@datagrok/sequence-translator 1.10.16 → 1.10.17

package/CREDITS.md

@@ -0,0 +1,236 @@
+# SequenceTranslator — Third-Party Libraries
+
+The `@datagrok/sequence-translator` package is distributed under the MIT
+license that covers the rest of the `public/` repository (see [`../../LICENSE.md`](../../LICENSE.md)). It
+incorporates the open-source components listed below; this file reproduces the
+attribution and notices required by their respective licenses.
+
+All runtime dependencies are under permissive licenses (BSD-3-Clause, MIT). No
+copyleft (GPL/LGPL/MPL) component is bundled into the published plugin
+artifact.
+
+---
+
+## 1. Bundled in the published artifact (`dist/`)
+
+### OpenChemLib (6.0.1)
+
+JavaScript cheminformatics toolkit used as the structure renderer and
+chirality engine for oligonucleotide molfile generation. Unlike most other
+Datagrok plugins, SequenceTranslator **bundles its own copy** of OpenChemLib
+(the platform's webpack-external `openchemlib/full.js` is intentionally
+disabled in `webpack.config.js`).
+
+- Upstream: https://github.com/cheminfo/openchemlib-js
+- License: **BSD-3-Clause**
+
+```
+Copyright (c) 2015-2017, cheminfo
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    * Neither the name of {{ project }} nor the names of its contributors
+      may be used to endorse or promote products derived from this software
+      without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+```
+
+### Lodash (4.17.x)
+
+General-purpose JavaScript utility library.
+
+- Upstream: https://lodash.com/
+- License: **MIT**
+
+```
+Copyright OpenJS Foundation and other contributors <https://openjsf.org/>
+
+Based on Underscore.js, copyright Jeremy Ashkenas,
+DocumentCloud and Investigative Reporters & Editors <http://underscorejs.org/>
+
+This software consists of voluntary contributions made by many
+individuals. For exact contribution history, see the revision history
+available at https://github.com/lodash/lodash
+
+The following license applies to all parts of this software except as
+documented below:
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+```
+
+### object-hash (3.x)
+
+Stable SHA-1 hashing of pattern objects (used for pattern identity in the
+Pattern Designer app).
+
+- Upstream: https://github.com/puleos/object-hash
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2014 object-hash contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+### save-svg-as-png (1.4.x)
+
+Exports the rendered Pattern-Designer SVG as a PNG.
+
+- Upstream: https://github.com/exupero/saveSvgAsPng
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2014 Eric Shull
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+```
+
+### typeahead-standalone (4.14.x)
+
+Autocomplete dropdown for monomer selection in the PolyTool dialogs.
+
+- Upstream: https://github.com/digitalfortress-tech/typeahead-standalone
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2020 Niket PATHAK
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+---
+
+## 2. Linked at runtime via the Datagrok platform (webpack externals)
+
+These libraries are not bundled into SequenceTranslator's `dist/` — they are
+provided once by the platform host and shared across all packages.
+
+| Component | Version | License    | Upstream                                |
+|-----------|---------|------------|-----------------------------------------|
+| RxJS      | 6.x     | Apache-2.0 | https://github.com/ReactiveX/rxjs       |
+| cash-dom  | 8.x     | MIT        | https://github.com/fabiospampinato/cash |
+| Day.js    | 1.x     | MIT        | https://github.com/iamkun/dayjs         |
+| wu.js     | 2.x     | MIT        | https://github.com/fitzgen/wu.js        |
+| ExcelJS   | 4.x     | MIT        | https://github.com/exceljs/exceljs      |
+
+(`openchemlib/full.js` is **not** in this section: SequenceTranslator
+intentionally bundles its own pinned copy — see Section 1.)
+
+---
+
+## 3. Fetched at runtime from third-party services
+
+None.
+
+---
+
+## 4. Docker container images
+
+None.
+
+---
+
+## 5. Development-only dependencies
+
+Tools used during the build/test cycle (not in the runtime tree, not bundled):
+the `datagrok-tools` CLI transitively pulls in `puppeteer-screen-recorder`,
+which references `@ffmpeg-installer/ffmpeg` (LGPL-2.1) and
+`@ffmpeg-installer/win32-x64` (GPLv3). These binaries are **not** redistributed
+as part of the published SequenceTranslator plugin and impose no obligation on
+users of the plugin.
+
+The dev dependencies on other Datagrok plugins (`@datagrok/bio`,
+`@datagrok/chem`, `@datagrok/helm`) and `@datagrok-libraries/helm-web-editor`,
+`@datagrok-libraries/js-draw-lite` are MIT — covered by the repo-wide
+`LICENSE.md`. Each of those components maintains its own `CREDITS.md`
+(or will) for its own third-party content.

package/detectors.js

@@ -73,6 +73,14 @@ class SequenceTranslatorPackageDetectors extends DG.Package {
             menu.item('PolyTool-Enumerate', () => { grok.functions.call(`${packageName}:getPtChemEnumeratorDialog`, {cell: item.cell}).catch(catchError); });
             break;
           }
+          case 'OligoNucleotide': {
+            // Same enumerator as HELM cells, but the result column is tagged
+            // as OligoNucleotide so the duplex renderer picks it up.
+            menu.item('PolyTool-Enumerate', () => {
+              grok.functions.call(`${packageName}:getPtOligoEnumeratorDialog`, {cell: item.cell}).catch(catchError);
+            });
+            break;
+          }
           }
         }
         this.logger.debug(`${logPrefix}, onContextMenu, end`);