From bf63a423fc91774772a1a647ff37f32b9d9d4c7e Mon Sep 17 00:00:00 2001 From: Jonathan Karr Date: Sat, 21 Aug 2021 02:01:38 -0400 Subject: [PATCH] fixed: corrected documentation of supported observables --- Dockerfile | 2 +- biosimulators.json | 57 ++++++++++++++---- biosimulators_tellurium/_version.py | 2 +- .../BIOMD0000000297-with-reports.omex | Bin 20048 -> 20230 bytes tests/test_core_main.py | 11 ++++ 5 files changed, 59 insertions(+), 13 deletions(-) diff --git a/Dockerfile b/Dockerfile index d879803..fa406d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ # Base OS FROM python:3.9-slim-buster -ARG VERSION="0.1.13" +ARG VERSION="0.1.14" ARG SIMULATOR_VERSION="2.2.0" # metadata diff --git a/biosimulators.json b/biosimulators.json index 50baf3f..36752c7 100644 --- a/biosimulators.json +++ b/biosimulators.json @@ -347,14 +347,21 @@ "namespace": "SIO", "id": "SIO_000418" }], - "dependentVariableTargetPatterns": [ - { + "dependentVariableTargetPatterns": [{ "variables": "species concentrations", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species" }, { "variables": "parameter values", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value" + }, + { + "variables": "reaction fluxes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction" + }, + { + "variables": "compartment sizes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment" } ], "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"], @@ -408,14 +415,21 @@ "namespace": "SIO", "id": "SIO_000418" }], - "dependentVariableTargetPatterns": [ - { + "dependentVariableTargetPatterns": [{ "variables": "species concentrations", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species" }, { "variables": "parameter values", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value" + }, + { + "variables": "reaction fluxes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction" + }, + { + "variables": "compartment sizes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment" } ], "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"], @@ -495,14 +509,21 @@ "namespace": "SIO", "id": "SIO_000418" }], - "dependentVariableTargetPatterns": [ - { + "dependentVariableTargetPatterns": [{ "variables": "species concentrations", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species" }, { "variables": "parameter values", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value" + }, + { + "variables": "reaction fluxes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction" + }, + { + "variables": "compartment sizes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment" } ], "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"], @@ -618,14 +639,21 @@ "namespace": "SIO", "id": "SIO_000418" }], - "dependentVariableTargetPatterns": [ - { + "dependentVariableTargetPatterns": [{ "variables": "species counts", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species" }, { "variables": "parameter values", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value" + }, + { + "variables": "reaction fluxes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction" + }, + { + "variables": "compartment sizes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment" } ], "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"], @@ -725,14 +753,21 @@ } ], "dependentDimensions": [], - "dependentVariableTargetPatterns": [ - { + "dependentVariableTargetPatterns": [{ "variables": "species