Merge pull request #2 from smaht-dac/naming_objects

.

pipeline_utils/__main__.py

@@ -58,6 +58,7 @@ def main(args=None):
     pipeline_deploy_parser.add_argument('--post-software', action='store_true', help='POST|PATCH Software objects')
     pipeline_deploy_parser.add_argument('--post-file-format', action='store_true', help='POST|PATCH FileFormat objects')
     pipeline_deploy_parser.add_argument('--post-file-reference', action='store_true', help='POST|PATCH ReferenceFile objects')
+    pipeline_deploy_parser.add_argument('--post-reference-genome', action='store_true', help='POST|PATCH ReferenceGenome objects')
     pipeline_deploy_parser.add_argument('--post-workflow', action='store_true', help='POST|PATCH Workflow objects')
     pipeline_deploy_parser.add_argument('--post-metaworkflow', action='store_true', help='POST|PATCH MetaWorkflow objects')
     pipeline_deploy_parser.add_argument('--post-wfl', action='store_true', help='Upload Workflow Description files (.cwl, .wdl)')

pipeline_utils/lib/yaml_parser.py

@@ -23,6 +23,7 @@
 from pipeline_utils.schemas.yaml_software import yaml_software_schema
 from pipeline_utils.schemas.yaml_reference_file import yaml_reference_file_schema
 from pipeline_utils.schemas.yaml_file_format import yaml_file_format_schema
+from pipeline_utils.schemas.yaml_reference_genome import yaml_reference_genome_schema
 
 
 ###############################################################
@@ -118,8 +119,11 @@ class YAMLTemplate(object):
     METAWORKFLOW_TYPE_SCHEMA = 'MetaWorkflow'
     FILEFORMAT_TYPE_SCHEMA = 'FileFormat'
     REFERENCEFILE_TYPE_SCHEMA = 'ReferenceFile'
+    REFERENCEGENOME_TYPE_SCHEMA = 'ReferenceGenome'
     SOFTWARE_TYPE_SCHEMA = 'Software'
     VARIANT_TYPE_SCHEMA = "variant_type"
+    CODE_SCHEMA = 'code'
+    IDENTIFIER_SCHEMA = 'identifier'
 
     def __init__(self, data, schema):
         """Constructor method.
@@ -145,17 +149,23 @@ def _clean_newline(self, line):
             line = line.replace('|', '')
         return line
 
-    def _link_title(self, name, version):
+    def _link_title(self, name, version=None):
         """Helper to create a "title" field.
         """
         title = getattr(self, self.TITLE_SCHEMA, None)
         if title:
-            if version in title:
-                return title
+            if version:
+                if version in title:
+                    return title
+                else:
+                    return f'{title} [{version}]'
             else:
-                return f'{title} [{version}]'
+                return title
         else:
-            return f'{name.replace("_", " ")} [{version}]'
+            if version:
+                return f'{name.replace("_", " ")} [{version}]'
+            else:
+                return f'{name.replace("_", " ")}'
 
     def _string_consortia(self, consortia):
         """Helper to create a string from "consortia" field.
@@ -549,7 +559,7 @@ def to_json(
         if getattr(self, self.SOURCE_URL_SCHEMA, None):
             sftwr_json[self.SOURCE_URL_SCHEMA] = self.source_url
 
-        sftwr_json[self.TITLE_SCHEMA] = self._link_title(self.name, version)
+        sftwr_json[self.TITLE_SCHEMA] = self._link_title(self.name)
         sftwr_json[self.ALIASES_SCHEMA] = [f'{self._string_consortia(consortia)}:{self.SOFTWARE_TYPE_SCHEMA}-{self.name}_{version}']
 
         # uuid, accession if specified
@@ -562,6 +572,10 @@ def to_json(
         if getattr(self, self.LICENSE_SCHEMA, None):
             sftwr_json[self.LICENSE_SCHEMA] = self.license
 
+        # code
+        if getattr(self, self.CODE_SCHEMA, None):
+            sftwr_json[self.CODE_SCHEMA] = self.code
+
         return sftwr_json
 
 
@@ -638,11 +652,10 @@ class YAMLFileFormat(YAMLTemplate):
     """
 
