Gonza10 v patch 1

README.md

@@ -1,3 +1,31 @@
 # Xperimental-data-convertor
 
 This is a utility to link excel2sbol and excel to flapjack converter, interlink the resulting data, and upload it to synbiohub and flapjack.
+
+## Plate-reader exports
+
+Create a Flapjack-compatible workbook from an XDC template and a BioTek-style
+CSV/TXT reader export. The template's `SBH_sampledesigns_collection` worksheet
+must map its sample-design names to SynBioHub SBOL object URIs.
+
+```python
+import os
+
+from xperimental_data_conv import create_flapjack_input
+
+create_flapjack_input(
+    "Align_TF_Study.xlsm",
+    "2025-07-02_Align-TF-Cytom-12-plasmids_growth-plate_1-1_Neo.txt",
+    "Flapjack_input.xlsx",
+    username=os.environ["SBH_USERNAME"],
+    password=os.environ["SBH_PASSWORD"],
+)
+```
+
+The output has `Data`, `Media`, `Strains`, `DNA`, and `Chemicals` worksheets.
+The `Data` worksheet retains the reader export; the other sheets are 96-well
+maps resolved from the SBOL graph. Media uses role `NCIT:C48164`, strain
+assemblies use role `NCIT:C14419`, chemicals use their functional-component
+definition and `Flapjack#concentration`, and plasmids become `DNA 1...N` maps.
+Use `token=os.environ["SBH_TOKEN"]` instead of username/password for token
+authentication.

requirements.txt

@@ -1,2 +1,4 @@
 excel2flapjack~=1.0.2
-excel2sbol~=1.0.24
+excel2sbol~=1.0.24
+sbol2>=1.4,<2
+openpyxl>=3.1,<4

setup.py

@@ -0,0 +1,17 @@
+from setuptools import find_packages, setup
+
+setup(name='xperimental-data-conv',
+      version='1.0.1b',
+      url='https://github.com/SynBioDex/Experimental-Data-Convertor',
+      license='BSD 3-clause',
+      maintainer='Gonzalo Vidal',
+      maintainer_email='Gonzalo.vidalpena@colorado.edu',
+      include_package_data=True,
+      description='Convert Excel resources into SBOL and Flapjack, uploads them to SynBioHub and Flapjack and connects them',
+      packages=find_packages(include=['xperimental_data_conv', 'xperimental_data_conv.*']),
+      long_description=open('README.md').read(),
+      install_requires=['excel2flapjack==1.0.8',
+                        'excel2sbol==1.0.29',
+                        'sbol2>=1.4,<2',
+                        'openpyxl>=3.1,<4'],
+      zip_safe=False)

