Bioprotocols Working Group commits | Ecosyste.ms: OpenCollective

Fix the malformed OWL restrictions.

Add Jupyter notebook with the code for finding and fixing ill-formed
owl:Restriction definitions...

github.com/Bioprotocols/labop - 36136cce296c69cba7b8ae7b21eb50c419908375 authored about 3 years ago by Robert P. Goldman <[email protected]>

added ipython dep

github.com/Bioprotocols/labop - 25b871427c32d5cd39412d3f57bea547814906f5 authored about 3 years ago by Daniel Bryce <[email protected]>

fix container ontology dep

github.com/Bioprotocols/labop - a9dccb1eea93f8830e3f6fecbf88ec56818c937c authored about 3 years ago by Daniel Bryce <[email protected]>

Typing hint was wrong type

github.com/Bioprotocols/labop - 8d5725a53ab1cc5172e41ed4a0b675654a711def authored about 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #12 from rpgoldman/merge-client-package

This merge pulls in a branch that is a cleaned-up version of the client-package, which has an ug...

github.com/Bioprotocols/container-ontology - a7dd08801bbbf5659966002db12e227d64a7a845 authored about 3 years ago by rpgoldman <[email protected]>

Update the ontology for the server.

- Add a local copy of SBOL3 to the server.

- Make `hasWellBottomShape` a functional property. ...

github.com/Bioprotocols/container-ontology - 2aefad6bec9a413c391f02a798ae14f554891b15 authored about 3 years ago by Robert P. Goldman <[email protected]>

Add instructions for install and use.

github.com/Bioprotocols/container-ontology - d4eab7e31e5af7b34bb82dfe58ff88e4530568fe authored about 3 years ago by Robert P. Goldman <[email protected]>

Client API for container ontology server.

The client API has two components:
1. Auto-generated API to the Owlery container server, based o...

github.com/Bioprotocols/container-ontology - f00bc37ca2fa3c3c1e8cfc7d4ee9731cc3bab9f2 authored about 3 years ago by Robert P. Goldman <[email protected]>

More info on Strateos catalog.

github.com/Bioprotocols/container-ontology - 38ca3d9148bdf024c63ca78b5e2f8ce99f7b17db authored about 3 years ago by Robert P. Goldman <[email protected]>

demo notebook with output.

github.com/Bioprotocols/labop - b9016eb9bc3786c5d4b2c92ede818e92dbe6edaf authored about 3 years ago by Daniel Bryce <[email protected]>

demo notebook with output.

github.com/Bioprotocols/labop - 112cfe9c64badcf292baf6cc85bb120efe812a9c authored about 3 years ago by Daniel Bryce <[email protected]>

notebook README.md

github.com/Bioprotocols/labop - 436c31bbc1cb9808aa818390d59a888b20b8bb25 authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - 2781fc5a74189476a4a1e6363373335ecec7368b authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - 97504b1f60d8bc47a9f4425b473d3d6c6d32beb4 authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - e87c1ffa4fec4f3c62d2c6dbab3546f41814619a authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - 30a33980e92fc42aaa30ef9fdcd8c6cc159b907b authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - 43f9561154f55340bf2374df13c24a87416ca8db authored about 3 years ago by Daniel Bryce <[email protected]>

add deps for tests

github.com/Bioprotocols/labop - b73240cdc6ae3fbb47e914599071a5fcb0e1433b authored about 3 years ago by Daniel Bryce <[email protected]>

demo final

github.com/Bioprotocols/labop - 4b1e6063ac94afc1209d5c54b36543aba45be8a9 authored about 3 years ago by Daniel Bryce <[email protected]>

stable demo code. still cleaning up notebooks.

github.com/Bioprotocols/labop - 6da58d8e15e4c5f3208cec47f3813fcaf3b5ae6b authored about 3 years ago by Daniel Bryce <[email protected]>

validation failing on execution, but bypassing

github.com/Bioprotocols/labop - 6fa6b6774354bb2ff10b8d3867684815b44780c1 authored about 3 years ago by Daniel Bryce <[email protected]>

fixed failing tests

github.com/Bioprotocols/labop - 59d86bc26630a3f95d3e290a8b9b34069f5a029d authored about 3 years ago by Daniel Bryce <[email protected]>

checkpoint on markdown conversion

github.com/Bioprotocols/labop - 724cf21c8e291960015247edccee32709569fdf3 authored about 3 years ago by Daniel Bryce <[email protected]>

