Merge pull request #292 from sartography/277-Document-pane

277 document pane

crc/api.yml

@@ -67,6 +67,37 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/User"
+  # /v1.0/document_directory/{study_id}
+  /document_directory/{study_id}:
+    parameters :
+      - name : study_id
+        required : true
+        in : path
+        description : The unique id of a study.
+        schema :
+          type : integer
+      - name : workflow_id
+        in : query
+        required : false
+        schema :
+          type : integer
+    get:
+      operationId: crc.api.file.get_document_directory
+      security:
+        - auth_admin: ['secret']
+      summary: Returns a directory of all files for study in a nested structure
+      tags:
+        - Document Categories
+      responses:
+        '200':
+          description: All IRB Categories defined in the file document.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/DocumentDirectory"
+
   # /v1.0/study
   /study:
     get:
@@ -565,6 +596,12 @@ paths:
         description: The unique key of a workflow task form field.  Make sure this matches a document in the irb_documents.xslx reference sheet.
         schema:
           type: string
+      - name: study_id
+        in: query
+        required: false
+        description: The study that the files are related to
+        schema:
+          type: integer
     get:
       operationId: crc.api.file.get_files
       summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
@@ -1429,6 +1466,29 @@ components:
           type: string
           x-nullable: true
           example: "27b-6-1212"
+    DocumentDirectory:
+      properties:
+        level:
+          type: string
+          x-nullable: true
+          example: "Ancillary Document"
+        description:
+          type: string
+          x-nullable: true
+          example: "Documents that are ancillary to the study"
+        file:
+          $ref: "#/components/schemas/File"
+          x-nullable: true
+        expanded:
+          type: boolean
+          example: False
+        filecount:
+          type: integer
+          example: 1
+        children:
+          type: array
+          items:
+            $ref: "#/components/schemas/File"
     DataStore:
       properties:
         id:

crc/api/file.py

@@ -6,24 +6,80 @@ from flask import send_file
 
 from crc import session
 from crc.api.common import ApiError
+from crc.models.api_models import DocumentDirectory, DocumentDirectorySchema
 from crc.models.file import FileSchema, FileModel, File, FileModelSchema, FileDataModel, FileType
 from crc.models.workflow import WorkflowSpecModel
 from crc.services.file_service import FileService
 
 
+def ensure_exists(output, categories, expanded):
+    """
+    This is a recursive function, it expects a list of
+    levels with a file object at the end (kinda like duck,duck,duck,goose)
+
+    for each level, it makes sure that level is already in the structure and if it is not
+    it will add it
+
+    function terminates upon getting an entry that is a file object ( or really anything but string)
+    """
+    current_item = categories[0]
+    found = False
+    if isinstance(current_item, str):
+        for item in output:
+            if item.level == current_item:
+                found = True
+                item.filecount = item.filecount + 1
+                item.expanded = expanded | item.expanded
+                ensure_exists(item.children, categories[1:], expanded)
+        if not found:
+            new_level = DocumentDirectory(level=current_item)
+            new_level.filecount = 1
+            new_level.expanded = expanded
+            output.append(new_level)
+            ensure_exists(new_level.children, categories[1:], expanded)
+    else:
+        new_level = DocumentDirectory(file=current_item)
+        new_level.expanded = expanded
+        output.append(new_level)
+
+
+def get_document_directory(study_id, workflow_id=None):
+    """
+    return a nested list of files arranged according to the category hirearchy
+    defined in the doc dictionary
+    """
+    output = []
+    doc_dict = FileService.get_doc_dictionary()
+    file_models = FileService.get_files_for_study(study_id=study_id)
+    files = (to_file_api(model) for model in file_models)
+    for file in files:
+        doc_code = doc_dict[file.irb_doc_code]
+        if workflow_id:
+            expand = file.workflow_id == int(workflow_id)
+        else:
+            expand = False
+        print(expand)
+        categories = [x for x in [doc_code['category1'],doc_code['category2'],doc_code['category3'],file] if x != '']
+        ensure_exists(output, categories, expanded=expand)
+    return DocumentDirectorySchema(many=True).dump(output)
+
+
 def to_file_api(file_model):
     """Converts a FileModel object to something we can return via the api"""
     return File.from_models(file_model, FileService.get_file_data(file_model.id),
                             FileService.get_doc_dictionary())
 
 
-def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None):
+def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None,study_id=None):
-    if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key]):
+    if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key,study_id]):
         raise ApiError('missing_parameter',
                        'Please specify either a workflow_spec_id or a '
                        'workflow_id with an optional form_field_key')
 
-    file_models = FileService.get_files(workflow_spec_id=workflow_spec_id,
+    if study_id is not None:
+        file_models = FileService.get_files_for_study(study_id=study_id)
+    else:
+        file_models = FileService.get_files(workflow_spec_id=workflow_spec_id,
                                         workflow_id=workflow_id,
                                         irb_doc_code=form_field_key)
 

crc/models/api_models.py

@@ -7,7 +7,7 @@ from marshmallow_enum import EnumField
 
 from crc import ma
 from crc.models.workflow import WorkflowStatus
-
+from crc.models.file import FileSchema
 
 class MultiInstanceType(enum.Enum):
     none = "none"
@@ -167,6 +167,27 @@ class NavigationItemSchema(ma.Schema):
         item.spec_type = spec_type
         return item
 
