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Recent Releases of isatools

isatools - Release 0.14.2

Enhancements and Cleanup:

ISA MODEL

  • The model.py file has been split into the model module. Each class has been split into a dedicated file.
  • Added a method from_dict() to the ISA Investigation class to let users load objects from a dictionary.
  • Added a method to_dict() to each ISA model class that let users dump ISA objects to dictionaries. (also see ISA JSONLD section)
  • Added a new GraphQL interface to ISA investigation (see below querying isa for more information)

ISA TAB

  • The isatab.py file has been split into the isatab module. Functions and classes have been split into three submodules: load (to read isatab files), dump (to write isafiles) and validate (to run validation rules against an isatab file). Usage remains the same.
  • The isatab validation pipeline have been reworked to allow the rules set to be extended with user custom rules. Please contact us if you would like to implement your own validation rules.

ISA JSON

  • the isajson.py file has been split into the isajson module. Functions and classes have been split into three files: load.py, dump.py and validate.py. Usage remains the same but there is now an alternative using dicts instead of files (see below)
  • load.py and dump.py are now wrappers. The code of the isa json serializer/deserializer has been moved to be part of the ISA model. Users can still use the old load() and dump() methods but are now able to do it directly from an investigation object. Example ```py from json import load from isatools.model import Investigation

isajsonfile = 'path/to/isa.json' # the json file path with open(isajsonfile, 'r') as f: isajsoninput = load(f) # load the dict from the file investigation = Investigation() # create en investigation investigation.fromdict(isajsoninput) # feed in the dictionary, will generated missing identifiers make inputs and outputs different isajsonoutput = investigation.todict() # Dump it back to a dict anotherinvestigation = Investigation() # create en investigation anotherinvestigation.fromdict(isajsonoutput) # feed in the dictionary assert investigation == anotherinvestigation # assert equality between the created investigations. assert investigation.todict() == anotherinvestigation.to-dict() # compare to_dict() methods ```

Note: identifiers may be missing from the json file and autogenerated by the ISA objects. In this case, output dictionnaries won't match which is why the investigation is being compared to another investigation.

ISA JSON-LD

  • Using the new to_dict() function from model.py, it is possible to produce JSON-LD. The The method takes an optional boolean parameter ld (default to False) that serializes to json-ld dictionaries by injecting @context, @id and @type attributes. See isa json below for more information.
  • Customisation of the JSON-LD serialization is achieved through the set_context() function of the model module.
  • Added support for SIO, WD, OBO and SDO annotations (see https://github.com/ISA-tools/isa-api/tree/master/isatools/resources/json-context).
  • Added support for generating URL identifiers (necessary for hosting triple stores).
  • Check https://github.com/ISA-tools/isa-api/blob/master/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb for examples.

SPARQL querying over ISA:

  • The outputs of the ISA JSON LD serializer have been tested as a valid RDF representation. Using MTBLS instances with rdflib and settting the contexts with set_context(vocab='wd', all_in_one=False, local=False, include_contexts=False) we were able to produce RDF triples and store them into a virtuosoDB and a berkeleyDB with SPARQL support.
  • Check https://github.com/ISA-tools/isa-api/blob/master/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb for examples.

GRAPHQL querying over ISA:

  • Each ISA Investigation now has a graphQL interface bound to it. A full documentation of the graphQL interface is available at https://github.com/ISA-tools/isa-api/tree/master/isatools/graphQL/README.md

MTBLS, the EMBL-EBI MetaboLights Client:

  • Refactored the MTBLS client but kept the same functions (and signature) exposed. You can now use MTBLInvestigation instead of the old functions. Example:

```py from isatools.net.mtbls import MTBLSInvestigation

investigation = MTBLSInvestigation('MTBLS1')

This creates a temp dir for the investigation that gets deleted when the object is destroyed through the automatic garbage collector. You can pass a directory if you want to persist the investigation.

investigation = MTBLSInvestigation(mtblsid='MTBLS1', outputdirectory="path/to/output/dir", output_format='tab')

You can then run all the old function through methods with the same name and chain methods without downloading the whole investigation again.

print(investigation.getcharacteristicssummary()) print(investigation.getfactornames()) ```

ISA SQL:

  • Created a relational SQL Alchemy model for ISA objects tested with PSQL and SQLite. All model files are available here: https://github.com/ISA-tools/isa-api/tree/master/isatools/database/models image

Other

Versions update:

  • Dropped python 3.6 and 3.7
  • Added compatibility for python 3.10 (production ready)
  • Added compatibility for python 3.11 (test only)
  • Bump numpy, pandas and mzml.

Cookbook

  • Added a cookbook for querying isa with sparql and grapql. See https://github.com/ISA-tools/isa-api/blob/master/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb

Testing:

  • The application has been further tested with CI, especially the model. Global coverage increased from 75% to 84%.
  • Build time was reduced due to mocking some network operations.

ISA-API performance profiler:

  • Added a small command line interface using cProfile to generate performance reports of different ISA features (in particular serialization and deserialization to tab and json).

Known issues:

  • There is a know performance issue with the coveralls/coverage modules on python 3.11 making the build very slow (see https://github.com/nedbat/coveragepy/issues/1287). Performances for end users shouldn't be affected.

Contributors:

  • Batista Dominique, University of Oxford (https://orcid.org/0000-0002-2109-489X)
  • Philipoe Rocca Serra, University of Oxford (https://orcid.org/0000-0001-9853-5668)

- Jupyter Notebook
Published by terazus about 3 years ago

isatools - Release v0.13.0 - Release Candidate 2

Release v0.13.0 - Release Candidate v2

Enhancements and Cleanup: - significant optimisation of isatab.dump() via reworking the study/assay graph implementation. This can improve up to 3 or 4 orders of magnitude the writing to ISA-tab for datasets with thousands of samples (PR #403). An additional tweak has been implemented to compute only once the study/assay process graph (8c2d09da6599dc89e3f6cfe8719c125c50fa3690) - All the major objects of the ISA models are now Commentable (PR #395) - isatools.create.connectors now supports both strings and Ontology Annotations for Subject Type and Sample Type (PR #405) - CI is now migrated from Travis CI to GitHub CI (#404)

Breaking changes: - Changes to the isatools.create.connectors module to align it with the Datascriptor study JSON config. Now the Datascriptor study config has a "design" property holding all the study design information (PR #405)

Bug Fixes: - all names for protocols in studies generated by isatools.create.connectors from Datascriptor study configs are unique (issue #398) - identifiers for studies and investigations are coerced to strings (commit 7e9f468d633b54d356c136fdf1f0ea765d33279d)

- Jupyter Notebook
Published by Zigur over 4 years ago

isatools - Release v0.13.0 - Release Candidate

Release v0.13.0 - Release Candidate

Enhancements and Cleanup: - significant optimisation of isatab.dump() via reworking the study/assay graph implementation. This can improve up to 3 or 4 orders of magnitude the writing to ISA-tab for datasets with thousands of samples (PR #403) - All the major objects of the ISA models are now Commentable (PR #395) - isatools.create.connectors now supports both strings and Ontology Annotations for Subject Type and Sample Type (PR #405) - CI is now migrated from Travis CI to GitHub CI (#404)

Breaking changes: - Changes to the isatools.create.connectors module to align it with the Datascriptor study JSON config. Now the Datascriptor study config has a "design" property holding all the study design information (PR #405)

Bug Fixes: - all names for protocols in studies generated by isatools.create.connectors from Datascriptor study configs are unique (issue #398) - identifiers for studies and investigations are coerced to strings (commit 7e9f468d633b54d356c136fdf1f0ea765d33279d)

- Jupyter Notebook
Published by Zigur over 4 years ago

isatools - Release v0.12.2 - bugfix release

This Bugfix release fixes the broken networkx dependency in setup.py.

- Jupyter Notebook
Published by Zigur almost 5 years ago

isatools - Release v0.12.1 - bugfix release

Update to fix: - missing Factor Values from isatools.create serialisation (PR #391)

- Jupyter Notebook
Published by Zigur almost 5 years ago

isatools - Release v0.12.0 - Stable

Release v0.12.0

Features:

  • Added the isatools.create.connectors module. This module contains the generate_study_design_from_config function to generate an isatools.create.StudyDesign from a JSON configuration document containing metadata about the study design, including sampling and assay plan. These JSON documents can be generated by the Datascriptor application.(issues #355, #356, #377)
  • Added support for observational variables to isatools.create.model.StudyArm (with the parameter source_characteristics) (PR #367)
  • StudyDesign.generate_isa_study()now generates one Assay per assay type (via StudyDesign._generate_samples()). (issue #369, #373)
    • The names of the assay nodes (extract, labelled, extract, protocol node, and data file) (issue #370, #373)
    • isatools.create.model.ProductNode now has an attribute extension (e.g. a file extension fo a DataFile node) (issue #378)

Enhancements and Cleanup: - Introduced support for (built-in, non-configurable) synonyms in protocol types. Protocol types have also been made case insensitive. (issue #382) - Refactored constants and error messages for the create mode, introducing the modules isatools.create.constants and isatools.create.errors (issue #342, #368) - Removed asterisk imports (*) from all the core modules (issue #368) - Removed leftover print() statements (issue #374) - overall test coverage increased from 67% to 75%. The increase is due both to an increase in the number of tests and the removal of some deprecated, experimental or spurious modules.

Breaking changes: - isatools.create.models has been renamed to isatools.create.model (issue #368) - IsaModelAttributeError has been replaced with AttributeError. We will favour standard Exceptions whenever applicable.

Bug Fixes: - Fixed typo in NAMEPROPERTYASSIGNMENT_ERROR (issue #328) - Silent expansion of Characteristic categories from str to OntologyAnnotation now supported. You can assign a string to a characteristic category and it will be automatically wrapped into an ontology annotation. (issue #332) - Fixed duplicated in OntologyAnnotation ids (issue #381) - Fixed raising of an error when correctly setting a comment value (issue #360) - Assigned correct header "Data Transformation Name" for protocol type "sequence analysis data transformation" (commit b8f2f55b4e046f1841ffba7d6fb190c87918375f)

- Jupyter Notebook
Published by Zigur about 5 years ago

isatools - Release v0.12.0 - Release Candidate 3

Release v0.12.0 - Release Candidate

Features:

  • Added the isatools.create.connectors module. This module contains the generate_study_design_from_config function to generate an isatools.create.StudyDesign from a JSON configuration document containing metadata about the study design, including sampling and assay plan. These JSON documents can be generated by the Datascriptor application.(issues #355, #356, #377)
  • Added support for observational variables to isatools.create.model.StudyArm (with the parameter source_characteristics) (PR #367)
  • StudyDesign.generate_isa_study()now generates one Assay per assay type (via StudyDesign._generate_samples()). (issue #369, #373)
    • The names of the assay nodes (extract, labelled, extract, protocol node, and data file) (issue #370, #373)
    • isatools.create.model.ProductNode now has an attribute extension (e.g. a file extension fo a DataFile node) (issue #378)

Enhancements and Cleanup: - Introduced support for (built-in, non-configurable) synonyms in protocol types. Protocol types have also been made case insensitive. (issue #382) - Refactored constants and error messages for the create mode, introducing the modules isatools.create.constants and isatools.create.errors (issue #342, #368) - Removed asterisk imports (*) from all the core modules (issue #368) - Removed leftover print() statements (issue #374) - overall test coverage increased from 67% to 75%. The increase is due both to an increase in the number of tests and the removal of some deprecated, experimental or spurious modules.

Breaking changes: - isatools.create.models has been renamed to isatools.create.model (issue #368) - IsaModelAttributeError has been replaced with AttributeError. We will favour standard Exceptions whenever applicable.

Bug Fixes: - Fixed typo in NAMEPROPERTYASSIGNMENT_ERROR (issue #328) - Silent expansion of Characteristic categories from str to OntologyAnnotation now supported. You can assign a string to a characteristic category and it will be automatically wrapped into an ontology annotation. (issue #332) - Fixed duplicated in OntologyAnnotation ids (issue #381) - Fixed raising of an error when correctly setting a comment value (issue #360) - Assigned correct header "Data Transformation Name" for protocol type "sequence analysis data transformation" (commit b8f2f55b4e046f1841ffba7d6fb190c87918375f)

- Jupyter Notebook
Published by Zigur about 5 years ago

isatools - Release v0.12.0 - Release Candidate 2

Release v0.12.0 - Release Candidate

Features:

