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