github.com/Bioprotocols/labop commits | Ecosyste.ms: OpenCollective

Merge branch 'main' into add-container-spec

6aa396dc39e581329832a42e338efb22cdbc27b7 authored over 3 years ago by rpgoldman <[email protected]>

Update cached test output.

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.

086cd258370fbd8325c1b4786325ca388a7088a1 authored over 3 years ago by Robert P. Goldman <[email protected]>

LUDOX protocol with new specification.

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...

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...

98dbba4b59b7892ac2988bbcbfc9211128f4197a authored over 3 years ago by rpgoldman <[email protected]>

add ipython dep

aa2aa911b184a7b3b2ca229e3dcb9a87f38d6734 authored over 3 years ago by Daniel Bryce <[email protected]>

reviving markdown with basic functionality

722712cd253514a93809e5e54df6a85b527c049c authored over 3 years ago by Daniel Bryce <[email protected]>

reverted date formatting

d8a19e5550ec9a4277dc90c5ef7e21f1e682d80c authored over 3 years ago by Daniel Bryce <[email protected]>

cleanup of execution trace plotting and addressed review comments.

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...

e492dd0b2873c2ac6557626eae7d119d834dd4df authored over 3 years ago by Robert P. Goldman <[email protected]>

Merge branch 'main' into notebooks

422f2ecaa3d5462958261171417b4ee1f36ee0ad authored over 3 years ago by Daniel Bryce <[email protected]>

minor bug fixes

dbf1ea30fe3e04fc17f479138781f66507a90310 authored over 3 years ago by Daniel Bryce <[email protected]>

added basic UI support to notebooks for authoring protocols

a86a205a6c4751b22d01a66528facaf9df62eb52 authored over 3 years ago by Daniel Bryce <[email protected]>

plotting for executions and notebook demo

f9cc6a697d299f235b7299f98d6ea7d477d4a3ef authored over 3 years ago by Daniel Bryce <[email protected]>

Use List, Set, etc. typing aliases for type hints

92b0a1359a14fd36235c5d27431f5ea93172cda6 authored over 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #45 from SD2E/compact-visualization

Create compact visualizations of protocols

49b87a6178699fd8872a95ae4369293b07184721 authored over 3 years ago by Jacob Beal <[email protected]>

added legend and fixes for ludox protocol

e7b5e6e07822cb105c5bd0f8ea5bc93d8cb46b1d authored over 3 years ago by Daniel Bryce <[email protected]>

Create compact visualizations of protocols

Also fix a bug in GG assembly revealed by visualization

92d4a061d4eef41bc050fc0a1a5e0df3d3908e59 authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #44 from SD2E/golden-gate

Example: Golden Gate protocol

011e7b75ff10a8fe25cc36c29116201ae3b45cdc authored over 3 years ago by Jacob Beal <[email protected]>

Merge pull request #41 from SD2E/30-validate_owl-1

OWL validation

283f5110135bc1c24c8a7254569881af723a4777 authored over 3 years ago by bbartley <[email protected]>

Syntactically correct version of Golden Gate protocol and validated output

Remove redundant (and incorrect) Protocol.initiating_nodes that was overriding Activity.initiatin...

6a4bfac01c2930061cbd93cba76b243b6b78131a authored over 3 years ago by Jake Beal <[email protected]>

Merge commit 'a790da333cf1aed9018602f983a65b2473d37a8b' into golden-gate

cda65ad1c35a48fdf580b0895603281627c2745a authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #42 from SD2E/execution-records-test

Execution records test

a790da333cf1aed9018602f983a65b2473d37a8b authored over 3 years ago by Daniel Bryce <[email protected]>

First draft of GoldenGate assembly protocol (not yet working)

Also adds a get_last_step() function for protocols, Autoprotocol "spin" primitive, and new "Trans...