  • Added the isatools.create.connectors module. This module contains the generate_study_design_from_config function to generate an isatools.create.StudyDesign from a JSON configuration document containing metadata about the study design, including sampling and assay plan. These JSON documents can be generated by the Datascriptor application.(issues #355, #356, #377)
  • Added support for observational variables to isatools.create.model.StudyArm (with the parameter source_characteristics) (PR #367)
  • StudyDesign.generate_isa_study()now generates one Assay per assay type (via StudyDesign._generate_samples()). (issue #369, #373)
    • The names of the assay nodes (extract, labelled, extract, protocol node, and data file) (issue #370, #373)
    • isatools.create.model.ProductNode now has an attribute extension (e.g. a file extension fo a DataFile node) (issue #378)

Enhancements and Cleanup: - Introduced support for (built-in, non-configurable) synonyms in protocol types. Protocol types have also been made case insensitive. (issue #382) - Refactored constants and error messages for the create mode, introducing the modules isatools.create.constants and isatools.create.errors (issue #342, #368) - Removed asterisk imports (*) from all the core modules (issue #368) - Removed leftover print() statements (issue #374) - overall test coverage increased from 67% to 75%. The increase is due both to an increase in the number of tests and the removal of some deprecated, experimental or spurious modules.

Breaking changes: - isatools.create.models has been renamed to isatools.create.model (issue #368) - IsaModelAttributeError has been replaced with AttributeError. We will favour standard Exceptions whenever applicable.

Bug Fixes: - Fixed typo in NAMEPROPERTYASSIGNMENT_ERROR (issue #328) - Silent expansion of Characteristic categories from str to OntologyAnnotation now supported. You can assign a string to a characteristic category and it will be automatically wrapped into an ontology annotation. (issue #332) - Fixed duplicated in OntologyAnnotation ids (issue #381) - Fixed raising of an error when correctly setting a comment value (issue #360) - Assigned correct header "Data Transformation Name" for protocol type "sequence analysis data transformation"

- Jupyter Notebook
Published by Zigur about 5 years ago

isatools - Release v0.12.0 - Release Candidate

Release v0.12.0 - Release Candidate

Features:

  • Added the isatools.create.connectors module. This module contains the generate_study_design_from_config function to generate an isatools.create.StudyDesign from a JSON configuration document containing metadata about the study design, including sampling and assay plan. These JSON documents can be generated by the Datascriptor application.(issues #355, #356, #377)
  • Added support for observational variables to isatools.create.model.StudyArm (with the parameter source_characteristics) (PR #367)
  • StudyDesign.generate_isa_study()now generates one Assay per assay type (via StudyDesign._generate_samples()). (issue #369, #373)
    • The names of the assay nodes (extract, labelled, extract, protocol node, and data file) (issue #370, #373)
    • isatools.create.model.ProductNode now has an attribute extension (e.g. a file extension fo a DataFile node) (issue #378)

Enhancements and Cleanup: - Introduced support for (built-in, non-configurable) synonyms in protocol types. Protocol types have also been made case insensitive. (issue #382) - Refactored constants and error messages for the create mode, introducing the modules isatools.create.constants and isatools.create.errors (issue #342, #368) - Removed asterisk imports (*) from all the core modules (issue #368) - Removed leftover print() statements (issue #374) - overall test coverage increased from 67% to 76%. The increase is due both to an increase in the number of tests and the removal of some deprecated, experimental or spurious modules.

Breaking changes: - isatools.create.models has been renamed to isatools.create.model (issue #368) - IsaModelAttributeError has been replaced with AttributeError. We will favour standard Exceptions whenever applicable.

Bug Fixes: - Fixed typo in NAMEPROPERTYASSIGNMENT_ERROR (issue #328) - Silent expansion of Characteristic categories from str to OntologyAnnotation now supported. You can assign a string to a characteristic category and it will be automatically wrapped into an ontology annotation. (issue #332) - Fixed duplicated in OntologyAnnotation ids (issue #381) - Fixed raising of an error when correctly setting a comment value (issue #360)

- Jupyter Notebook
Published by Zigur about 5 years ago

isatools - Release v0.11.0 - Major upgrade of the Create mode

This release of isatools introduces a major overhaul of the pre-existing create mode for the generation of ISA documents from study design metadata. We have also introduced some (mostly) minor fixes to the core ISA API, enforcing a stricter validation on some objects.

