pyxetabase 4.0.0.dev62__py3-none-any.whl → 4.0.0.dev74__py3-none-any.whl

pyxetabase/rest_clients/clinical_analysis_client.py

@@ -445,6 +445,88 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='load', subcategory='clinical', data=data, **options)
 
+    def run_pipeline_affy(self, data=None, **options):
+        """
+        Execute the clinical genomics pipeline that performs QC (FastQC,...),
+            mapping (BWA, Bowtie,...) , variant calling (GATK,...) and variant
+            indexing in OpenCGA storage.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/affy/run
+
+        :param dict data: JSON with parameters to execute the command
+            affy-pipeline. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :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='analysis', resource='run', subcategory='clinical/pipeline/affy', data=data, **options)
+
+    def run_pipeline_genomics(self, data=None, **options):
+        """
+        Execute the clinical genomics pipeline that performs QC (FastQC,...),
+            mapping (BWA, Bowtie,...) , variant calling (GATK,...) and variant
+            indexing in OpenCGA storage.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/genomics/run
+
+        :param dict data: JSON with parameters to execute the command
+            ngs-pipeline-genomics. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :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='analysis', resource='run', subcategory='clinical/pipeline/genomics', data=data, **options)
+
+    def run_pipeline_prepare(self, data=None, **options):
+        """
+        Prepare the clinical pipeline.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/prepare/run
+
+        :param dict data: JSON with parameters to execute the command
+            ngs-pipeline-prepare. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :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='analysis', resource='run', subcategory='clinical/pipeline/prepare', data=data, **options)
+
     def aggregation_stats_rga(self, field, **options):
         """
         RGA aggregation stats.
@@ -1029,6 +1111,9 @@ class ClinicalAnalysis(_ParentRestClient):
             analysts is being updated. Allowed values: ['ADD SET REMOVE']
         :param str files_action: Action to be performed if the array of files
             is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str reported_files_action: Action to be performed if the array
+            of reported files is being updated. Allowed values: ['ADD SET
+            REMOVE']
         :param str panels_action: Action to be performed if the array of
             panels is being updated. Allowed values: ['ADD SET REMOVE']
         :param str annotation_sets_action: Action to be performed if the array
@@ -1203,11 +1288,10 @@ class ClinicalAnalysis(_ParentRestClient):
             project can be either the ID or UUID.
         :param str comments_action: Action to be performed if the array of
             comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
-        :param str supporting_evidences_action: Action to be performed if the
-            array of supporting evidences is being updated. Allowed values:
-            ['ADD SET REMOVE']
-        :param str files_action: Action to be performed if the array of files
-            is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str signatures_action: Action to be performed if the array of
+            signatures is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str references_action: Action to be performed if the array of
+            references is being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """

pyxetabase/rest_clients/file_client.py

@@ -407,11 +407,11 @@ class File(_ParentRestClient):
         :param str format: File format. Allowed values: ['VCF BCF GVCF TBI
             BIGWIG SAM BAM BAI CRAM CRAI FASTQ FASTA PED TAB_SEPARATED_VALUES
             COMMA_SEPARATED_VALUES XML PROTOCOL_BUFFER JSON AVRO PARQUET PDF
-            IMAGE PLAIN BINARY NONE UNKNOWN']
+            IMAGE PLAIN BINARY JAVASCRIPT NONE UNKNOWN']
         :param str file_format: [DEPRECATED] File format. Allowed values:
             ['VCF BCF GVCF TBI BIGWIG SAM BAM BAI CRAM CRAI FASTQ FASTA PED
             TAB_SEPARATED_VALUES COMMA_SEPARATED_VALUES XML PROTOCOL_BUFFER
-            JSON AVRO PARQUET PDF IMAGE PLAIN BINARY NONE UNKNOWN']
+            JSON AVRO PARQUET PDF IMAGE PLAIN BINARY JAVASCRIPT NONE UNKNOWN']
         :param str bioformat: File bioformat. Allowed values:
             ['MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT
             MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX
@@ -422,7 +422,7 @@ class File(_ParentRestClient):
             OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF
             OTHER_PED VCF4 CVDB VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
             REFERENCE_GENOME NONE UNKNOWN']
-        :param str checksum: Expected MD5 file checksum.
+        :param str checksum: Expected SHA-256 file checksum.
         :param bool resource: Boolean field indicating whether the file is a
             resource or not.
         :param str study: Study [[organization@]project:]study where study and
@@ -569,6 +569,19 @@ class File(_ParentRestClient):
 
         return self._post(category='files', resource='annotations/update', query_id=file, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
 