1861d1591339899930ab2fc8ab6737f64e7320ac authored over 3 years ago by Jake Beal <[email protected]>

support for input and output parameters of protocol.

f942cb1095fa5cfbb514cab2c4436c8403be1675 authored over 3 years ago by Daniel Bryce <[email protected]>

Remove test_invalid for now until we find a better test case

a2130da6a180e0a673353a72be5171cc5b98797f authored over 3 years ago by Bryan Bartley <[email protected]>

Clean up some junk

7ea3b52caca97d8c76cfe9c446c76ad61e86c014 authored over 3 years ago by Bryan Bartley <[email protected]>

Add a test case with malformed OWL

06db2113fb6bdc0d9c830a709787216566563410 authored over 3 years ago by Bryan Bartley <[email protected]>

Merge branch 'main' into 30-validate_owl-1

2f257be2ae91082e006665212b6f3d2efea0a47b authored over 3 years ago by Bryan Bartley <[email protected]>

Modify github action yaml to run OWL validation tests

e1b0615e8b960e11991b1a89964c3c7ed4dc2266 authored over 3 years ago by Bryan Bartley <[email protected]>

completed support for optional pins

f9d9db907822090f2104057004004e1f2e199884 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #40 from SD2E/execution-records-test

Execution records test

936e13b32d27edb08df35833463a57f479492be5 authored over 3 years ago by Jacob Beal <[email protected]>

turning off file stability check for now on execution

8959b8a5341468be0594f2588205cc624b003202 authored over 3 years ago by Jake Beal <[email protected]>

don't try to show a PDF in a headless environment

7233d6f43bf576768978443b10f3dcf168fc439c authored over 3 years ago by Jake Beal <[email protected]>

add graphviz to workflow

4dd1f8d58fff342089d7d8069d94e5deb82e0151 authored over 3 years ago by Jake Beal <[email protected]>

use safe execution path

d629e0300121b9c1bf2774483ef94b600d8b4581 authored over 3 years ago by Jake Beal <[email protected]>

version pin is ==, not =

b5983e3d6eec1f92e191a7b03c341789ece0f809 authored over 3 years ago by Jake Beal <[email protected]>

pin sbol factory version

39ed7690fc02341d8bac18bb982f9d0199bd0b9a authored over 3 years ago by Jake Beal <[email protected]>

validation tests passing

e458994026961b20fc2ec61e8e0d7a5366252b90 authored over 3 years ago by Jake Beal <[email protected]>

Merge branch 'execution-records-test' of https://github.com/SD2E/paml into execution-records-test

3e2000f9da730b763a033bda06f323a0751324bc authored over 3 years ago by Jake Beal <[email protected]>

added protocol input for ludox test

5ecb153b49a2872817c2fdaadccf8a4e8ce4e968 authored over 3 years ago by Jake Beal <[email protected]>

missing test rubric file

73d3bf440ed8e264d5c554995a0eaaf5dda3997f authored over 3 years ago by Daniel Bryce <[email protected]>

broken state adding protocol outputs.

9b5a152422712e94f23e7b3844bb25c156fba8ed authored over 3 years ago by Daniel Bryce <[email protected]>

passing comparison after stashing expected output.

33be2afd019820c399bd4a358f3a15041c280981 authored over 3 years ago by Daniel Bryce <[email protected]>

Allow edge flows to have no edge. Used to capture link between input pins and activity that has an implicit edge.

fb9ae52150975fe4d6730c51ccec808fd382e5d6 authored over 3 years ago by Daniel Bryce <[email protected]>

stable execution checkpoint. Still getting validation errors due to tokens without values.

753e7f69fd47bd5519e49a991a048156672a35cb authored over 3 years ago by Daniel Bryce <[email protected]>

Create gradle.yml

20ad77445653344b88c2cc78429797765d04fce5 authored over 3 years ago by bbartley <[email protected]>

checkpoint on execution. Need to update paml for ordered parameters in the lib functions.

bd7f5e38b4be740bda302b95eb7f1f3df363dc03 authored over 3 years ago by Daniel Bryce <[email protected]>

partially drafted commit for execution engine class

034ec3897a71cfd9954b987d43dfa1a94436e2cd authored over 3 years ago by Jake Beal <[email protected]>

Add parameter value records and "completedNormally" field

Kludge in prov:Activity properties while cannot inherit directly due to sbol_factory issues 22 an...

51d24b7018455027936a04cbc3f0d43a10405ea6 authored over 3 years ago by Jake Beal <[email protected]>

Adjust validation to allow make incoming edges optional for ActivityParameterNode

b8c2599244c1e50d3d160223f301a18fa5f7a22a authored over 3 years ago by Jake Beal <[email protected]>

Allow literals to be constructed as references

Add helper functions for checking required inputs and outputs for behaviors, finding the root of ...