Among the most noteworthy changes there are: * Support of complex longitudinal study designs with the introduction of Element, Treatment, StudyCell and StudyArm classes #318, #321 * Increased flexibility of the sample and assay plans, with the introduction of the AssayGraph and the overhaul of the SampleAssayPlan class, now renamed SampleAndAssayPlan #329, #333, #296 * Increased flexibility for Quality Control support through the QualityControlService utility class * Reworked serialization to JSON/deserialization from JSON of all the study design objects #313 * Check added when submitting quantitative Parameter Values: only numerical values are allowed #347

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by Zigur about 6 years ago

isatools - Release v0.10.3a - Create Mode for Metabolomics (update)

- Jupyter Notebook
Published by djcomlab over 7 years ago

isatools - Release v0.10.3 - Create Mode for Metabolomics (update)

Update to fix various bugs/issues.

- Jupyter Notebook
Published by djcomlab over 7 years ago

isatools - Release v0.10.2 - Create Mode for Metabolomics (update)

Updates to create model.

- Jupyter Notebook
Published by djcomlab over 7 years ago

isatools - Release v0.10.1 - Create Mode for Metabolomics (update)

- Jupyter Notebook
Published by djcomlab over 7 years ago

isatools - Release v0.10.0 - Create Mode for Metabolomics

Various updates to the Create Mode for Metabolomics templating, found in isatools.create.models, and updates to address various general issues.

- Jupyter Notebook
Published by djcomlab over 7 years ago

isatools - v0.9.5 PhenoMeNal Cerebellin

ISA API for the PhenoMeNal Cerebellin release.

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Published by djcomlab almost 8 years ago

isatools - v0.9.5 PhenoMeNal Cerebellin

ISA API for the PhenoMeNal Cerebellin release.

- Jupyter Notebook
Published by djcomlab almost 8 years ago

isatools - Release v0.9.5 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

This minor release is an update to address several minor bugs found in v0.9.4.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab about 8 years ago

isatools - Release v0.9.4 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

  • Study planning and serialization #229, #230, #236, #232, #166, #283, #252, #251, #245
  • ArrayExpress I/O #220, #213
  • Refactoring of ISA API structure #216
  • Generate report on study groups based on factor values #224, #280
  • Fixes issues #205, #210, #208, #214, #238, #267, #266, #264, #261, #260, #256, #255, #250, #246, #244, #243, #242, #239

This minor release is an update to the study and assay planning classes and object factory.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab about 8 years ago

isatools - Release v0.9.3 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

  • Study planning and serialization #229, #230, #236, #232, #166
  • ArrayExpress I/O #220, #213
  • Refactoring of ISA API structure #216
  • Generate report on study groups based on factor values #224
  • Fixes issues #205, #210, #208, #214, #238

This minor release is an update to the build requirements from using bs4 to beautifulsoup4 package to enable build packaging to conda.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.9.2 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

  • Study planning and serialization #229, #230, #236, #232, #166
  • ArrayExpress I/O #220, #213
  • Refactoring of ISA API structure #216
  • Generate report on study groups based on factor values #224
  • Fixes issues #205, #210, #208, #214, #238

This minor release is a fix for a distribution bug in v0.9.1 reported in #241.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.9.1 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

  • Study planning and serialization #229, #230, #236, #232, #166
  • ArrayExpress I/O #220, #213
  • Refactoring of ISA API structure #216
  • Generate report on study groups based on factor values #224
  • Fixes issues #205, #210, #208, #214, #238

This minor release is a fix for a distribution bug in v0.9.0 reported in #241.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.9.0 - Sample and Assay planning

This release of isatools implements new sets of study planning (sample and assay planning) classes, and generation of ISA template content based planning parameters. Additionally, ArrayExpress network I/O (retrieving MAGE-TABs and ISA-Tab from ArrayExpress database) has been implemented, and a report generator for analysing study groups in ISA-Tab created.

A major refactoring of the ISA-API package structure to clarify conversions from network importers has also been done.

  • Study planning and serialization #229, #230, #236, #232, #166
  • ArrayExpress I/O #220, #213
  • Refactoring of ISA API structure #216
  • Generate report on study groups based on factor values #224
  • Fixes issues #205, #210, #208, #214, #238

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.8.3 - MAGE-TAB format support

This release of isatools implements new MAGE-TAB format read/write capability, including import and export between MAGE-TAB and ISA formats (ISA-Tab and ISA-JSON).

  • MAGE-TAB import to ISA #203
  • MAGE-TAB export from ISA #124
  • Fixes issues #101, #177, #191, #205, #210, #221, #222, #222, #223, #226
  • For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.8.2 to address ISA-Tab loading issues reported in #222, #223 and #226.