Autoprotocol done

github.com/Bioprotocols/labop - 174bdf6394600d983c67d8bdc1edd526ec4e521c authored about 3 years ago by Daniel Bryce <[email protected]>

working container resolution through container ontology.

github.com/Bioprotocols/labop - a22617c86e13eef27de1d3ca9ddd0bbdc47c3d44 authored about 3 years ago by Daniel Bryce <[email protected]>

remove markdown test and testing container creation

github.com/Bioprotocols/labop - 075b9ea0262628f5ca092366b96de73d9429cc71 authored about 3 years ago by Daniel Bryce <[email protected]>

started markdown specialization

github.com/Bioprotocols/labop - 66506b46ed05ffeeb986719d28ad4e57812e16e0 authored about 3 years ago by Daniel Bryce <[email protected]>

started markdown specialization

github.com/Bioprotocols/labop - ebba1e84e0568af7335dad797b7fecf92639d171 authored about 3 years ago by Daniel Bryce <[email protected]>

Merge branch 'markdown' into to-autoprotocol

github.com/Bioprotocols/labop - 05669d99543d624db113d4020f5ef8cfa20dc85b authored about 3 years ago by Daniel Bryce <[email protected]>

notebook for autoprotocol conversion demo

github.com/Bioprotocols/labop - 397a6857e45b150b12851491e6a7a104223c53eb authored about 3 years ago by Daniel Bryce <[email protected]>

checkpoint on conversion, needing uri resolution against Strateos

github.com/Bioprotocols/labop - 724841b59eb6a6b8b9d27ad7b71a90498779864b authored about 3 years ago by Daniel Bryce <[email protected]>

add logger

github.com/Bioprotocols/labop - f1d11180e7dabc29b983003489988e205e1bde1b authored about 3 years ago by Daniel Bryce <[email protected]>

checkpoint on conversion, needing uri resolution against Strateos

github.com/Bioprotocols/labop - 86b6a37b32dc294acc4f4619d861cb2ac7cf3d18 authored about 3 years ago by Daniel Bryce <[email protected]>

get existing container from inventory by query on type

github.com/Bioprotocols/labop - 913fb9b669c4f832611cfae52dc34b2f5d8c5894 authored about 3 years ago by Daniel Bryce <[email protected]>

checkpoint on conversion, needing uri resolution against Strateos

github.com/Bioprotocols/labop - 564e5723396c302ad5227e3a956528bde37680af authored about 3 years ago by Daniel Bryce <[email protected]>

initial prototyping of execution to autoprotocol

github.com/Bioprotocols/labop - 4d1aaf2b4f9ae6a09d2b0688e1e29ec451d44bbe authored about 3 years ago by Jack Ladwig <[email protected]>

add ipython dep

github.com/Bioprotocols/labop - 07503c6132a11241ac7eef3414bf6c6a6b1b377b authored about 3 years ago by Daniel Bryce <[email protected]>

reviving markdown with basic functionality

github.com/Bioprotocols/labop - 8d42ffcaeb2dc0f13e394f363f23a9a94252c63e authored about 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #61 from rpgoldman/revise-imports

github.com/Bioprotocols/labop - 0ef8dbc5e110890d09567f083fd162064f9b7189 authored about 3 years ago by rpgoldman <[email protected]>

Add a snapshot of the draft as a stopgap on automated production

github.com/Bioprotocols/labop-specification - 3108db2cb3adab4cd68635a45719c56425b75dbb authored about 3 years ago by Jake Beal <[email protected]>

Update README.md

github.com/Bioprotocols/labop - 278d86dbbc7cb268fdf288995f81478a0176b867 authored about 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #62 from SD2E/cleanup

WIP: Cleanup

github.com/Bioprotocols/labop - 9015e97c7cd87f7fbf18aa4c1deb9ac6eeb8fcdb authored about 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #64 from SD2E/demo

Demo

github.com/Bioprotocols/labop - 74483b62ce96e212055d931a980f0b5e6cb8d2e1 authored about 3 years ago by Daniel Bryce <[email protected]>

removed rdflib-jsonld

github.com/Bioprotocols/labop - 531112681bc50776ea54873270289bc9d3d27762 authored about 3 years ago by Daniel Bryce <[email protected]>

refactored spec building and added to readme

updated dep versions in setup.py

github.com/Bioprotocols/labop - 9593c56cfe52138e3ea90d68c8149771edea2a7d authored about 3 years ago by Daniel Bryce <[email protected]>

refined demo notebook and made legend optional for plotting.

