person who contributed to the Font Software.
+
+PERMISSION & CONDITIONS
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,
+in Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+redistributed and/or sold with any software, provided that each copy
+contains the above copyright notice and this license. These can be
+included either as stand-alone text files, human-readable headers or
+in the appropriate machine-readable metadata fields within text or
+binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+Name(s) unless explicit written permission is granted by the corresponding
+Copyright Holder. This restriction only applies to the primary font name as
+presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+Software shall not be used to promote, endorse or advertise any
+Modified Version, except to acknowledge the contribution(s) of the
+Copyright Holder(s) and the Author(s) or with their explicit written
+permission.
+
+5) The Font Software, modified or unmodified, in part or in whole,
+must be distributed entirely under this license, and must not be
+distributed under any other license. The requirement for fonts to
+remain under this license does not apply to any document created
+using the Font Software.
+
+TERMINATION
+This license becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+OTHER DEALINGS IN THE FONT SOFTWARE.