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.8.2 - MAGE-TAB format support

This release of isatools implements new MAGE-TAB format read/write capability, including import and export between MAGE-TAB and ISA formats (ISA-Tab and ISA-JSON).

  • MAGE-TAB import to ISA #203
  • MAGE-TAB export from ISA #124
  • Fixes issues #101, #177, #191, #205, #210, #221

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.8.1 to address ISA-Tab loading issues reported in #221.

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.8.1 - MAGE-TAB format support

This release of isatools implements new MAGE-TAB format read/write capability, including import and export between MAGE-TAB and ISA formats (ISA-Tab and ISA-JSON).

  • MAGE-TAB import to ISA #203
  • MAGE-TAB export from ISA #124
  • Fixes issues #101, #177, #191, #205, #210 For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.8.0 to address ISA-Tab loading issues reported in https://github.com/workflow4metabolomics/mtbls-dwnld/issues/4

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.8.0 - MAGE-TAB format support

This release of isatools implements new MAGE-TAB format read/write capability, including import and export between MAGE-TAB and ISA formats (ISA-Tab and ISA-JSON).

  • MAGE-TAB import to ISA #203
  • MAGE-TAB export from ISA #124
  • Fixes issues #101, #177, #191

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 8 years ago

isatools - Release v0.7.5 - SampleTab format support

This release of isatools implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

  • SampleTab import to ISA #190
  • SampleTab export from ISA #120
  • Support for command-line calls to SampleTab converters #182
  • Fixes ISA-Tab r/w for NMR #187
  • Fixes issues #154, #199, #200, #201, #202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.7.4 for PhenoMeNal project features.

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.7.4 - SampleTab format support

This release of isatools implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

  • SampleTab import to ISA #190
  • SampleTab export from ISA #120
  • Support for command-line calls to SampleTab converters #182
  • Fixes ISA-Tab r/w for NMR #187
  • Fixes issues #154, #199, #200, #201, #202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.7.3 to add functionality to the mtbls project to summarise variable metadata in ISA-Tab files for PhenoMeNal project.

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.7.3 - SampleTab format support

This release of isatools implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

  • SampleTab import to ISA #190
  • SampleTab export from ISA #120
  • Support for command-line calls to SampleTab converters #182
  • Fixes ISA-Tab r/w for NMR #187
  • Fixes issues #154, #199, #200, #201, #202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.7.2.

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.7.2 - SampleTab format support

This release of isatools implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

  • SampleTab import to ISA #190
  • SampleTab export from ISA #120
  • Support for command-line calls to SampleTab converters #182
  • Fixes ISA-Tab r/w for NMR #187
  • Fixes issues #154, #199, #200, #201, #202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to 0.7.0 to fix containerisation issue reported in https://github.com/phnmnl/container-mtblisa/issues/1

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.7.0 - SampleTab format support

This release of isatools implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

  • SampleTab import to ISA #190
  • SampleTab export from ISA #120
  • Support for command-line calls to SampleTab converters #182
  • Fixes ISA-Tab r/w for NMR #187
  • Fixes issues #154, #199, #200, #201, #202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.6.2 - Enhanced ISA-Tab r/w performance and more

This release of isatools focuses on further performance enhancements to the existing API functionality, in particular the ISA-Tab r/w, and a range of new features:

  • Performance enhancements to ISA-Tab read and write #184
  • New feature to load and dump only Investigation file of ISA-Tab #185
  • New feature to export ISArchive zip from ISA content #180
  • New feature to search Ontology Lookup Service and return OntologyAnnotation object #1
  • New feature to search Entrez for publications and return Publication object #157
  • New feature to merge Study and Assay table ISA-Tab files (of same assay type) #186
  • Refactoring of example data and tests data to pull from centralised https://github.com/ISA-tools/ISAdatasets repository #78 #183
  • Bug fixes to ISA-Tab investigation file loading issues #196 #197

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to v0.6.0 that fixes ISA-Tab load issues reported in #199 and #202.

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.6.0 - Enhanced ISA-Tab r/w performance and more