+class DocumentDirectorySchema(ma.Schema):
+    level = marshmallow.fields.String()
+    file = marshmallow.fields.Nested(FileSchema)
+    filecount = marshmallow.fields.Integer()
+    expanded = marshmallow.fields.Boolean()
+    children = marshmallow.fields.Nested("self",many=True)
+
+
+class DocumentDirectory(object):
+    def __init__(self, level=None, file=None, children=None):
+
+        self.level = level
+        self.file = file
+        self.expanded = False
+        self.filecount = 0
+        if children is None:
+            self.children = list()
+        else:
+            self.children=children
+
+
 class WorkflowApi(object):
     def __init__(self, id, status, next_task, navigation,
                  spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks,

crc/models/file.py

@@ -108,7 +108,7 @@ class File(object):
                                                        doc_dictionary[model.irb_doc_code]['category2'],
                                                        doc_dictionary[model.irb_doc_code]['category3']]))
             instance.description = doc_dictionary[model.irb_doc_code]['description']
-            instance.download_name = ".".join([instance.category, model.type.value])
+            instance.download_name = "/".join([instance.category, model.name])
         else:
             instance.category = ""
             instance.description = ""

crc/services/file_service.py

@@ -17,6 +17,21 @@ from crc.api.common import ApiError
 from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
 from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecDependencyFile
 from crc.services.cache_service import cache
+import re
+
+
+def camel_to_snake(camel):
+    """
+    make a camelcase from a snakecase
+    with a few things thrown in - we had a case where
+    we were parsing a spreadsheet and using the headings as keys in an object
+    one of the headings was "Who Uploads?"
+    """
+    camel = camel.strip()
+    camel = re.sub(' ', '', camel)
+    camel = re.sub('?', '', camel)
+    return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
+
 
 class FileService(object):
     """Provides consistent management and rules for storing, retrieving and processing files."""
@@ -25,10 +40,27 @@ class FileService(object):
 
     __doc_dictionary = None
 
+    @staticmethod
+    def verify_doc_dictionary(dd):
+        """
+        We are currently getting structured information from an XLS file, if someone accidentally
+        changes a header we will have problems later, so we will verify we have the headers we need
+        here
+        """
+        required_fields = ['category1','category2','category3','description']
+
+        # we only need to check the first item, as all of the keys should be the same
+        key = list(dd.keys())[0]
+        for field in required_fields:
+            if field not in dd[key].keys():
+                raise ApiError(code="Invalid document list %s"%FileService.DOCUMENT_LIST,
+                               message='Please check the headers in %s'%FileService.DOCUMENT_LIST)
+
     @staticmethod
     def get_doc_dictionary():
         if not FileService.__doc_dictionary:
             FileService.__doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
+        FileService.verify_doc_dictionary(FileService.__doc_dictionary)
         return FileService.__doc_dictionary
 
     @staticmethod

crc/services/workflow_processor.py

@@ -98,10 +98,6 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
 
 
 
-    @staticmethod
-    def camel_to_snake(camel):
-        camel = camel.strip()
-        return re.sub(r'(?<!^)(?=[A-Z])', '_', camel).lower()
 
 
 class MyCustomParser(BpmnDmnParser):

postgres/package-lock.json

@@ -1,3 +1,481 @@
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-  "lockfileVersion": 1
+  "requires": true,
+  "lockfileVersion": 1,
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+      "dev": true,
+      "optional": true,
+      "requires": {
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+      }
+    },
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 }

tests/study/test_study_api.py

@@ -97,7 +97,7 @@ class TestStudyApi(BaseTest):
         self.assertEqual(1, len(study.files))
         self.assertEqual("UVA Compliance/PRC Approval", study.files[0]["category"])
         self.assertEqual("Cancer Center's PRC Approval Form", study.files[0]["description"])
-        self.assertEqual("UVA Compliance/PRC Approval.png", study.files[0]["download_name"])
+        self.assertEqual("UVA Compliance/PRC Approval/anything.png", study.files[0]["download_name"])
 
         # TODO: WRITE A TEST FOR STUDY FILES
 

tests/test_document_directories.py

@@ -0,0 +1,41 @@
+import json
+from tests.base_test import BaseTest
+from crc.services.file_service import FileService
+
+
+
+
+
+class TestDocumentDirectories(BaseTest):
+
+    def test_directory_list(self):
+        self.load_example_data()
+        irb_code_1 = 'UVACompl_PRCAppr'
+        irb_code_2 = 'Study_App_Doc'
+
+        workflow = self.create_workflow('empty_workflow')
+        first_task = self.get_workflow_api(workflow).next_task
+        study_id = workflow.study_id
+
+        # Add a file
+        FileService.add_workflow_file(workflow_id=workflow.id,
+                                      name="something.png", content_type="text",
+                                      binary_data=b'1234', irb_doc_code=irb_code_1)
+        # Add second file
+        FileService.add_workflow_file(workflow_id=workflow.id,
+                                      name="anything.png", content_type="text",
+                                      binary_data=b'5678', irb_doc_code=irb_code_2)
+
+        # Get back the list of documents and their directories.
+        rv = self.app.get('/v1.0/document_directory/%i' % study_id, headers=self.logged_in_headers())
+        self.assert_success(rv)
+        json_data = json.loads(rv.get_data(as_text=True))
+        print(json_data)
+        self.assertEquals(2, len(json_data))
+        self.assertEquals('UVA Compliance', json_data[0]['level'])
+        self.assertEquals('PRC Approval', json_data[0]['children'][0]['level'])
+        self.assertEquals('something.png', json_data[0]['children'][0]['children'][0]['file']['name'])
+        self.assertEquals('Study', json_data[1]['level'])
+        self.assertEquals('Application', json_data[1]['children'][0]['level'])
+        self.assertEquals('Document', json_data[1]['children'][0]['children'][0]['level'])
+        self.assertEquals('anything.png',  json_data[1]['children'][0]['children'][0]['children'][0]['file']['name'])