tests/test_flapjack_export.py

@@ -0,0 +1,155 @@
+import tempfile
+import unittest
+from pathlib import Path
+
+from openpyxl import load_workbook
+
+from xperimental_data_conv import (
+    FlapjackPlateExporter,
+    SampleDesignMetadata,
+    SynBioHubSampleDesignResolver,
+    TemplateSample,
+)
+
+
+FIXTURES = Path(__file__).parent / "test_files"
+
+
+class FakeObject:
+    def __init__(
+        self,
+        display_id,
+        *,
+        roles=(),
+        properties=None,
+        modules=(),
+        functional_components=(),
+    ):
+        self.displayId = display_id
+        self.roles = roles
+        self.properties = properties or {}
+        self.modules = modules
+        self.functionalComponents = functional_components
+
+
+class FakeReference:
+    def __init__(self, definition, display_id):
+        self.definition = definition
+        self.displayId = display_id
+
+
+class FakeSynBioHubClient:
+    def __init__(self, objects):
+        self.objects = objects
+
+    def get_object(self, uri):
+        return self.objects[uri]
+
+
+class StaticResolver:
+    def __init__(self):
+        self.resolved_uris = []
+
+    def resolve(self, sample):
+        self.resolved_uris.append(sample.sample_design_uri)
+        return SampleDesignMetadata(
+            medium="m9",
+            strain="Ecolisc2",
+            plasmids=("pIJAI477", "pIJAI478"),
+            chemicals={"Arabinose": 0.004},
+        )
+
+
+class TestSynBioHubSampleDesignResolver(unittest.TestCase):
+    def test_resolves_sbol_modules_by_roles_and_extended_properties(self):
+        sample_uri = "https://example.org/sample/1"
+        medium_uri = "https://example.org/m9/1"
+        chemical_module_uri = "https://example.org/arabinose_004/1"
+        chemical_uri = "https://example.org/arabinose/1"
+        strain_uri = "https://example.org/strain/1"
+        plasmid_uris = ["https://example.org/p{0}/1".format(index) for index in range(1, 5)]
+
+        objects = {
+            sample_uri: FakeObject(
+                "sample_design",
+                modules=(
+                    FakeReference(medium_uri, "m9"),
+                    FakeReference(chemical_module_uri, "arabinose_004"),
+                    FakeReference(strain_uri, "Ecolisc2"),
+                ),
+            ),
+            medium_uri: FakeObject(
+                "m9", roles=("http://identifiers.org/ncit/NCIT:C48164",)
+            ),
+            chemical_module_uri: FakeObject(
+                "arabinose_004",
+                properties={
+                    "https://wiki.synbiohub.org/wiki/Terms/Flapjack#concentration": [
+                        "0.004"
+                    ]
+                },
+                functional_components=(FakeReference(chemical_uri, "Arabinose"),),
+            ),
+            chemical_uri: FakeObject("Arabinose"),
+            strain_uri: FakeObject(
+                "Ecolisc2",
+                roles=("https://identifiers.org/obo/ncit:C14419",),
+                functional_components=tuple(
+                    FakeReference(uri, "p{0}".format(index))
+                    for index, uri in enumerate(plasmid_uris, start=1)
+                ),
+            ),
+        }
+        objects.update(
+            {
+                uri: FakeObject("pIJAI{0}".format(476 + index))
+                for index, uri in enumerate(plasmid_uris, start=1)
+            }
+        )
+
+        resolver = SynBioHubSampleDesignResolver(FakeSynBioHubClient(objects))
+        metadata = resolver.resolve(
+            TemplateSample("sample1", "A", 1, "sample_design", sample_uri)
+        )
+
+        self.assertEqual("m9", metadata.medium)
+        self.assertEqual("Ecolisc2", metadata.strain)
+        self.assertEqual(
+            ("pIJAI477", "pIJAI478", "pIJAI479", "pIJAI480"),
+            metadata.plasmids,
+        )
+        self.assertEqual({"Arabinose": 0.004}, metadata.chemicals)
+
+
+class TestFlapjackPlateExporter(unittest.TestCase):
+    def test_creates_flapjack_workbook_from_align_tf_files(self):
+        with tempfile.TemporaryDirectory() as temporary_directory:
+            output = Path(temporary_directory) / "flapjack_input.xlsx"
+            resolver = StaticResolver()
+            result = FlapjackPlateExporter(
+                FIXTURES / "Align_TF_Study.xlsm", resolver
+            ).export(
+                FIXTURES / "2025-07-02_Align-TF-Cytom-12-plasmids_growth-plate_1-1_Neo.txt",
+                output,
+            )
+
+            self.assertEqual(output, result)
+            self.assertTrue(resolver.resolved_uris)
+            workbook = load_workbook(output, data_only=True, read_only=True)
+            try:
+                self.assertEqual(
+                    ["Data", "Media", "Strains", "DNA", "Chemicals"],
+                    workbook.sheetnames,
+                )
+                self.assertEqual("Software Version", workbook["Data"]["A2"].value)
+                self.assertEqual("3.11.19", workbook["Data"]["B2"].value)
+                self.assertEqual("m9", workbook["Media"]["B2"].value)
+                self.assertEqual("Ecolisc2", workbook["Strains"]["B2"].value)
+                self.assertEqual("DNA 1", workbook["DNA"]["A1"].value)
+                self.assertEqual("pIJAI477", workbook["DNA"]["B2"].value)
+                self.assertEqual("DNA 2", workbook["DNA"]["A11"].value)
+                self.assertEqual("pIJAI478", workbook["DNA"]["B12"].value)
+                self.assertEqual("Arabinose", workbook["Chemicals"]["A1"].value)
+                self.assertEqual(0.004, workbook["Chemicals"]["B2"].value)
+            finally:
+                workbook.close()

tests/test_xdc.py

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+from xperimental_data_conv.main import XDC
+import unittest
+import os
+
+
+fj_url = "charmmefj.synbiohub.org"
+fj_user = ""
+fj_pass = ""
+
+sbh_url = "https://synbiohub.org"
+sbh_user = "test@test.test"
+sbh_pass = "test123"
+sbh_collec = "XDC_package_test"
+
+test_file_path ='../test_files'
+excel_path = os.path.join(test_file_path, 'Medias.xlsm')
+
+homespace = 'https://synbiohub.org/synbiotest'
+
+fj_overwrite = False
+sbh_overwrite=False
+
+xdc = XDC(input_excel_path = excel_path,
+            fj_url = fj_url,
+            fj_user = fj_user, 
+            fj_pass = fj_pass, 
+            sbh_url = sbh_url, 
+            sbh_user = sbh_user, 
+            sbh_pass = sbh_pass, 
+            sbh_collection = sbh_collec, 
+            sbh_collection_description = 'XDC package test collection',
+            sbh_overwrite = sbh_overwrite, 
+            fj_overwrite = fj_overwrite, 
+            homespace = homespace,
+            fj_token = None, 
+            sbh_token = None)
+
+class Test_XDC(unittest.TestCase):
+    def test_initialize(self):
+        xdc.initialize()
+

xperimental-data-conv/__init__.py

@@ -0,0 +1 @@
+#no shared content