github.com/Bioprotocols/labop - 3a3f0bd82af9ce743841eeadaf3f0a4f240f7f7e authored about 3 years ago by Daniel Bryce <[email protected]>

ignores

github.com/Bioprotocols/labop - fedd0b746af103215fc69e06194d0b2d913ab134 authored about 3 years ago by Daniel Bryce <[email protected]>

Move content from top level to subdirs. Remove output files from top level.

github.com/Bioprotocols/labop - 80db6a989c7d09476ca7d91b47b8198a605ff352 authored about 3 years ago by Daniel Bryce <[email protected]>

modify plotting for demo

github.com/Bioprotocols/labop - 0bb820a3d6b436b570e45e5655d4206f894e5f90 authored about 3 years ago by Daniel Bryce <[email protected]>

Remove definitions of owl properties.

`owl:minCardinality` and `owl:maxCardinality` are defined as `owl:AnnotationProperty`'s in uml.t...

github.com/Bioprotocols/labop - d48ed57aad15db9000a2e77bd1fd8545a97ee215 authored about 3 years ago by Robert P. Goldman <[email protected]>

Modify imports.

Replace use of prefix IRIs with ontology IRIs in `owl:imports`.

github.com/Bioprotocols/labop - 0cbe8240cc153a468297a7842e53c6bbb0a65593 authored about 3 years ago by Robert P. Goldman <[email protected]>

Merge pull request #57 from SD2E/model-comments

Add descriptions for SampleCollection, SampleData, and ContainerSpec.

github.com/Bioprotocols/labop - ca50d5c516ff6660e19e3a8cd59cbee4d0c2d03c authored about 3 years ago by Jacob Beal <[email protected]>

Add generated PAML data model and update generated UML data model.

Restore header explanation of UML imports
Improve SBOL import explanation, add PROV-O imports

github.com/Bioprotocols/labop-specification - 815669b5accf312c3f8ca2b7ff59763aa33c8757 authored about 3 years ago by Jake Beal <[email protected]>

Merge pull request #7 from SD2E/autogenerate_uml_docs

Reformat master LaTeX file to facilitate automatic documentation generation

github.com/Bioprotocols/labop-specification - 8de1dd5428fa7fe9e470674aa17e71ea121ba41c authored about 3 years ago by Jacob Beal <[email protected]>

Merge branch 'main' into autogenerate_uml_docs

github.com/Bioprotocols/labop-specification - 40d7801528856f287d61330b0df1fd7148a5409e authored about 3 years ago by Bryan Bartley <[email protected]>

Update generator script for latest version of sbol_factory

github.com/Bioprotocols/labop - 01db0d76f52f6fb2cc423578b6fa8860cefb817d authored about 3 years ago by Jake Beal <[email protected]>

Edit paml.tex to work with sbol_factory's automatic documentation

github.com/Bioprotocols/labop-specification - 5f5bda637d61562098e41e4aecbf824c905e0a14 authored about 3 years ago by Bryan Bartley <[email protected]>

Nearly complete draft of PAML specification

github.com/Bioprotocols/labop-specification - 603aecf16c1823671a1238882e019cf154a82955 authored over 3 years ago by Jake Beal <[email protected]>

Add script for generating specification content, assuming that PAML and PAML-specification are sibling directories on Mac or Unix.

github.com/Bioprotocols/labop - ff85b63217c8c51ff814cc55eba9ebd98e172ac1 authored over 3 years ago by Jake Beal <[email protected]>

Add descriptions for SampleCollection, SampleData, and ContainerSpec.

First pass on PAML descriptions is complete.

github.com/Bioprotocols/labop - c7bfefcf2fd2737d63c042248a01b2d2bf42ffdb authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #56 from SD2E/model-descriptions

Model descriptions

github.com/Bioprotocols/labop - 7d811e40863fdc1299dea828aa8cc918bea7a1d0 authored over 3 years ago by bbartley <[email protected]>

Add descriptions for ActivityNodeExecution and CallBehaviorExecution

github.com/Bioprotocols/labop - 3614c31ee3010fcbba36f296ac63b62b2f5d8147 authored over 3 years ago by Jake Beal <[email protected]>

