Merge 143dbac into c7a3f81

pyproject.toml

@@ -15,7 +15,7 @@ packages = [
 python = ">=3.6.1,<3.10"
 python-magic = ">=0.4.12"
 attrs = ">=21.4"
-xlrd3 = "1.1.0"
+openpyxl = "^3.0.9"
 xlwt = "1.3.0"
 dcicutils = ">=3.11.0"
 # awscli is not directly imported but is required for aws cp operation

tests/conftest.py

@@ -1,6 +1,8 @@
 # flake8: noqa
 import pytest
 from wranglertools.get_field_info import FDN_Key, FDN_Connection
+from pathlib import Path
+import openpyxl
 
 
 class MockedResponse(object):
@@ -365,6 +367,18 @@ def embed_properties():
             }
 
 
+@pytest.fixture
+def workbooks():
+    workbooks = {}
+    WORKBOOK_DIR = './tests/data_files/workbooks/'
+    filenames = Path(WORKBOOK_DIR).glob('*.xlsx')
+    for fn in filenames:
+        if fn.name.startswith('~'):
+            continue
+        workbooks[fn.name] = openpyxl.load_workbook(fn)
+    return workbooks
+
+
 @pytest.fixture
 def file_metadata():
     from collections import OrderedDict
@@ -414,6 +428,15 @@ def returned_award_schema():
     return MockedResponse(data, 200)
 