     # schema constants
-    IDENTIFIER_SCHEMA = 'identifier'
     STANDARD_FILE_EXTENSION_SCHEMA = 'standard_file_extension'
-    # VALID_ITEM_TYPES_SCHEMA = 'valid_item_types'
+    VALID_ITEM_TYPES_SCHEMA = 'valid_item_types'
     EXTRA_FILE_FORMATS_SCHEMA = 'extra_file_formats'
-    # FILE_TYPES_SCHEMA = 'file_types'
+    FILE_TYPES_SCHEMA = 'file_types'
 
     def __init__(self, data):
         """Constructor method.
@@ -672,7 +685,7 @@ def to_json(
         frmt_json[self.CONSORTIA_SCHEMA] = consortia
         frmt_json[self.DESCRIPTION_SCHEMA] = self.description
         frmt_json[self.STANDARD_FILE_EXTENSION_SCHEMA] = self.extension
-        # frmt_json[self.VALID_ITEM_TYPES_SCHEMA] = getattr(self, self.FILE_TYPES_SCHEMA, ['ReferenceFile', 'FileProcessed'])
+        frmt_json[self.VALID_ITEM_TYPES_SCHEMA] = getattr(self, self.FILE_TYPES_SCHEMA, ['ReferenceFile', 'OutputFile'])
         # check for secondary formats
         if getattr(self, self.SECONDARY_FORMATS_SCHEMA, None):
             frmt_json[self.EXTRA_FILE_FORMATS_SCHEMA] = getattr(self, self.SECONDARY_FORMATS_SCHEMA)
@@ -685,3 +698,52 @@ def to_json(
             frmt_json[self.ACCESSION_SCHEMA] = self.accession
 
         return frmt_json
+
+###############################################################
+#   YAMLReferenceGenome, YAML ReferenceGenome
+###############################################################
+class YAMLReferenceGenome(YAMLTemplate):
+    """Class to work with YAML documents representing ReferenceGenome objects.
+    """
+
+    def __init__(self, data):
+        """Constructor method.
+        """
+        super().__init__(data, yaml_reference_genome_schema)
+        # validate data with schema
+        self._validate()
+        # load attributes
+        for key, val in data.items():
+            setattr(self, key, val)
+
+    def to_json(
+               self,
+               submission_centers, # alias list
+               consortia # alias list
+               ):
+        """Function to build the corresponding object in JSON format.
+        """
+        gen_json = {}
+
+        # common metadata
+        gen_json[self.IDENTIFIER_SCHEMA] = self.name
+        gen_json[self.ALIASES_SCHEMA] = [f'{self._string_consortia(consortia)}:{self.REFERENCEGENOME_TYPE_SCHEMA}-{self.name}_{self.version}']
+        gen_json[self.SUBMISSION_CENTERS_SCHEMA] = submission_centers
+        gen_json[self.CONSORTIA_SCHEMA] = consortia
+        gen_json[self.TITLE_SCHEMA] = self._link_title(self.name, self.version)
+        gen_json[self.CODE_SCHEMA] = self.code
+
+        # uuid, accession if specified
+        if getattr(self, self.UUID_SCHEMA, None):
+            gen_json[self.UUID_SCHEMA] = self.uuid
+        if getattr(self, self.ACCESSION_SCHEMA, None):
+            gen_json[self.ACCESSION_SCHEMA] = self.accession
+
+        # check linked files
+        if getattr(self, self.FILES_SCHEMA, None):
+            gen_json[self.FILES_SCHEMA] = []
+            for file in self.files:
+                gen_json[self.FILES_SCHEMA].append(
+                    f'{self._string_consortia(consortia)}:{self.REFERENCEFILE_TYPE_SCHEMA}-{file.replace("@", "_")}')
+
+        return gen_json

pipeline_utils/pipeline_deploy.py

@@ -76,6 +76,7 @@ def __init__(self, args, repo, version='VERSION', pipeline='PIPELINE'):
             'Software': yaml_parser.YAMLSoftware,
             'FileFormat': yaml_parser.YAMLFileFormat,
             'ReferenceFile': yaml_parser.YAMLReferenceFile,
+            'ReferenceGenome': yaml_parser.YAMLReferenceGenome,
             'Workflow': yaml_parser.YAMLWorkflow,
             'MetaWorkflow': yaml_parser.YAMLMetaWorkflow
         }
@@ -84,10 +85,12 @@ def __init__(self, args, repo, version='VERSION', pipeline='PIPELINE'):
             'Software': 'portal_objects/software.yaml',
             'FileFormat': 'portal_objects/file_format.yaml',
             'ReferenceFile': 'portal_objects/file_reference.yaml',
+            'ReferenceGenome': 'portal_objects/reference_genome.yaml',
             # .yml files
             'Software_yml': 'portal_objects/software.yml',
             'FileFormat_yml': 'portal_objects/file_format.yml',
             'ReferenceFile_yml': 'portal_objects/file_reference.yml',
+            'ReferenceGenome_yml': 'portal_objects/reference_genome.yml',
             # folders
             'Workflow': 'portal_objects/workflows',
             'MetaWorkflow': 'portal_objects/metaworkflows',
@@ -206,7 +209,7 @@ def _yaml_to_json(self, data_yaml, YAMLClass, **kwargs):
 
