Backend REST API Consistency Restructure (#162)

* Manually rebased/merged discussions feature with the REST API consolidation effort to streamline the backend API service endpoints to be consistent

* Re-ordered the frontend methods to be together and consistent; fixed the frontend to include the anlaysis discussion tag

* Analysis Supporting Evidence endpoints refactored

* Refactor the annotation attachments endpoint to allow attachments to a dataset

.gitignore

@@ -63,7 +63,7 @@ backend/example_file_to_upload.txt
 # Pandoc JOSS artifacts
 media/
 *.jats
-*.pdf
+/*.pdf
 *.crossref
 
 # SSL/TLS Certificates

backend/.pylintrc

@@ -419,8 +419,7 @@ disable=useless-return,
         suppressed-message,
         useless-suppression,
         deprecated-pragma,
-        use-symbolic-message-instead,
-        duplicate-code
+        use-symbolic-message-instead
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

backend/src/enums.py

@@ -4,6 +4,15 @@
 from enum import Enum
 
 
+class SectionRowType(str, Enum):
+    """The types of data stored within a field in an Analysis' sections."""
+
+    TEXT = 'text'
+    IMAGE = 'image'
+    DOCUMENT = 'document'
+    LINK = 'link'
+
+
 class GenomicUnitType(str, Enum):
     """Enumeration of the different types of genomic units that can be analyzed"""
 

backend/src/main.py

@@ -23,6 +23,18 @@
         "name": "analysis",
         "description": "Analyses of cases with information such as target gene, variation, phenotyping, and more.",
     },
+    {
+        "name": "analysis sections",
+        "description": "Adds, updates, and removes content from an Analysis Section's fields within an analysis.",
+    },
+    {
+        "name": "analysis discussions",
+        "description": "Adds, updates, and removes discussion messages from an Analysis.",
+    },
+    {
+        "name": "analysis attachments",
+        "description": "Adds, updates, and removes attachments from an Analysis.",
+    },
     {
         "name": "annotation",
         "description":

backend/src/models/analysis.py

@@ -4,10 +4,10 @@
 """
 # pylint: disable=too-few-public-methods
 from datetime import date
-from multiprocessing import Event
+import json
 import re
 from typing import List, Optional
-from pydantic import BaseModel, computed_field
+from pydantic import BaseModel, computed_field, model_validator
 
 from .event import Event
 
@@ -29,6 +29,14 @@ class Section(BaseModel, frozen=True):
     attachment_field: Optional[str] = None
     content: List = []
 
+    @model_validator(mode='before')
+    @classmethod
+    def validate_to_json(cls, value):
+        """Allows FastAPI to valid and unpack the JSON of data into the model"""
+        if isinstance(value, str):
+            return cls(**json.loads(value))
+        return value
+
 
 class BaseAnalysis(BaseModel):
     """The share parts of an analysis and it's summary"""
@@ -107,6 +115,22 @@ def units_to_annotate(self):
 
         return units
 
+    def find_section_field_by_attachment_id(self, attachment_id):
+        """
+        Returns a tuple of the Section and field of section that the attachment is in, otherwise returns (None, None)
+        """
+
+        def attribute_type_in_field(attribute_key, field_value):
+            return attribute_key if attribute_key in field_value else ''
+
+        for section in self.sections:
+            for field in section.content:
+                for value in field['value']:
+                    for key in ['file_id', 'attachment_id']:
+                        if attribute_type_in_field(key, value) and value[key] == attachment_id:
+                            return (section, field)
+        return (None, None)
+
     def find_discussion_post(self, discussion_post_id):
         """
         Finds a specific discussion post in an analysis by the discussion post id otherwise returns none