Merge pull request #32 from C-Accel-CRIPT/develop

updates and Bug fix

.gitignore

@@ -137,8 +137,8 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# Custom
-config.yaml
-
 # IDE config folder
-.idea/
+.idea/
+
+# Local
+config.yaml

main.py

@@ -9,10 +9,10 @@
 import requests
 
 import ascii_art
-import parse
-import create
-from create import error_list
-import upload
+import src.parse as parse
+import src.create as create
+from src.create import error_list
+import src.upload as upload
 
 
 ###
@@ -204,8 +204,9 @@
 upload.upload(api, data, "Data")
 upload.upload(api, materials, "Material")
 upload.upload(api, processes, "Process")
+upload.add_sample_preparation_to_process(api, parsed_sheets["data"], data, processes)
 upload.upload(api, files, "File")
-upload.add_sample_preparation_to_process(parsed_sheets["data"], data, processes, api)
+
 
 ###
 # Finish

requirements.txt

@@ -1,5 +1,5 @@
-cript==0.4.1
+cript==0.4.7
 openpyxl==3.0.10
-pandas==1.4.3
+pandas==1.4.4
 PyYAML==6.0
 tqdm==4.64.0

parse.py → src/parse.py

@@ -24,6 +24,8 @@ def __init__(self, path, sheet_name, required_columns, unique_columns):
  self.df.dropna(how="all", inplace=True)
  self.columns = self.df.columns
 
+ # TODO should be tested last, once component functions are found to be working.
+ # Check against manually created parsed objects.
  def parse(self):
  """Parses a DataFrame conversion of an excel sheet and returns parsed information as a
  dictionary of dictionaries. Each dictionary within the main dictionary contains relevant cell
@@ -78,7 +80,7 @@ def _skip_column(self, key, value):
  value-any
  return-boolean"""
  # Check if col starts with '#'
- if key[0] == "#":
+ if key.startswith("#"):
  return True
 
  # Check if val empty
@@ -165,5 +167,5 @@ def _clean_key(self, raw_key):
  For example, *name -> name or [3]temperature-> temperature
  raw_key-string
  return-string"""
- raw_key.strip()
+ raw_key = raw_key.strip()
  return re.sub("\[.*\]", "", raw_key.strip("*"))

upload.py → src/upload.py

@@ -18,13 +18,16 @@ def upload(api, obj_dict, obj_type):
  unit="item",
  )
  for key, obj in obj_dict.items():
- api.save(obj, update_existing=True)
+ # Creates name for File object made from external source
+ if obj_type == "File" and obj.name is None:
+ obj.name = obj.source
+ api.save(obj, update_existing=True, max_level=0)
  pbar.update(1) # Increment progress bar
 
  pbar.close()
 
 
-def add_sample_preparation_to_process(parsed_data, data, processes, api):
+def add_sample_preparation_to_process(api, parsed_data, data, processes):
  """Adds Process Nodes to a Data nodes "sample_preparation" field if applicable and saves updated node.
  parsed_data-dict
  data-dict of CRIPT Data objects

tests/README.md

@@ -0,0 +1,5 @@
+# TESTING
+
+Download "testing_template_v0.xlsx" from cript google drive.
+Put it in the "tests" folder and make sure to use it as path
+variable when running unit tests.

tests/test_create.py

@@ -0,0 +1,72 @@
+import src.create as create
+from src.create import error_list
+import pytest
+
+"""
+TODO
+Will have to make related_objs(dict of dicts), cell_value(str), parsed_cell(dict).
+Test for succesful and exception part of the try and except statement.
+"""
+
+
+def test_get_relation():
+ pass
+
+
+"""
+TODO 
+for each create_ check that each if statement is going off fine. Will double as checking
+the create_object function since pretty much all of them end in calling create_object.
+"""
+
+
+def test_create_experiments():
+ pass
+
+
+def test_create_citations():
+ pass
+
+
+def test_create_data():
+ pass
+
+
+def test_create_materials():
+ pass
+
+
+def test_create_mixtures():
+ pass
+
+
+def test_create_processes():
+ pass
+
+
+def test_create_mixtures():
+ pass
+
+
+def test_create_prerequisites():
+ pass
+
+
+def test_create_ingredients():
+ pass
+
+
+def test_create_products():
+ pass
+
+
+def test_create_equipment():
+ pass
+
+
+def test_create_property():
+ pass
+
+
+def test_create_condition():
+ pass

tests/test_main.py

@@ -0,0 +1,8 @@
+import src.main as main
+import pytest
+
+"""
+TODO -wait until Brilant is done.
+Multiple upload tests, use different small excel sheets.
+Also have an upload with config empty and config filled out.
+"""