8118f96c10d1f23fad4b56c3f764406afe1acf44 authored over 3 years ago by Jake Beal <[email protected]>

Draft implementation of representation for recording protocol executions

aa5e593be191162c124f55dde17b6d4c82f6a909 authored over 3 years ago by Jake Beal <[email protected]>

Allow literals to be constructed as references

Add helper functions for checking required inputs and outputs for behaviors, finding the root of ...

39eae402be05b83f9a9f3ce9cabe6c438b19ef32 authored over 3 years ago by Jake Beal <[email protected]>

added test case for executions

26d00c59ee84ccc83954c0465a5c5ac2e3d7332c authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #24 from SD2E/time

Time

cd026c524d67f6a1ed6aa0edf760594f2ea7d42c authored over 3 years ago by Daniel Bryce <[email protected]>

removed abstract properties and changed string to uri.

60b2210eeb1387c8c8b716d8e83c2e3326e68918 authored over 3 years ago by Daniel Bryce <[email protected]>

fixed order of parameter handling and setup gantt chart

9330b8fade6cb790934b099c1ace1d7937941355 authored over 3 years ago by Daniel Bryce <[email protected]>

Update setup.py

3dd3bd16640e678ebc198bc077c9e432e4cc3daf authored over 3 years ago by Daniel Bryce <[email protected]>

Ordered parameters for time constraints.

19dfc6298cd15be30a879decc870e94d6f28980e authored over 3 years ago by Daniel Bryce <[email protected]>

checkpoint

732b56a8f747fcc515a1bd1110d0d00e6bc1a15a authored over 3 years ago by Daniel Bryce <[email protected]>

added pointer from time constraints to protocols

fe419f3bbd37dd5f96db0b51e19cf4436d001dcf authored over 3 years ago by Daniel Bryce <[email protected]>

checkpoint on ordered values

3e1900b2f169c789768701c13245596957723659 authored over 3 years ago by Daniel Bryce <[email protected]>

fixed time constraints to be at top level and have identities.

58581614b1b7ebce46556a7181bfd3b81c8fab47 authored over 3 years ago by Daniel Bryce <[email protected]>

rebased on main after ordered values addition

6960bbffce1f3736ab200051838cdb4ed7ec5d28 authored over 3 years ago by Daniel Bryce <[email protected]>

update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

9d12bf7a4156b3cedaa87f185dd80c835c5ebcc8 authored over 3 years ago by Daniel Bryce <[email protected]>

updated timepoints for control, primitive, and protocol

755ecad9eafe702fee3d4144a7df6f9dea8d5112 authored over 3 years ago by Daniel Bryce <[email protected]>

renamed logic constraints

45e8f50c4280dc0ecf8ec69779f909f83120a641 authored over 3 years ago by Daniel Bryce <[email protected]>

update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

97c4c34cf98ff62a3711d6168b26c79977ee334b authored over 3 years ago by Daniel Bryce <[email protected]>

make time optional to fix tests

9447306d0dfee802ad65b85ae880118e3832bdd4 authored over 3 years ago by Daniel Bryce <[email protected]>

added expressions to ttl

bb40b4a8e5007ce95e08f844bae3eb71906260ea authored over 3 years ago by Daniel Bryce <[email protected]>

update to remove timepoints from activities. Having bug with prov uri string that leads to unassigned property on time variables.

f5a49232063966c950f24adccb4dfed506b72070 authored over 3 years ago by Daniel Bryce <[email protected]>

updated time property to be a datatype property

41f502d131d5ec38961cb565c0b60e6359da7580 authored over 3 years ago by Daniel Bryce <[email protected]>

simplified api for temporal constraints.

