.. _study_section: Study Section ============= The configuration section for a study follows the general INI format. Its name must be ``study`` - this will indicate that it is a study configuration section. This configuration section must properly describe one study. Either this section or the `ref:` section must be present in the config file. Example Configuration --------------------- .. code-block:: ini [study] enabled = yes name = Study id = study prefix = data file_format = vcf description = %(work_dir)s/data/description.md studyType = WE year = 2019 hasDenovo = yes hasTransmitted = no hasComplex = no hasCNV = no commonReport = True genotypeBrowser = True phenotypeBrowser = True enrichmentTool = False phenotypeTool = False [study] ------- The properties for this section are explained below. name ____ .. code-block:: ini name = Name which will be used as display name for the study. Default value for it is the value of the ``id`` property from the study. id __ .. code-block:: ini id = Identifier of the study. description ___________ .. code-block:: ini description = This property shows if the ``Dataset Description`` tab is enabled for the study. It can contain a description as a string in markdown format or as an absolute or relative path to a markdown file. You can see more about the ``Dataset Description`` tab :ref:`here `. prefix ______ .. code-block:: ini prefix = This property shows the location of the directory that contains the study's data files. It can be an absolute or relative path. If it is a relative path, it must be relative to the directory containing the study's configuration file. file_format ___________ .. code-block:: ini file_format = This property shows the file format of the study data files. Supported formats are ``impala`` and ``vcf``. In the ``impala`` format, files are queried with the help of ``Apache Impala`` and the expected file format is ``Apache Parquet``. On the other hand, if ``vcf`` is the chosen file format, files are expected to be valid ``tsv`` files in the VCF format. Querying in the VCF file format is implemented with the help of ``pandas``. phenoDB _______ .. code-block:: ini phenoDB = The corresponding :ref:`pheno DB ` for the study. It must be a valid pheno DB id. studyType _________ .. code-block:: ini studyType = This property gives the type of the study. Possible types are: * ``WE`` - Whole Exome * ``WG`` - Whole Genome * ``TG`` - Targeted Genome year ____ .. code-block:: ini year = This property specifies the release year of the study. pubMed ______ .. code-block:: ini pubMed = This property contains the id of an article from PubMed associated with the study. You can see more about PubMed on their website - https://www.ncbi.nlm.nih.gov/pubmed/. .. _study_section_has_denovo: hasDenovo _________ .. FIXME: Remove this property after implementing getting of its value from the study backend. .. code-block:: ini hasDenovo = This property specifies if the study contains variants with ``denovo`` inheritance. This property takes a :ref:`boolean ` value. .. _study_section_has_transmitted: hasTransmitted ______________ .. FIXME: Remove this property after implementing getting of its value from the study backend. .. code-block:: ini hasTransmitted = This property specifies if the study contains variants with ``transmitted`` type inheritance. This property takes a :ref:`boolean ` value. .. _study_section_has_complex: hasComplex __________ .. FIXME: Remove this property after implementing getting of its value from the study backend. .. code-block:: ini hasComplex = This property specifies if the study contains variants with ``complex`` variant type. This property takes a :ref:`boolean ` value. .. _study_section_has_CNV: hasCNV ______ .. FIXME: Remove this property after implementing getting of its value from the study backend. .. code-block:: ini hasCNV = This property shows if the study contains variants with ``CNV``, ``CNV+`` or ``CNV-`` effect types or ``CNV`` variant type. This property takes a :ref:`boolean ` value. .. _study_section_common_report: commonReport ____________ .. code-block:: ini commonReport = This property specifies if the ``Dataset Statistics`` tab is enabled for the study. You can see more about the ``Dataset Statistics`` tab :ref:`here `. This property takes a :ref:`boolean ` value. .. _study_section_genotype_browser: genotypeBrowser _______________ .. code-block:: ini genotypeBrowser = This property specifies if the ``Genotype Browser`` tab is enabled for the study. You can see more about the ``Genotype Browser`` tab :ref:`here `. This property takes a :ref:`boolean ` value. .. _study_section_phenotype_browser: phenotypeBrowser ________________ .. code-block:: ini phenotypeBrowser = This property specifies if the ``Phenotype Browser`` tab is enabled for the study. You can see more about the ``Phenotype Browser`` tab :ref:`here `. This property takes a :ref:`boolean ` value. .. _study_section_enrichment_tool: enrichmentTool ______________ .. code-block:: ini enrichmentTool = This property specifies if the ``Enrichment Tool`` tab is enabled for the study. You can see more about the ``Enrichment Tool`` tab :ref:`here `. This property takes a :ref:`boolean ` value. .. _study_section_phenotype_tool: phenotypeTool _____________ .. code-block:: ini phenotypeTool = This property specifies if the ``Phenotype Tool`` tab is enabled for the study. You can see more about the ``Phenotype Tool`` tab :ref:`here `. This property takes a :ref:`boolean ` value. enabled _______ .. code-block:: ini enabled = DEFAULT ``True`` This property enables the study. This property takes a :ref:`boolean ` value.