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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit GillesPy2 1.6.5 #458

Closed biosimulators-daemon closed 2 years ago

biosimulators-daemon commented 3 years ago

id: gillespy2 version: 1.6.5 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/099b976e19ee66771ca27d349bf63f6353bc54d3/biosimulators.json specificationsPatch: version: 1.6.5 image: url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.6.5 digest: "sha256:ff232e7725fb508f5ef37ab58ef94cc97926f5351125b33e0c9cafe32dd750cd" validateImage: true commitSimulator: true

biosimulators-daemon commented 3 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Failures

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (5.7 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Exception: ``` The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.6.5' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `ODE_stochastic` may be invalid. - The model file `model_ODE_stochastic.xml` may be invalid. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_' in the math element of the can only act on variables with the same units. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(-(C * Kr_AR_binding) + A * Kf_AR_binding * R) * cell' in the element of the with id 'AR_binding' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_) * cell' in the element of the with id 'A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_) * cell' in the element of the with id 'active_A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R) * cell' in the element of the with id 'R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R) * cell' in the element of the with id 'active_R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound) * cell' in the element of the with id 'PrmA_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound) * cell' in the element of the with id 'PrmR_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R) * cell' in the element of the with id 'R_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_) * cell' in the element of the with id 'A_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00332107756632545 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'C_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_A_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'AR_binding') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmA_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmR_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - Model `ODE_stochastic_0` may be invalid. - The model file `model_ODE_stochastic.xml` may be invalid. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_' in the math element of the can only act on variables with the same units. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(-(C * Kr_AR_binding) + A * Kf_AR_binding * R) * cell' in the element of the with id 'AR_binding' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_) * cell' in the element of the with id 'A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_) * cell' in the element of the with id 'active_A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R) * cell' in the element of the with id 'R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R) * cell' in the element of the with id 'active_R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound) * cell' in the element of the with id 'PrmA_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound) * cell' in the element of the with id 'PrmR_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R) * cell' in the element of the with id 'R_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_) * cell' in the element of the with id 'A_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00332107756632545 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'C_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_A_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'AR_binding') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmA_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmR_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - The changes of the model may be invalid. - Change 1 may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_mRNA_R` may be invalid. - Variable `var_tsk_1_1_mRNA_R` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_A` may be invalid. - Variable `var_tsk_1_1_A` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_R` may be invalid. - Variable `var_tsk_1_1_R` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_PrmA` may be invalid. - Variable `var_tsk_1_1_PrmA` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_PrmR` may be invalid. - Variable `var_tsk_1_1_PrmR` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_C` may be invalid. - Variable `var_tsk_1_1_C` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_PrmA_bound` may be invalid. - Variable `var_tsk_1_1_PrmA_bound` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_PrmR_bound` may be invalid. - Variable `var_tsk_1_1_PrmR_bound` may be invalid. - XPath could not be validated. - Data generator `dataGen_tsk_1_1_mRNA_A_` may be invalid. - Variable `var_tsk_1_1_mRNA_A_` may be invalid. - XPath could not be validated. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Model `ODE_stochastic` may be invalid. - The model file `model_ODE_stochastic.xml` may be invalid. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_' in the math element of the can only act on variables with the same units. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(-(C * Kr_AR_binding) + A * Kf_AR_binding * R) * cell' in the element of the with id 'AR_binding' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_) * cell' in the element of the with id 'A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_) * cell' in the element of the with id 'active_A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R) * cell' in the element of the with id 'R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R) * cell' in the element of the with id 'active_R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound) * cell' in the element of the with id 'PrmA_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound) * cell' in the element of the with id 'PrmR_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R) * cell' in the element of the with id 'R_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_) * cell' in the element of the with id 'A_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00332107756632545 