0381103364e67a335164c40037bc560c2955c2dc authored over 3 years ago by Daniel Bryce <[email protected]>

refactored time extensions to build upon uml

a27656297b46f75c4a9f6d636a3e1f1b0ac27735 authored over 3 years ago by Daniel Bryce <[email protected]>

testing constraint checking

778cc1af141559ad5b8ea6c42683047d455816f1 authored over 3 years ago by Daniel Bryce <[email protected]>

setting timepoints and durations for ludox protocol

64d7bf805a2981abcff20fcb3264b14a1bb5b9e4 authored over 3 years ago by Daniel Bryce <[email protected]>

Don't use rdfs:subPropertyOf

3a4e875c8c0a7de1a256e1055dbe93e0adcdbe49 authored over 3 years ago by Bryan Bartley <[email protected]>

support for additional, general constraints

c6bb3a766105bee62e02e48e84ba4206d0cdcae4 authored over 3 years ago by Daniel Bryce <[email protected]>

Added Time to paml ontology

8c135f067d60a51e2e85028175e684e7cadbeda9 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #38 from SD2E/ordered-values

Ordered values

2eab6b4d2a49538ffb838349d28dfe9e2660c810 authored over 3 years ago by Jacob Beal <[email protected]>

Merge branch 'main' into ordered-values

a4f482ced552055e9468d1640ed31721d3e3d3e4 authored over 3 years ago by Daniel Bryce <[email protected]>

addressed Jake's comments

2c1578153e560f70d73fee1ee0b139a2436c3728 authored over 3 years ago by Daniel Bryce <[email protected]>

addressed Jake's comments

addressed Jake's comments

070ba4b64bf86d5456514376b976863ed9b106b2 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #39 from SD2E/37-update_package_config

Update for compatibility with SBOLFactory v1.0a6

e90b9d65d27b9bf40b852d8235dbbe79f3eb520a authored over 3 years ago by bbartley <[email protected]>

Update for compatibility with SBOLFactory v1.0a6

4fd14c084999bd2ee08251f5bbee7aad40f78c90 authored over 3 years ago by Bryan Bartley <[email protected]>

missed a rubric

629bb2275fac183f4494557d57bf1a9e4844a4d6 authored over 3 years ago by Daniel Bryce <[email protected]>

updated test rubric and downgraded rdflib

0859fcb513fe78eae0e619f91e966e69079686fa authored over 3 years ago by Daniel Bryce <[email protected]>

use ordered values in behavior parameters

b8ccda2551d5a1bb55a52b27fea5be58bbe6aa52 authored over 3 years ago by Daniel Bryce <[email protected]>

use ordered values in behavior parameters

e7ecf9d580f7fb613f8b98f4650dd4d16e3cf207 authored over 3 years ago by Daniel Bryce <[email protected]>

tests for parameter ordering

43c1726cc6579cda17545dddb8ae3c0ef6319e35 authored over 3 years ago by Daniel Bryce <[email protected]>

added ordered parameter

971cc07939caeb2a2a022eea285c021eb2f02ce3 authored over 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #36 from SD2E/fix/issue-35

Fix issue 35.

d0796dedb58ecedd0151ef82af27007dee807f47 authored over 3 years ago by Jacob Beal <[email protected]>

Fix issue 35. Depending on the order of nodes added to a UML Activity was fragile (and broken); track steps explicitly in a scratch property instead.

dc22bd7343d006ce6b71e28d55314dbbe5c0e5a0 authored over 3 years ago by Jake Beal <[email protected]>

Fix pervasive syntax errors in OWL Restrictions (#33)

These were in an abbreviated form that for some reason, none of our tools flagged clearly as err...

ba730d4cfa97954f75c83f583668b6529fd35d02 authored over 3 years ago by rpgoldman <[email protected]>

Merge pull request #31 from SD2E/update-primitive-types

Primitives hadn't been updated from old Location class to new SampleArray class.

1a2743465e295e4482a0b7a85fedda385ecbc320 authored over 3 years ago by Jacob Beal <[email protected]>

Primitives hadn't been updated from old Location class to new SampleArray array class.

This commit makes that changes and all of its related changes down the tree.

0fe0e737246cdddcbc25053b41bd8b3578d7a55f authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #29 from SD2E/fix-owl-errors

Fix broken OWL

f153a126d417a60696cf693c44a3b197d952dd83 authored over 3 years ago by rpgoldman <[email protected]>

Fix broken OWL: all values of owl:onClass should actually be owl:allValuesFrom

847f298823436d1a0c93f39b5a9077412a2ef4fa authored over 3 years ago by Jake Beal <[email protected]>