 
+@pytest.fixture
+def returned_bcc_schema():
+    """ trimmed schema with examples of various permutations of properties including descriptions, comments, enums, suggested enums
+        and also a calcprop and schema version that have import-item permission for testing sheet generation
+    """
+    data = {"title": "Cell culture details for biosample preparation","id": "/profiles/biosample_cell_culture.json","$schema": "http://json-schema.org/draft-04/schema#","type": "object","required": ["culture_start_date", "award", "lab"],"identifyingProperties": ["uuid", "aliases"],"additionalProperties": False,"mixinProperties": [{ "$ref": "mixins.json#/schema_version" },],"mixinFacets" : [{ "$ref": "mixins.json#/facets_common" }],"properties": {"description": {"title": "Description","description": "A short description of the cell culture procedure - eg. Details on culturing a preparation of K562 cells","type": "string","lookup": 20,"formInput": "textarea"},"culture_start_date": {"title": "Culture start date","description": "YYYY-MM-DD format date for most recently thawed cell culture.","comment": "Date can be submitted in as YYYY-MM-DD or YYYY-MM-DDTHH:MM:SSTZD","type": "string","lookup": 40,"anyOf": [{"format": "date-time"},{"format": "date"}]},"culture_harvest_date": {"title": "Culture harvest date","type": "string","lookup": 50,"anyOf": [{"format": "date-time"},{"format": "date"}]},"culture_duration":{"title":"Total Days in Culture","description":"Total number of culturing days since receiving original vial","type":"number","lookup": 60},"passage_number": {"title": "Passage Number","type": "integer","lookup": 70},"protocols_additional": {"title": "Additional Protocols used in Cell Culture","description": "Protocols including additional culture manipulations such as stem cell differentiation or cell cycle synchronization.","type": "array","lookup": 150,"items": {"title": "Culture Protocol","type": "string","linkTo": "Protocol"}},"in_vitro_differentiated": {"title": "Differentiated in vitro","description": "Relevant for pluripotent and stem cell lines - set to Yes if cells have undergone in vitro differentiation","type": "string","enum": ["Yes", "No"],"default": "No","lookup": 98},"tissue": {"title": "Differentiation Tissue/Cell Type","description": "The resulting tissue or cell type for cells that have undergone differentiation.","type": "string","linkTo": "OntologyTerm","lookup": 99,"suggested_enum": ["cardiac muscle myoblast","cardiac muscle cell"]},"synchronization_stage": {"title": "Synchronization Stage","description": "If a culture is synchronized the cell cycle stage from which the biosample used in an experiment is prepared","type": "string","lookup": 120,"suggested_enum": ["non synchronized","G1",],"ignored_enum": ["3h after mitotic shakeoff"]},"@type":{"calculatedProperty":True,"title":"Type","type":"array","items":{"type":"string"}}, "schema_version":{"requestMethod":[],"type":"string","default":"1","pattern":"^\\d+(\\.\\d+)*$","title":"Schema Version", "permission":"import_items"}}}
+    return MockedResponse(data, 200)
+
+
 @pytest.fixture
 def returned_vendor_schema():
     data = {"title":"Vendor","description":"Schema for submitting an originating lab or vendor.","id":"/profiles/vendor.json","$schema":"http://json-schema.org/draft-04/schema#","type":"object","required":["title"],"identifyingProperties":["uuid","name"],"additionalProperties":False,"mixinProperties":[{"$ref":"mixins.json#/schema_version"},{"$ref":"mixins.json#/uuid"},{"$ref":"mixins.json#/status"},{"$ref":"mixins.json#/notes"},{"$ref":"mixins.json#/submitted"},{"$ref":"mixins.json#/attribution"},{"$ref":"mixins.json#/aliases"}],"properties":{"aliases":{"type":"array","default":[],"uniqueItems":True,"title":"Lab aliases","description":"Lab specific identifiers to reference an object.","items":{"comment":"Current convention is colon separated lab name and lab identifier. (e.g. john-doe:42).","pattern":"^\\S+:\\S+","uniqueKey":"alias","title":"Lab alias","description":"A lab specific identifier to reference an object.","type":"string"}},"award":{"comment":"See award.json for list of available identifiers.","title":"Grant","description":"Grant associated with the submission.","linkTo":"Award","type":"string"},"lab":{"description":"Lab associated with the submission.","linkSubmitsFor":True,"title":"Lab","comment":"See lab.json for list of available identifiers.","linkTo":"Lab","type":"string"},"date_created":{"anyOf":[{"format":"date-time"},{"format":"date"}],"serverDefault":"now","readonly":True,"type":"string","comment":"Do not submit, value is assigned by the server. The date the object is created.","title":"Date created","rdfs:subPropertyOf":"dc:created","permission":"import_items"},"submitted_by":{"serverDefault":"userid","readonly":True,"type":"string","comment":"Do not submit, value is assigned by the server. The user that created the object.","linkTo":"User","title":"Submitted by","rdfs:subPropertyOf":"dc:creator","permission":"import_items"},"notes":{"elasticsearch_mapping_index_type":{"title":"Field mapping index type","description":"Defines one of three types of indexing available","type":"string","enum":["analyzed","not_analyzed","no"],"default":"analyzed"},"description":"DCIC internal notes.","type":"string","title":"Notes"},"status":{"readonly":True,"default":"in review by lab","title":"Status","type":"string","enum":["released","current","revoked","deleted","replaced","in review by lab","in review by project","released to project"],"permission":"import_items"},"uuid":{"serverDefault":"uuid4","readonly":True,"requestMethod":"POST","type":"string","title":"UUID","format":"uuid","permission":"import_items"},"schema_version":{"default":"1","pattern":"^\\d+(\\.\\d+)*$","requestMethod":[],"title":"Schema Version","comment":"Do not submit, value is assigned by the server. The version of the JSON schema that the server uses to validate the object. Schema version indicates generation of schema used to save version to to enable upgrade steps to work. Individual schemas should set the default.","type":"string"},"description":{"title":"Description","description":"A plain text description of the source.","type":"string","default":""},"title":{"title":"Name","description":"The complete name of the originating lab or vendor. ","type":"string"},"name":{"uniqueKey":True,"type":"string","description":"DON'T SUBMIT, auto-generated, use for referencing vendors in other sheets.","pattern":"^[a-z0-9\\-]+$"},"url":{"title":"URL","description":"An external resource with additional information about the source.","type":"string","format":"uri"},"@type":{"calculatedProperty":True,"title":"Type","type":"array","items":{"type":"string"}},"@id":{"calculatedProperty":True,"title":"ID","type":"string"}},"boost_values":{"name":1,"title":1},"@type":["JSONSchema"]}