     def _post_patch_file(self, type):
         """
-            'Software', 'FileFormat', 'ReferenceFile'
+            'Software', 'FileFormat', 'ReferenceFile', 'ReferenceGenome'
         """
         logger.info(f'@ {type}...')
 
@@ -414,6 +417,10 @@ def run_post_patch(self):
         if self.post_file_reference:
             self._post_patch_file('ReferenceFile')
 
+        # ReferenceGenome
+        if self.post_reference_genome:
+            self._post_patch_file('ReferenceGenome')
+
         # Workflow
         if self.post_workflow:
             self._post_patch_folder('Workflow')

pipeline_utils/schemas/yaml_file_format.py

@@ -20,14 +20,14 @@
             schema.DESCRIPTION: 'Extension of the FileFormat',
             schema.TYPE: schema.STRING
         },
-        # 'file_types': {
-        #     schema.DESCRIPTION: 'File types that can use the FileFormat',
-        #     schema.TYPE: schema.ARRAY,
-        #     schema.ITEMS: {
-        #         schema.TYPE: schema.STRING,
-        #         schema.PATTERN: 'ReferenceFile|FileProcessed|FileSubmitted|FileFastq'
-        #     }
-        # },
+        'file_types': {
+            schema.DESCRIPTION: 'File types that can use the FileFormat',
+            schema.TYPE: schema.ARRAY,
+            schema.ITEMS: {
+                schema.TYPE: schema.STRING,
+                schema.PATTERN: 'ReferenceFile|OutputFile|AlignedReads|UnalignedReads|VariantCalls'
+            }
+        },
         'status': {
             schema.TYPE: schema.STRING
         },

pipeline_utils/schemas/yaml_reference_genome.py

@@ -0,0 +1,32 @@
+from pipeline_utils.schemas import schema
+
+yaml_reference_genome_schema = {
+    ## Schema #########################
+    schema.SCHEMA: 'https://json-schema.org/draft/2020-12/schema',
+    schema.ID: '/schemas/YAMLReferenceGenome',
+    schema.TITLE: 'YAMLReferenceGenome',
+    schema.DESCRIPTION: 'Schema to validate a YAML description of a ReferenceGenome',
+    schema.TYPE: schema.OBJECT,
+    schema.PROPERTIES: {
+        'name': {
+            schema.DESCRIPTION: 'Name of the ReferenceGenome',
+            schema.TYPE: schema.STRING
+        },
+        'version': {
+            schema.DESCRIPTION: 'Version of the ReferenceGenome',
+            schema.TYPE: schema.STRING
+        },
+        'code': {
+            schema.DESCRIPTION: 'Code for the ReferenceGenome',
+            schema.TYPE: schema.STRING
+        },
+        'files': {
+            schema.DESCRIPTION: 'Associated reference files',
+            schema.TYPE: schema.ARRAY,
+            schema.ITEMS: {
+                schema.TYPE: schema.STRING
+            }
+        }
+    },
+    schema.REQUIRED: ['name', 'version', 'code']
+}

tests/repo_correct/portal_objects/reference_genome.yaml

@@ -0,0 +1,12 @@
+################################################################
+# GRCh38 Genome Reference
+################################################################
+name: GRCh38
+version: GCA_000001405.15
+files:
+  - complete-reference-fasta-no-alt@GCA_000001405.15_GRCh38_no_decoy
+  - complete-reference-bwt-no-alt@GCA_000001405.15_GRCh38_no_decoy
+# Required for displaying in the file name
+code: GRCh38
+# This is required to sync with a previously generated object
+uuid: e89937e6-80d3-4605-8dea-4a74c7981a9f

tests/repo_correct/portal_objects/software.yaml

@@ -7,6 +7,7 @@ source_url: 'http:/broad'
 description: gatk software package
 category:
   - Aligner
+code: pippo
 