Merge commit '5381793c094143443d7e7005ca4b2f0b2d6fe373' into model-descriptions

github.com/Bioprotocols/labop - 38657cdecfc9238e1283e0e70daeedab3b2f0d6c authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #55 from SD2E/uml_documentation

Add documentation to UML ontology using rdfs:comment

github.com/Bioprotocols/labop - 5381793c094143443d7e7005ca4b2f0b2d6fe373 authored over 3 years ago by bbartley <[email protected]>

Add documentation to UML ontology using rdfs:comment

github.com/Bioprotocols/labop - dadd1d166fc5a09adfd5b92abfce5e5c239052f1 authored over 3 years ago by Bryan Bartley <[email protected]>

Improve description of BehaviorExecution, add descriptions for Material, ProtocolExecution, and ActivityEdgeFlow

github.com/Bioprotocols/labop - f6edc0c4cd0c3eb2c25a6ea51c04f358d8466c02 authored over 3 years ago by Jake Beal <[email protected]>

Fix use of wrong OM property.

Had mistakenly used `hasDimension` where I should have used `hasUnit`.

github.com/Bioprotocols/container-ontology - 0bc4d2518affbbff5637c57d77933af3e8614cb0 authored over 3 years ago by Robert P. Goldman <[email protected]>

Full specification comments for PAML classes Protocol, Primitive, BehaviorExecution, and ParameterValue

github.com/Bioprotocols/labop - 608bf2b46797b2aca1bf6074d162aea88671ae87 authored over 3 years ago by Jake Beal <[email protected]>

add uml refs to macros, add paml insert

github.com/Bioprotocols/labop-specification - 084824b08d08a1c627390f7edb6b2a0b343c2994 authored over 3 years ago by Jake Beal <[email protected]>

Update catalog of OWL files.

github.com/Bioprotocols/container-ontology - 0f0affe5fb967b164596217a111caa2f299d8234 authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge pull request #49 from SD2E/notebooks

Notebooks

github.com/Bioprotocols/labop - 8f9018927d114231eb8013fd848848af9ee2eb5d authored over 3 years ago by Daniel Bryce <[email protected]>

Merge branch 'main' into notebooks

github.com/Bioprotocols/labop - 0c22cd3d8e55781aee4b01aac72b4ec60ef1d8cf authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #52 from rpgoldman/container-spec

github.com/Bioprotocols/labop - 2ed01e655d27f2da88d0ca56a4da9b0d4a007b63 authored over 3 years ago by rpgoldman <[email protected]>

Replace xsd:float with xsd:decimal.

xsd:float is disjoint with all other numeric types, unlike xsd:decimal, so we are using that as ...

github.com/Bioprotocols/container-ontology - 264095450722a78a87e1dc7d269f96449d6b3ba6 authored over 3 years ago by Robert P. Goldman <[email protected]>

Update LUDOX test rubric.

github.com/Bioprotocols/labop - e78cc5130d1fa81ba53dc7a11ca6167af8ae22d5 authored over 3 years ago by Robert P. Goldman <[email protected]>

Use paml:ContainerSpec instead of string.

Add a ContainerSpec Identified object that pairs a string with a prefix map, suitable for use wi...

github.com/Bioprotocols/labop - 2281134458c88ad6d1a77112a572080f1498e98d authored over 3 years ago by Robert P. Goldman <[email protected]>

Add definition of PAML ContainerSpec class.

github.com/Bioprotocols/labop - bf2faa9a89445b810fc004a0fe3e7edad8b5257a authored over 3 years ago by Robert P. Goldman <[email protected]>

Test ability to run owlery server.

github.com/Bioprotocols/container-ontology - c0bfa46b3ec1af6790625487aaf45c4afd8956f4 authored over 3 years ago by Robert P. Goldman <[email protected]>

Add more shape and color properties to Strateos catalog.

github.com/Bioprotocols/container-ontology - 109c55775cc62c9215ce8679dd13039bdb2a7b53 authored over 3 years ago by Robert P. Goldman <[email protected]>

Updates to container ontology.