This release of isatools focuses on further performance enhancements to the existing API functionality, in particular the ISA-Tab r/w, and a range of new features: - Performance enhancements to ISA-Tab read and write #184 - New feature to load and dump only Investigation file of ISA-Tab #185 - New feature to export ISArchive zip from ISA content #180 - New feature to search Ontology Lookup Service and return OntologyAnnotation object #1 - New feature to search Entrez for publications and return Publication object #157 - New feature to merge Study and Assay table ISA-Tab files (of same assay type) #186 - Refactoring of example data and tests data to pull from centralised https://github.com/ISA-tools/ISAdatasets repository #78 #183 - Bug fixes to ISA-Tab investigation file loading issues #196 #197

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab almost 9 years ago

isatools - Release v0.5.0 - Performance enhancements

This release of isatools focuses on implementing new performance enhancements to the existing API functionality: - Bug fixes and minor enhancements in issues #147, #174 and #176 - Implementation of a wholesale replacement for the ISA-Tab parser, now found in theisatab.load() function, which loads ISA-Tab content into ISA model objects. This represents work towards harmonisation of the loading of ISA-Tab content into the same model as the ISA JSON loader, and a big improvement on loading performance (e.g. loading BII-I-1 test data down from 3.7s to 0.6s in tests using the timeit module) #168 - Implementation of a ISA JSON Encoder to write out ISA model objects to the ISA-JSON representation. This is implemented as the ISAJSONEncoder class that can be passed to the Python json package used to dump JSON. - Integration of the new ISA-Tab loader and the new ISA JSON Encoder into the isatab2json converter #181 - Where the isatab2json is used elsewhere in the API, updates have been made to use the enhanced performance converter, where appropriate.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab about 9 years ago

isatools - Release v0.4.0 - Creation of ISA content and enhancements

This release of isatools firms up ISA content creation with example code and added documentation; implemented a range of enhancements and bug fixes, including boosting test coverage from 55% to 73%. New features and enhancements include: - A more complete user guide to creating ISA content using objects - Validator reports generated as JSON - Batch validation scripts - Integration of the mzml2isa tool into the ISA API

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab about 9 years ago

isatools - Release v0.3.6 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update that fixes ISA-Tab writer issue #172.

- Jupyter Notebook
Published by djcomlab about 9 years ago

isatools - Release v0.3.5 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a third minor update that fixes ISA-Tab validator issues reported in #162 and #163.

- Jupyter Notebook
Published by djcomlab about 9 years ago

isatools - Release v0.3.4 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a second minor update that fixes the SRA XML submission issues to ENA reported in #158.

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.3.3 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update that fixes the SRA XML submission issues to ENA reported in #158.

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.3.2 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update that adds contribution in pull #156 to query MetaboLights ISA-Tab metadata.

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.3.1 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update that fixes a distribution bug reported in #142.

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - 0.3.0 - New SRA exporter, DB importers

This release of isatools implements new ISA to SRA exporters, and 4 data importers into ISA-Tab: - ISA JSON to SRA export - Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable) - Importer for MetaboLights to ISA-Tab and ISA JSON - Importer for MetabolomicsWorkbench to ISA-Tab - Importer for Biocrates to ISA-Tab - Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.2.4 - ISA validators (minor update)

This minor update release of isatools fixes some bugs reported up to #119.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.2.3 - ISA validators (minor update)

This minor update release of isatools fixes a bug reported in #116.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.2.2 - New ISA validators

This release of isatools implements two new ISA validators: - ISA JSON content validation, checking content is properly formed and linked within documents - Replacement fo the legacy ISA tab validation (the Java converter) with a pure Python implementation.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

- Jupyter Notebook
Published by djcomlab over 9 years ago

isatools - Release v0.1.3

  • Fix for issues #92
  • Updates to travis config

- Jupyter Notebook
Published by agbeltran almost 10 years ago

isatools - Initial release v0.1.2

Minor updates to distribution errors in previous tag.

- Jupyter Notebook
Published by djcomlab almost 10 years ago

isatools - Initial release v0.1.0

- Jupyter Notebook
Published by agbeltran almost 10 years ago