+    def update_content(self, file, data=None, **options):
+        """
+        Overwrite the content of a file.
+        PATH: /{apiVersion}/files/{file}/content/update
+
+        :param dict data: File parameters. (REQUIRED)
+        :param str file: File id or name. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        """
+
+        return self._post(category='files', resource='update', query_id=file, subcategory='content', data=data, **options)
+
     def download(self, file, **options):
         """
         Download file.

pyxetabase/rest_clients/job_client.py

@@ -56,6 +56,12 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
+        :param str tool.minimum_requirements.queue: Queue where the job is
+            expected to be executed.
+        :param str tool.minimum_requirements.processor_type: Processor type
+            required to run the job. Allowed values: [CPU, GPU, FPGA].
+        :param str execution.queue.id: Queue id where the job has been
+            submitted to be executed.
         :param str user_id: User that created the job.
         :param str priority: Priority of the job.
         :param str status: Filter by status.
@@ -118,6 +124,12 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
+        :param str tool.minimum_requirements.queue: Queue where the job is
+            expected to be executed.
+        :param str tool.minimum_requirements.processor_type: Processor type
+            required to run the job. Allowed values: [CPU, GPU, FPGA].
+        :param str execution.queue.id: Queue id where the job has been
+            submitted to be executed.
         :param str tool.external_executor.id: Id of the external executor.
             This field is only applicable for jobs executed by an external
             executor.
@@ -202,6 +214,12 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
+        :param str tool.minimum_requirements.queue: Queue where the job is
+            expected to be executed.
+        :param str tool.minimum_requirements.processor_type: Processor type
+            required to run the job. Allowed values: [CPU, GPU, FPGA].
+        :param str execution.queue.id: Queue id where the job has been
+            submitted to be executed.
         :param str tool.external_executor.id: Id of the external executor.
             This field is only applicable for jobs executed by an external
             executor.

{pyxetabase-4.0.0.dev62.dist-info → pyxetabase-4.0.0.dev74.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev62
+Version: 4.0.0.dev74
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev62.dist-info → pyxetabase-4.0.0.dev74.dist-info}/RECORD