1. Connect the cont:Plate class with the NCIT class for Microwell Plate
2. Add cont:NotFlatWellB...

github.com/Bioprotocols/container-ontology - dd1633295b6d461e44a8d68437fa40599f083bf7 authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge pull request #51 from rpgoldman/add-container-spec

github.com/Bioprotocols/labop - 2104a1d5a4aa1bab1c9f8197d513ed5cf3554fa7 authored over 3 years ago by rpgoldman <[email protected]>

Fix test whitespace.

github.com/Bioprotocols/labop - 5ee8f8162d4697cd5133b805389f1ddf63a0e135 authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge branch 'main' into add-container-spec

github.com/Bioprotocols/labop - 6aa396dc39e581329832a42e338efb22cdbc27b7 authored over 3 years ago by rpgoldman <[email protected]>

Update cached test output.

github.com/Bioprotocols/labop - 59ae5974ea8748e7e31bdbd8a4415db2722a9894 authored over 3 years ago by Robert P. Goldman <[email protected]>

Fix HTML bug in protocol to dot translation.

We use HTML for some node labels, so we must ensure that the label contents are HTML-escaped.

github.com/Bioprotocols/labop - 086cd258370fbd8325c1b4786325ca388a7088a1 authored over 3 years ago by Robert P. Goldman <[email protected]>

LUDOX protocol with new specification.

github.com/Bioprotocols/labop - 494e7270209b0d5194c0d445fb3ed7022c485098 authored over 3 years ago by Robert P. Goldman <[email protected]>

Change type of EmptyContainer specification

Changed from `paml:Identified` to `xsd:string`. This permits us to store an OWL DL query string...

github.com/Bioprotocols/labop - 003e30a9e0bffec56c53984e3659f8bbb3d03c20 authored over 3 years ago by Robert P. Goldman <[email protected]>

Pull LUDOX protocol out of tests. (#50)

This makes it possible to build the LUDOX protocol in any environment. It *does* preserve the re...

github.com/Bioprotocols/labop - 98dbba4b59b7892ac2988bbcbfc9211128f4197a authored over 3 years ago by rpgoldman <[email protected]>

add ipython dep

github.com/Bioprotocols/labop - aa2aa911b184a7b3b2ca229e3dcb9a87f38d6734 authored over 3 years ago by Daniel Bryce <[email protected]>

reviving markdown with basic functionality

github.com/Bioprotocols/labop - 722712cd253514a93809e5e54df6a85b527c049c authored over 3 years ago by Daniel Bryce <[email protected]>

Replace temporary IRI prefix.

Previously I was using https://raw.githubusercontent.com/rpgoldman/container-ontology/main/owl/ ...

github.com/Bioprotocols/container-ontology - 944e29aec95bd6a8fee32ec2df9776b9a1b3c406 authored over 3 years ago by Robert P. Goldman <[email protected]>

reverted date formatting

github.com/Bioprotocols/labop - d8a19e5550ec9a4277dc90c5ef7e21f1e682d80c authored over 3 years ago by Daniel Bryce <[email protected]>

cleanup of execution trace plotting and addressed review comments.

github.com/Bioprotocols/labop - b1482f8b5830414e72657536b861c682bc31e14c authored over 3 years ago by Daniel Bryce <[email protected]>

Pull LUDOX protocol out of tests.

Take the building of the LUDOX protocol object and file out of the body of the test, and move it...

github.com/Bioprotocols/labop - e492dd0b2873c2ac6557626eae7d119d834dd4df authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge branch 'main' into notebooks

github.com/Bioprotocols/labop - 422f2ecaa3d5462958261171417b4ee1f36ee0ad authored over 3 years ago by Daniel Bryce <[email protected]>

minor bug fixes

github.com/Bioprotocols/labop - dbf1ea30fe3e04fc17f479138781f66507a90310 authored over 3 years ago by Daniel Bryce <[email protected]>

Fix loading redirect.

github.com/Bioprotocols/container-ontology - 2d93bc72dcd07f9693a2f2b4a09ac14a83565a57 authored over 3 years ago by Robert P. Goldman <[email protected]>

Update NEST PCR plate description.

github.com/Bioprotocols/container-ontology - 2904bf38550f3eae083e8c99ebe5ffe8062ea304 authored over 3 years ago by Robert P. Goldman <[email protected]>

added basic UI support to notebooks for authoring protocols

github.com/Bioprotocols/labop - a86a205a6c4751b22d01a66528facaf9df62eb52 authored over 3 years ago by Daniel Bryce <[email protected]>

Export check_doc function. (#11)

Modified `__init__.py` and `check_doc.py` to export this function
name.

github.com/Bioprotocols/labop-check - b6f7e77bf6b340308270a7450240d1f22ac54b4a authored over 3 years ago by rpgoldman <[email protected]>