 ---
 
@@ -19,3 +20,14 @@ category:
 commit: 324ePT
 uuid: efdac7ec-7da3-4f23-9056-7a04abbc5e8b
 accession: GAPMKF1LL29K
+
+---
+
+# Sentieon
+name: Sentieon_BWA-MEM
+code: sentieon_bwamem
+version: '202308.01'
+source_url: https://www.sentieon.com
+category:
+  - Alignment
+uuid: b42e44e5-a829-4687-aeff-65cd040b1528

tests/test_yaml_file_format.py

@@ -20,8 +20,8 @@ def test_file_format():
                 "submission_centers": ["hms-dbmi"],
                 "consortia": ["cgap-core"],
                 "standard_file_extension": "bam",
-                "status": "obsolete"
-                # "valid_item_types": ["ReferenceFile", "FileProcessed"]
+                "status": "obsolete",
+                "valid_item_types": ["ReferenceFile", "OutputFile"]
             },
             {
                 "accession": 'GAPFIXRDPDK1',
@@ -32,7 +32,7 @@ def test_file_format():
                 "consortia": ["cgap-core"],
                 "standard_file_extension": "bam.bai",
                 "status": "released",
-                # "valid_item_types": ["ReferenceFile", "FileProcessed"],
+                "valid_item_types": ["ReferenceFile", "OutputFile"],
                 "uuid": '1936f246-22e1-45dc-bb5c-9cfd55537fe9'
             }
         ]

tests/test_yaml_reference_genome.py

@@ -0,0 +1,36 @@
+#################################################################
+#   Libraries
+#################################################################
+import sys, os
+import pytest
+from pipeline_utils.lib import yaml_parser
+
+#################################################################
+#   Tests
+#################################################################
+def test_software():
+    """
+    """
+    res = [
+        {"code": "GRCh38",
+         "title": "GRCh38 [GCA_000001405.15]",
+         "consortia": ["cgap-core"],
+         "identifier": "GRCh38",
+         "submission_centers": ["hms-dbmi"],
+         "uuid": "e89937e6-80d3-4605-8dea-4a74c7981a9f",
+         "files": [
+            "cgap-core:ReferenceFile-complete-reference-fasta-no-alt_GCA_000001405.15_GRCh38_no_decoy",
+            "cgap-core:ReferenceFile-complete-reference-bwt-no-alt_GCA_000001405.15_GRCh38_no_decoy"
+         ],
+         "aliases": ["cgap-core:ReferenceGenome-GRCh38_GCA_000001405.15"]}
+
+        ]
+
+    for i, d in enumerate(yaml_parser.load_yaml('tests/repo_correct/portal_objects/reference_genome.yaml')):
+        # creating JSON object
+        d_ = yaml_parser.YAMLReferenceGenome(d).to_json(
+                            submission_centers=["hms-dbmi"],
+                            consortia=["cgap-core"]
+                            )
+        # check
+        assert d_ == res[i]

tests/test_yaml_software.py

@@ -21,7 +21,8 @@ def test_software():
                 "source_url": "http:/broad",
                 "title": "gatk 4.1.2",
                 "version": "4.1.2",
-                "category": ["Aligner"]
+                "category": ["Aligner"],
+                "code": "pippo"
             },
             {
                 "accession": "GAPMKF1LL29K",
@@ -30,10 +31,23 @@ def test_software():
                 "submission_centers": ["hms-dbmi"],
                 "name": "picard",
                 "consortia": ["cgap-core"],
-                "title": "picard [324ePT]",
+                "title": "picard",
                 "uuid": "efdac7ec-7da3-4f23-9056-7a04abbc5e8b",
                 "category": ["Variant Caller"]
+            },
+            {
+                "aliases": ["cgap-core:Software-Sentieon_BWA-MEM_202308.01"],
+                "version": "202308.01",
+                "submission_centers": ["hms-dbmi"],
+                "name": "Sentieon_BWA-MEM",
+                "consortia": ["cgap-core"],
+                "title": "Sentieon BWA-MEM",
+                "uuid": "b42e44e5-a829-4687-aeff-65cd040b1528",
+                "category": ["Alignment"],
+                "code": "sentieon_bwamem",
+                "source_url": "https://www.sentieon.com",
             }
+
         ]
 
     for i, d in enumerate(yaml_parser.load_yaml('tests/repo_correct/portal_objects/software.yaml')):