@@ -9,16 +9,16 @@ pyxetabase/rest_clients/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 pyxetabase/rest_clients/_parent_rest_clients.py,sha256=OuCnmaziUCENpmpA3CzKJGEhMY_Z-7Q_rlkH75QDi7I,5854
 pyxetabase/rest_clients/admin_client.py,sha256=SzUuUBw1WNaCEOaS15UsHhn0OPgJ0WTEEoR043Z2zwM,7206
 pyxetabase/rest_clients/alignment_client.py,sha256=srY1fmjMZCPWlbqhrD2gYVhS2zu7fgPx61tZOqQi4Wc,18509
-pyxetabase/rest_clients/clinical_analysis_client.py,sha256=jtEciqNiloadVxKmrq7UW-hYQlv9rHBR7G28IVTeXBM,65945
+pyxetabase/rest_clients/clinical_analysis_client.py,sha256=JvDSSxkdGIXP7nTX_CsxodjB6JNP8q_Df5vxW_kc6_M,70461
 pyxetabase/rest_clients/cohort_client.py,sha256=_OIKohOlZcz3kRfP-FEneLkdCDVewlbG75YrhMT0aTg,17104
 pyxetabase/rest_clients/cvdb_client.py,sha256=V7ny5nQEeJqsbALAe7JLyoV6b0XyYF7c9lsn-qK-i8o,143102
 pyxetabase/rest_clients/disease_panel_client.py,sha256=YQIykUElEUGtOKGivnl9vNyHIrrZ_tXMnA1cvK8eE1A,18066
 pyxetabase/rest_clients/family_client.py,sha256=n-kyjnrV09R50JxyiHjFs8rCQkOKFU0Z1O7oVYuaKxg,18586
 pyxetabase/rest_clients/federation_client.py,sha256=p5B8dRq9gj-fdgIfIPhmkT7mNU65cRFtH06kaGtmbWE,5066
-pyxetabase/rest_clients/file_client.py,sha256=xOndKo1z5pTUySKLn9dQK10tIdopwH4Fe0Sp2-wwJeU,34210
+pyxetabase/rest_clients/file_client.py,sha256=pbGgpRHlxRCNWTuVnuA1U5Zm3fKpwmJye1tKXElE90g,34777
 pyxetabase/rest_clients/ga4gh_client.py,sha256=fPnmiblnfpz_zcZPJblGqOFksrdiF3MUer3fv2nwQwk,3506
 pyxetabase/rest_clients/individual_client.py,sha256=C59zr_t7tTxNR7ZBeAPY6fyYl59fE7KY05MaLyXWmXw,23225
-pyxetabase/rest_clients/job_client.py,sha256=ROODPyg0prlJ1rZb7rvy3A-LK5dXVs7hzXoKek-c9gc,19851
+pyxetabase/rest_clients/job_client.py,sha256=oN55qQsj2C7LF4VG5tQQtyCNZNf4Y1MdmZCNiMP4Dnw,20955
 pyxetabase/rest_clients/meta_client.py,sha256=uExVRfdSKiXteLYe7R3q9x3zCp9mMWWMyPDU56TtoDo,2308
 pyxetabase/rest_clients/organization_client.py,sha256=tnwUTCqJoGiKXMQLMv4ymHA16JxnR5iL2SMLaJDBRs8,9465
 pyxetabase/rest_clients/project_client.py,sha256=M8naPsj47z2ylTrJNU_JyHReKzXrB038PoEtKKrtxmc,5212
@@ -29,8 +29,8 @@ pyxetabase/rest_clients/user_tool_client.py,sha256=QCqFpwB0B6w0likPj8y_lhQ3VXBME
 pyxetabase/rest_clients/variant_client.py,sha256=mmBuVE0JBThJr5zsLGci5nykNcCKyfZXRKl-h3HT9PA,75436
 pyxetabase/rest_clients/variant_operation_client.py,sha256=ceZ2-ii0D1oCDMRz_EURwUf_VjtsV5lzJuY-ZwG1b6Q,36840
 pyxetabase/rest_clients/workflow_client.py,sha256=HYu4YInpzQvDRDNtFkT8LmxUHuMaPdPP59wSvHkBZtc,12487
-pyxetabase-4.0.0.dev62.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-pyxetabase-4.0.0.dev62.dist-info/METADATA,sha256=oxyOqvlJ16jGd0QlDxM44U3K-CcxKWILwrI-jPHzOSM,5540
-pyxetabase-4.0.0.dev62.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pyxetabase-4.0.0.dev62.dist-info/top_level.txt,sha256=0m5pDpBX-lM8QpPl7bTpTQAm4kgu2-nr-pcaEu4Tn_8,11
-pyxetabase-4.0.0.dev62.dist-info/RECORD,,
+pyxetabase-4.0.0.dev74.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+pyxetabase-4.0.0.dev74.dist-info/METADATA,sha256=u5_mUMi6ZXCYfvq9lKkllXvC4DbTSd3yjzOzRSX1Kz0,5540
+pyxetabase-4.0.0.dev74.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pyxetabase-4.0.0.dev74.dist-info/top_level.txt,sha256=0m5pDpBX-lM8QpPl7bTpTQAm4kgu2-nr-pcaEu4Tn_8,11
+pyxetabase-4.0.0.dev74.dist-info/RECORD,,