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'C_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_decay') are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_A_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'mRNA_R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'AR_binding') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_decay') are second (exponent = -1, multiplier = 1, scale = 0), item (exponent = 1, multiplier = 1, scale = 0), metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_A_trnscr') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'active_R_trnsc') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmA_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'PrmR_activation') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'R_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - The units of the 'math' formula in a definition are expected to be the equivalent of _substance per time_. Reference: L3V1 Sections 4.11.7, 4.2.4 AND 4.9.4 In level 3 the expected units are extent_per_time. Expected units are item (exponent = 1, multiplier = 1, scale = 0), second (exponent = -1, multiplier = 1, scale = 0) but the units returned by the expression in the (from the with id 'A_trnsl') are metre (exponent = 3, multiplier = 1, scale = -6). - Model `ODE_stochastic_0` may be invalid. - The model file `model_ODE_stochastic.xml` may be invalid. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula '-(C * Kr_AR_binding) + A * Kf_AR_binding * R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R' in the math element of the can only act on variables with the same units. - The units of the expressions used as arguments to a function call are expected to match the units expected for the arguments of that function. Reference: L3V1 Section 3.4 The formula 'Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_' in the math element of the can only act on variables with the same units. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(-(C * Kr_AR_binding) + A * Kf_AR_binding * R) * cell' in the element of the with id 'AR_binding' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnscr * PrmA - Kr_A_trnscr * PrmA * mRNA_A_) * cell' in the element of the with id 'A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_A_trnscr * PrmA_bound - Kr_active_A_trnscr * PrmA_bound * mRNA_A_) * cell' in the element of the with id 'active_A_trnscr' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsc * PrmR - Kr_R_trnsc * PrmR * mRNA_R) * cell' in the element of the with id 'R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_active_R_trnsc * PrmR_bound - Kr_active_R_trnsc * PrmR_bound * mRNA_R) * cell' in the element of the with id 'active_R_trnsc' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmA_activation * PrmA - Kr_PrmA_activation * PrmA_bound) * cell' in the element of the with id 'PrmA_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(A * Kf_PrmR_activation * PrmR - Kr_PrmR_activation * PrmR_bound) * cell' in the element of the with id 'PrmR_activation' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_R_trnsl * mRNA_R - Kr_R_trnsl * R * mRNA_R) * cell' in the element of the with id 'R_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - The unit of measurement associated with the mathematical formula in the MathML math element of every KineticLaw object in a model should be identical to all KineticLaw objects in the model. Reference: L3V1 Section 3.4 The formula '(Kf_A_trnsl * mRNA_A_ - A * Kr_A_trnsl * mRNA_A_) * cell' in the element of the with id 'A_trnsl' produces units that are inconsistent with units of earlier KineticLaw elements. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00332107756632545 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression '0.00166053878316273 / KMOLE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - ...
biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.8 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (5.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Warnings: ``` Unexpected reports were produced: BIOMD0000000002_sim.sedml/Figure_4b ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_16' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_16' does not have a 'units' attribute. - The changes of the model may be invalid. - Change 1 may be invalid. - XPath could not be validated. - Data generator `data_generator_BLL` may be invalid. - Variable `var_BLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_IL` may be invalid. - Variable `var_IL` may be invalid. - XPath could not be validated. - Data generator `data_generator_AL` may be invalid. - Variable `var_AL` may be invalid. - XPath could not be validated. - Data generator `data_generator_A` may be invalid. - Variable `var_A` may be invalid. - XPath could not be validated. - Data generator `data_generator_BL` may be invalid. - Variable `var_BL` may be invalid. - XPath could not be validated. - Data generator `data_generator_B` may be invalid. - Variable `var_B` may be invalid. - XPath could not be validated. - Data generator `data_generator_DLL` may be invalid. - Variable `var_DLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_D` may be invalid. - Variable `var_D` may be invalid. - XPath could not be validated. - Data generator `data_generator_ILL` may be invalid. - Variable `var_ILL` may be invalid. - XPath could not be validated. - Data generator `data_generator_DL` may be invalid. - Variable `var_DL` may be invalid. - XPath could not be validated. - Data generator `data_generator_I` may be invalid. - Variable `var_I` may be invalid. - XPath could not be validated. - Data generator `data_generator_ALL` may be invalid. - Variable `var_ALL` may be invalid. - XPath could not be validated. - Data generator `data_generator_L` may be invalid. - Variable `var_L` may be invalid. - XPath could not be validated. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `./BIOMD0000000002_sim.sedml` may be invalid. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_16' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_16' does not have a 'units' attribute. - The changes of the model may be invalid. - Change 1 may be invalid. - XPath could not be validated. - Data generator `data_generator_BLL` may be invalid. - Variable `var_BLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_IL` may be invalid. - Variable `var_IL` may be invalid. - XPath could not be validated. - Data generator `data_generator_AL` may be invalid. - Variable `var_AL` may be invalid. - XPath could not be validated. - Data generator `data_generator_A` may be invalid. - Variable `var_A` may be invalid. - XPath could not be validated. - Data generator `data_generator_BL` may be invalid. - Variable `var_BL` may be invalid. - XPath could not be validated. - Data generator `data_generator_B` may be invalid. - Variable `var_B` may be invalid. - XPath could not be validated. - Data generator `data_generator_DLL` may be invalid. - Variable `var_DLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_D` may be invalid. - Variable `var_D` may be invalid. - XPath could not be validated. - Data generator `data_generator_ILL` may be invalid. - Variable `var_ILL` may be invalid. - XPath could not be validated. - Data generator `data_generator_DL` may be invalid. - Variable `var_DL` may be invalid. - XPath could not be validated. - Data generator `data_generator_I` may be invalid. - Variable `var_I` may be invalid. - XPath could not be validated. - Data generator `data_generator_ALL` may be invalid. - Variable `var_ALL` may be invalid. - XPath could not be validated. - Data generator `data_generator_L` may be invalid. - Variable `var_L` may be invalid. - XPath could not be validated. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000002` may be invalid. - The changes of the model may be invalid. - Change 1 may be invalid. - XPath could not be validated. - Data generator `data_generator_BLL` may be invalid. - Variable `var_BLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_IL` may be invalid. - Variable `var_IL` may be invalid. - XPath could not be validated. - Data generator `data_generator_AL` may be invalid. - Variable `var_AL` may be invalid. - XPath could not be validated. - Data generator `data_generator_A` may be invalid. - Variable `var_A` may be invalid. - XPath could not be validated. - Data generator `data_generator_BL` may be invalid. - Variable `var_BL` may be invalid. - XPath could not be validated. - Data generator `data_generator_B` may be invalid. - Variable `var_B` may be invalid. - XPath could not be validated. - Data generator `data_generator_DLL` may be invalid. - Variable `var_DLL` may be invalid. - XPath could not be validated. - Data generator `data_generator_D` may be invalid. - Variable `var_D` may be invalid. - XPath could not be validated. - Data generator `data_generator_ILL` may be invalid. - Variable `var_ILL` may be invalid. - XPath could not be validated. - Data generator `data_generator_DL` may be invalid. - Variable `var_DL` may be invalid. - XPath could not be validated. - Data generator `data_generator_I` may be invalid. - Variable `var_I` may be invalid. - XPath could not be validated. - Data generator `data_generator_ALL` may be invalid. - Variable `var_ALL` may be invalid. - XPath could not be validated. - Data generator `data_generator_L` may be invalid. - Variable `var_L` may be invalid. - XPath could not be validated. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots: BIOMD0000000002_sim.sedml: Tasks (1): BIOMD0000000002_task Reports (1): report: 14 data sets Plots (1): Figure_4b: 5 curves Executing SED-ML file 1: BIOMD0000000002_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (1): Succeeded: 1 Skipped: 0 Failed: 0 Outputs (2): Succeeded: 2 Skipped: 0 Failed: 0 ```
biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (4.8 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. "Cannot POST /logs/validate" ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_16' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_16' does not have a 'units' attribute.  warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `./BIOMD0000000002_sim.sedml` may be invalid. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_16' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_16' does not have a 'units' attribute.  warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000002_sim.sedml: Tasks (1): BIOMD0000000002_task Reports (1): report: 10 data sets Executing SED-ML file 1: BIOMD0000000002_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (1): Succeeded: 1 Skipped: 0 Failed: 0 Outputs (1): Succeeded: 1 Skipped: 0 Failed: 0 ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (4.9 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. "Cannot POST /logs/validate" ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_0 * B * L - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_1 * BL * L - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_3 * A * L - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_4 * AL * L - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_7 * I * L - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_8 * IL * L - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_12 * D * L - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_13 * DL * L - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_0' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_1' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_2' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_3' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_4' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_5' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_6' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_7' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_8' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_9' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_10' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_11' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_12' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_13' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_14' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_15' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kf_16' does not have a 'units' attribute. - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'kr_16' does not have a 'units' attribute.  warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `./BIOMD0000000002_sim.sedml` may be invalid. - Model `BIOMD0000000002` may be invalid. - The model file `BIOMD0000000002_url.xml` may be invalid. - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression ...
biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1409067374). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1409067374).
jonrkarr commented 2 years ago

Closing because v1.6.5 appears to have a regression on importing SBML as revealed by the Vilar example.

Reported as StochSS/GillesPy2#646.