concentrations", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species" }, { "variables": "parameter values", "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value" + }, + { + "variables": "reaction fluxes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction" + }, + { + "variables": "compartment sizes", + "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment" } ], "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"], @@ -787,4 +822,4 @@ "validated": false, "validationTests": null } -} +} \ No newline at end of file diff --git a/biosimulators_tellurium/_version.py b/biosimulators_tellurium/_version.py index 377e1f6..112abf1 100644 --- a/biosimulators_tellurium/_version.py +++ b/biosimulators_tellurium/_version.py @@ -1 +1 @@ -__version__ = '0.1.13' +__version__ = '0.1.14' diff --git a/tests/fixtures/BIOMD0000000297-with-reports.omex b/tests/fixtures/BIOMD0000000297-with-reports.omex index a400702eb0fd9bb927abfdcdbaeeaf3816273e99..368472311ce413819e21818089190b03b2e82b5a 100644 GIT binary patch delta 1159 zcmV;21bF+7p`U~cnkHk*?Q|_fk}!>EvL0KXKfSXD)~o9WqldPQrkr3&A{6{a)A`+- z{Eiq6mXq1XYUHzy`@G|J zkZnT{K_WN=6H3I``Yz>W=s2L+G3%s!T{Im=eiG(7g@b1yCBWP*lZR(LK-y?1f|ylq z+wHakLg5#bZeHoux2|E}h*2Tut0j#yh9$@%S3%Dbx=MNciN<7_W`A4|M5D1KXbiDw zLM6p4KQ^|2Vw%ZKCYKU(`ImN+L|SqCpe0!x5I$esr8JR3i#i+x#B7~%;1;7FRN(aX z?b!NoyL>YrcJq&WWjV#noSmtuM4a7BOn$R8BCJd;&O0g{)dH$GS!Z|+)694>1okl- zmYRZUApwCxIAL--pMSmW>W_Ezq66S9r;2YPnb4oG_)$id&{l!-27pxY7i2{^EJRYx zM^rhOV+y?qWt>fsI1-9Hgv{P%A^3yQBOplT87@se(EOqK;xLzgPRjtbgonPpxbB>T2N3;1u;W z`)Ji>8`5jkoFs$^sR@}|musql=^(nvjqf(meVyEVI~m=^^}(s`1I{@jz9w>Psokp9 zoo=aBp_|1T-;j_JQJkkcUtfdsBfLq)%gK%Y{dOtpD!-PHPg&yk|6-nN(&|cnOl{mi; zd+N|~8SY6H+Af0M+f#$HOR!skb_;Mn_@9dZ5dU29*Cg?Oi0xVTENb8hgzqqi!brjk z$eXfX!<<`Q7;~9f%Y^+6Kl9$u4F4armGOOHt|rqa`G19b7V*U?SB?e2p?XTvA}_i% z&WlT5I#f<=UNgcph6N>KlE`xa*T^ME_5glevcY62l8lP*jaldnuI0nn4(OkDxvlRHg00+mIRc1=10HAj=O ZO*#S3lkH7A0&hx_Do!8<2uuI~007LpF>3$- delta 169 zcmZph$9Q25qjZ2bGm8i_0|N&`z$~vIk*S|9ssni&co`TZC+o9_Z~m(2!@Svq<$*gN zs{CXnA4{=@)Tmr;hU<(C7MeL=8qA+u=%d3F$2{49MRM{EA1x+c#mV;-r6>RQ@ngzX zne6ZD%qTT^vTrP-?&OcYmQ43uChPcFG1a?G&hWEhl$^ZS&zfnc=i~=|3T#2%3_t(? DmB2FG diff --git a/tests/test_core_main.py b/tests/test_core_main.py index 12b18ab..f943d70 100644 --- a/tests/test_core_main.py +++ b/tests/test_core_main.py @@ -124,11 +124,22 @@ def _assert_combine_archive_outputs(self, dirname, reports=True, plots=True): ], ) + if reports and not plots: + report.data_sets.append(DataSet(id='data_set_kswe', label='kwse')) + report.data_sets.append(DataSet(id='data_set_kswe_prime', label="kwse'")) + report.data_sets.append(DataSet(id='data_set_R1', label="Clb-Sic dissociation")) + report.data_sets.append(DataSet(id='data_set_compartment', label="compartment")) + report_results = ReportReader().run(report, dirname, 'ex1/BIOMD0000000297.sedml/report_1_task1') for data_set_result in report_results.values(): self.assertFalse(numpy.any(numpy.isnan(data_set_result))) numpy.testing.assert_allclose(report_results[report.data_sets[0].id], numpy.linspace(0., 140., 140 + 1)) + if reports and not plots: + print(report_results.keys()) + numpy.testing.assert_allclose(report_results['data_set_kswe_prime'], numpy.full((140 + 1,), 2.)) + numpy.testing.assert_allclose(report_results['data_set_compartment'], numpy.full((140 + 1,), 1.)) + # check that expected plots where created at the expected locations if plots: if not reports: