pyxetabase 3.1.0.dev25__py3-none-any.whl → 4.0.0.dev29__py3-none-any.whl

pyopencga/rest_clients/admin_client.py

@@ -1,172 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class Admin(_ParentRestClient):
-    """
-    This class contains methods for the 'Admin' webservices
-    PATH: /{apiVersion}/admin
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Admin, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def group_by_audit(self, fields, entity, **options):
-        """
-        Group by operation.
-        PATH: /{apiVersion}/admin/audit/groupBy
-
-        :param str entity: Entity to be grouped by. Allowed values: ['AUDIT
-            NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL
-            COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION
-            VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL WORKFLOW
-            RESOURCE'] (REQUIRED)
-        :param str fields: Comma separated list of fields by which to group
-            by. (REQUIRED)
-        :param bool count: Count the number of elements matching the group.
-        :param int limit: Maximum number of documents (groups) to be returned.
-        :param str action: Action performed.
-        :param str before: Object before update.
-        :param str after: Object after update.
-        :param str date: Date <,<=,>,>=(Format: yyyyMMddHHmmss) and
-            yyyyMMddHHmmss-yyyyMMddHHmmss.
-        """
-
-        options['fields'] = fields
-        options['entity'] = entity
-        return self._get(category='admin', resource='groupBy', subcategory='audit', **options)
-
-    def install_catalog(self, data=None, **options):
-        """
-        Install OpenCGA database.
-        PATH: /{apiVersion}/admin/catalog/install
-
-        :param dict data: JSON containing the mandatory parameters. (REQUIRED)
-        """
-
-        return self._post(category='admin', resource='install', subcategory='catalog', data=data, **options)
-
-    def jwt_catalog(self, data=None, **options):
-        """
-        Change JWT secret key.
-        PATH: /{apiVersion}/admin/catalog/jwt
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str organization: Organization id.
-        """
-
-        return self._post(category='admin', resource='jwt', subcategory='catalog', data=data, **options)
-
-    def fetch_resource(self, data=None, **options):
-        """
-        Fetch resources from the public server and save them into the OpenCGA
-            local installation.
-        PATH: /{apiVersion}/admin/resource/fetch
-
-        :param dict data: Download-resources tool parameters. (REQUIRED)
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='admin', resource='fetch', subcategory='resource', data=data, **options)
-
-    def create_users(self, data=None, **options):
-        """
-        Create a new user.
-        PATH: /{apiVersion}/admin/users/create
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        """
-
-        return self._post(category='admin', resource='create', subcategory='users', data=data, **options)
-
-    def import_users(self, data=None, **options):
-        """
-        Import users or a group of users from LDAP or AAD.
-        PATH: /{apiVersion}/admin/users/import
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str organization: Organization id.
-        """
-
-        return self._post(category='admin', resource='import', subcategory='users', data=data, **options)
-
-    def permissions_users(self, **options):
-        """
-        User permissions.
-        PATH: /{apiVersion}/admin/users/permissions
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str entry_ids: Comma separated list of entry ids.
-        :param str permissions: Comma separated list of permissions to be
-            retrieved.
-        :param str category: Category corresponding to the id's provided.
-        """
-
-        return self._get(category='admin', resource='permissions', subcategory='users', **options)
-
-    def search_users(self, **options):
-        """
-        User search method.
-        PATH: /{apiVersion}/admin/users/search
-
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param bool count: Get the total number of results matching the query.
-            Deactivated by default.
-        :param str organization: Organization id.
-        :param str user: User ID.
-        :param str authentication_id: Authentication origin ID.
-        """
-
-        return self._get(category='admin', resource='search', subcategory='users', **options)
-
-    def sync_users(self, data=None, **options):
-        """
-        [DEPRECATED] Moved to /users/sync.
-        PATH: /{apiVersion}/admin/users/sync
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str organization: Organization id.
-        """
-
-        return self._post(category='admin', resource='sync', subcategory='users', data=data, **options)
-
-    def users_update_groups(self, user, data=None, **options):
-        """
-        Add or remove users from existing groups.
-        PATH: /{apiVersion}/admin/users/{user}/groups/update
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str user: User ID. (REQUIRED)
-        :param str organization: Organization id.
-        :param str action: Action to be performed: ADD or REMOVE user to/from
-            groups. Allowed values: ['ADD REMOVE']
-        """
-
-        return self._post(category='admin/users', resource='update', query_id=user, subcategory='groups', data=data, **options)
-

pyopencga/rest_clients/alignment_client.py

@@ -1,373 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class Alignment(_ParentRestClient):
-    """
-    This class contains methods for the 'Analysis - Alignment' webservices
-    PATH: /{apiVersion}/analysis/alignment
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Alignment, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def run_bwa(self, data=None, **options):
-        """
-        BWA is a software package for mapping low-divergent sequences against
-            a large reference genome.
-        PATH: /{apiVersion}/analysis/alignment/bwa/run
-
-        :param dict data: BWA parameters. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/bwa', data=data, **options)
-
-    def run_coverage_index(self, data=None, **options):
-        """
-        Compute the coverage from a given BAM alignment file, e.g., create a
-            .bw file from a .bam file.
-        PATH: /{apiVersion}/analysis/alignment/coverage/index/run
-
-        :param dict data: Coverage computation parameters. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/coverage/index', data=data, **options)
-
-    def coverage_qc_gene_coverage_stats_run(self, data=None, **options):
-        """
-        Compute gene coverage stats for a given alignment file and a list of
-            genes.
-        PATH: /{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run
-
-        :param dict data: Gene coverage stats parameters for a given BAM file
-            and a list of genes. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/coverage/qc/geneCoverageStats', data=data, **options)
-
-    def query_coverage(self, file, **options):
-        """
-        Query the coverage of an alignment file for regions or genes.
-        PATH: /{apiVersion}/analysis/alignment/coverage/query
-
-        :param str file: File ID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str region: Comma separated list of regions 'chr:start-end,
-            e.g.: 2,3:63500-65000.
-        :param str gene: Comma separated list of genes, e.g.: BCRA2,TP53.
-        :param int offset: Offset to extend the region, gene or exon at up and
-            downstream.
-        :param bool only_exons: Only exons are taking into account when genes
-            are specified.
-        :param str range: Range of coverage values to be reported. Minimum and
-            maximum values are separated by '-', e.g.: 20-40 (for coverage
-            values greater or equal to 20 and less or equal to 40). A single
-            value means to report coverage values less or equal to that value.
-        :param int window_size: Window size for the region coverage (if a
-            coverage range is provided, window size must be 1).
-        :param bool split_results: Split results into regions (or gene/exon
-            regions).
-        """
-
-        options['file'] = file
-        return self._get(category='analysis', resource='query', subcategory='alignment/coverage', **options)
-
-    def ratio_coverage(self, file1, file2, **options):
-        """
-        Compute coverage ratio from file #1 vs file #2, (e.g. somatic vs
-            germline).
-        PATH: /{apiVersion}/analysis/alignment/coverage/ratio
-
-        :param str file2: Input file #2 (e.g. germline file). (REQUIRED)
-        :param str file1: Input file #1 (e.g. somatic file). (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool skip_log2: Do not apply Log2 to normalise the coverage
-            ratio.
-        :param str region: Comma separated list of regions 'chr:start-end,
-            e.g.: 2,3:63500-65000.
-        :param str gene: Comma separated list of genes, e.g.: BCRA2,TP53.
-        :param int offset: Offset to extend the region, gene or exon at up and
-            downstream.
-        :param bool only_exons: Only exons are taking into account when genes
-            are specified.
-        :param int window_size: Window size for the region coverage (if a
-            coverage range is provided, window size must be 1).
-        :param bool split_results: Split results into regions (or gene/exon
-            regions).
-        """
-
-        options['file1'] = file1
-        options['file2'] = file2
-        return self._get(category='analysis', resource='ratio', subcategory='alignment/coverage', **options)
-
-    def stats_coverage(self, file, gene, **options):
-        """
-        Compute coverage stats per transcript for a list of genes.
-        PATH: /{apiVersion}/analysis/alignment/coverage/stats
-
-        :param str gene: Comma separated list of genes, e.g.: BCRA2,TP53.
-            (REQUIRED)
-        :param str file: File ID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param int threshold: Only regions whose coverage depth is under this
-            threshold will be reported.
-        """
-
-        options['file'] = file
-        options['gene'] = gene
-        return self._get(category='analysis', resource='stats', subcategory='alignment/coverage', **options)
-
-    def run_deeptools(self, data=None, **options):
-        """
-        Deeptools is a suite of python tools particularly developed for the
-            efficient analysis of high-throughput sequencing data, such as
-            ChIP-seq, RNA-seq or MNase-seq.
-        PATH: /{apiVersion}/analysis/alignment/deeptools/run
-
-        :param dict data: Deeptools parameters. Supported Deeptools commands:
-            bamCoverage, bamCompare. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/deeptools', data=data, **options)
-
-    def run_fastqc(self, data=None, **options):
-        """
-        A high throughput sequence QC analysis tool.
-        PATH: /{apiVersion}/analysis/alignment/fastqc/run
-
-        :param dict data: FastQC parameters. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/fastqc', data=data, **options)
-
-    def run_index(self, data=None, **options):
-        """
-        Index a given alignment file BAM/CRAM, e.g., create a .bai file from a
-            .bam file.
-        PATH: /{apiVersion}/analysis/alignment/index/run
-
-        :param dict data: Alignment index params. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/index', data=data, **options)
-
-    def run_picard(self, data=None, **options):
-        """
-        Picard is a set of command line tools (in Java) for manipulating
-            high-throughput sequencing (HTS) data and formats such as
-            SAM/BAM/CRAM and VCF. Supported Picard commands: CollectHsMetrics,
-            CollectWgsMetrics, BedToIntervalList.
-        PATH: /{apiVersion}/analysis/alignment/picard/run
-
-        :param dict data: Picard parameters. Supported Picard commands:
-            CollectHsMetrics, CollectWgsMetrics, BedToIntervalList. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/picard', data=data, **options)
-
-    def run_qc(self, data=None, **options):
-        """
-        Compute quality control (QC) metrics for a given alignment file:
-            samtools stats, samtools flag stats and FastQC metrics.
-        PATH: /{apiVersion}/analysis/alignment/qc/run
-
-        :param dict data: Alignment quality control (QC) parameters. It
-            computes: stats, flag stats and fastqc metrics. The BAM file ID is
-            mandatory and in order to skip some metrics, use the following
-            keywords (separated by commas): stats, flagstats, fastqc.
-            (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/qc', data=data, **options)
-
-    def query(self, file, **options):
-        """
-        Search over indexed alignments.
-        PATH: /{apiVersion}/analysis/alignment/query
-
-        :param str file: File ID. (REQUIRED)
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param bool count: Get the total number of results matching the query.
-            Deactivated by default.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str region: Comma separated list of regions 'chr:start-end,
-            e.g.: 2,3:63500-65000.
-        :param str gene: Comma separated list of genes, e.g.: BCRA2,TP53.
-        :param int offset: Offset to extend the region, gene or exon at up and
-            downstream.
-        :param bool only_exons: Only exons are taking into account when genes
-            are specified.
-        :param int min_mapping_quality: Minimum mapping quality.
-        :param int max_num_mismatches: Maximum number of mismatches.
-        :param int max_num_hits: Maximum number of hits.
-        :param bool properly_paired: Return only properly paired alignments.
-        :param int max_insert_size: Maximum insert size.
-        :param bool skip_unmapped: Skip unmapped alignments.
-        :param bool skip_duplicated: Skip duplicated alignments.
-        :param bool region_contained: Return alignments contained within
-            boundaries of region.
-        :param bool force_m_d_field: Force SAM MD optional field to be set
-            with the alignments.
-        :param bool bin_qualities: Compress the nucleotide qualities by using
-            8 quality levels.
-        :param bool split_results: Split results into regions (or gene/exon
-            regions).
-        """
-
-        options['file'] = file
-        return self._get(category='analysis', resource='query', subcategory='alignment', **options)
-
-    def run_samtools(self, data=None, **options):
-        """
-        Samtools is a program for interacting with high-throughput sequencing
-            data in SAM, BAM and CRAM formats. Supported Samtools commands:
-            sort, index, view, stats, flagstat, dict, faidx, depth,
-            plot-bamstats.
-        PATH: /{apiVersion}/analysis/alignment/samtools/run
-
-        :param dict data: Samtools parameters. Supported Samtools commands:
-            sort, index, view, stats, flagstat, dict, faidx, depth,
-            plot-bamstats. (REQUIRED)
-        :param str study: study.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='alignment/samtools', data=data, **options)
-