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CHANGELOG.md

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Qiita changelog

Version 0.2.0-dev (Changes since version 0.2.0 go here)

  • Users can now change values and add samples and/or columns to sample and prep templates using the Update button (see the prep template and sample template tabs).
  • The raw files of a RawData can be now updated using the qiita db update_raw_data CLI command.
  • instrument_model is now a required prep template column for EBI submissions.
  • PostgreSQL 9.3.0 is now the minimum required version because we are using the SQL type JSON, included for first time in 9.3.0.
  • The objects RawData, PreprocessedData and ProcessedData have been removed from the system and substituted by a general Artifact object.
  • The CLI commands load_raw, load_preprocessed and load_processed have been removed from the system and substituted by load_artifact.
  • We incorporated the idea of plugins into the system. Now, all processing could be plugins.
  • QIIME workflows for splitting libraries (SFF/FASTA-QUAL and FASTQ/per-sample-FASTQ) and for picking OTUs has been moved to a new target gene plugin.
  • An initial RESTapi has been introduced as a result of the plugin system, in which OAuth2 authentication is required to access the data.
  • The system has been ported to use HTTPS instead of HTTP.
  • The website now supports Mozilla Firefox 48 and above.

Version 0.2.0 (2015-08-25)

  • Creating an empty RawData is no longer needed in order to add a PrepTemplate. Now, the PrepTemplate is required in order to add a RawData to a study. This is the normal flow of a study, as the PrepTemplate information is usually available before the RawData information is available.
  • A user can upload a QIIME mapping file instead of a SampleTemplate. The system will create a SampleTemplate and a PrepTemplate from the information present in the QIIME mapping file. The QIIME required columns for this functionality to work are 'BarcodeSequence', 'LinkerPrimerSequence' and 'Description'. For more information about QIIME mapping files, visit http://qiime.org/documentation/file_formats.html#mapping-file-overview.
  • The command line interface has been reorganized:
  • qiita_env has been renamed qiita-env
  • qiita_test_install has been renamed qiita-test-install
  • qiita ebi has been moved to qiita ware ebi
  • qiita log has been moved to qiita maintenance log
  • A new qiita pet command subgroup has been created
  • qiita webserver has been moved to qiita pet webserver
  • Cluster names now use dashes instead of underscores (e.g., qiita_general is now qiita-general)
  • qiita-general is now used as a default argument to qiita-env start_cluster and qiita-env stop_cluster if no cluster name is specified
  • Qiita now now allows for processing of already demultiplexed data without any technical (barcode and primer) section of the read.
  • Qiita now includes full portal support, limiting study and analysis access at below the qiita_db level. This allows one database to act as if subsets of studies/analyses are their own specific interface. Commands added for portals creation and maintenance, under qiita db portal ... and qiita-env. Portal specific web user interface support has also been added; each portal is fully CSS customizable.
  • 403 errors are now not logged in the logging table
  • Qiita will execute all DB interactions in transactions. The queue code was moved and improved from SQLConnectionHandler to a new Transaction object. The system implements the singleton pattern. That is, there is only a single transaction in the system, represented by the variable TRN, and all DB interactions go through it.

Version 0.1.0 (2015-04-30)

Initial alpha release.