update to make sbol2 data source more robust

excel2sbol/excel2sbol/temp.py

@@ -5,9 +5,9 @@
 print(cwd)
 
 file_path_in = os.path.join(cwd, "excel2sbol", 'tests', 'test_files',
-                            'SBOL3_simple_library4.xlsx')
+                            'SBOL2_parts_project.xlsx')
 file_path_out = os.path.join(cwd, "excel2sbol", 'tests', 'test_files',
-                             'SBOL3_simple_library4.nt')
+                             'SBOL2_parts_project.xml')
 
 conv.converter(file_path_in, file_path_out)
 # conv.converter(file_path_in, file_path_out, sbol_version=2,

excel2sbol/tests/test_files/SBOL2_parts_project.xml

@@ -0,0 +1,70 @@
+<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">
+  <sbol:ComponentDefinition rdf:about="http://examples.org/mKate2__u38__BS_u40_Pe_u41_/1">
+    <prov:wasDerivedFrom rdf:resource="https://www.addgene.org/105210/"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/mKate2__u38__BS_u40_Pe_u41_"/>
+    <dcterms:description>coding sequence for module 1</dcterms:description>
+    <sbol:displayId>mKate2__u38__BS_u40_Pe_u41_</sbol:displayId>
+    <sbol:sequence rdf:resource="http://examples.org/mKate2__u38__BS_u40_Pe_u41__sequence/1"/>
+    <sbol:version>1</sbol:version>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://examples.org/SSX1/1">
+    <sbol:sequence rdf:resource="http://examples.org/SSX1_sequence/1"/>
+    <prov:wasDerivedFrom rdf:resource="https://www.addgene.org/105210/"/>
+    <dcterms:description>also known as P1 promoter</dcterms:description>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:displayId>SSX1</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/SSX1"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://examples.org/ECFP__u38__BS_u40_B_u41_/1">
+    <sbol:version>1</sbol:version>
+    <sbol:displayId>ECFP__u38__BS_u40_B_u41_</sbol:displayId>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/ECFP__u38__BS_u40_B_u41_"/>
+    <prov:wasDerivedFrom rdf:resource="https://www.addgene.org/105203/"/>
+    <dcterms:description>coding sequence for module 2</dcterms:description>
+    <sbol:sequence rdf:resource="http://examples.org/ECFP__u38__BS_u40_B_u41__sequence/1"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://examples.org/MAFK/1">
+    <sbol:displayId>MAFK</sbol:displayId>
+    <prov:wasDerivedFrom rdf:resource="https://www.addgene.org/105203/"/>
+    <sbol:sequence rdf:resource="http://examples.org/MAFK_sequence/1"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <dcterms:description>also known as P2 promoter</dcterms:description>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/MAFK"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:Sequence rdf:about="http://examples.org/mKate2__u38__BS_u40_Pe_u41__sequence/1">
+    <sbol:persistentIdentity rdf:resource="http://examples.org/mKate2__u38__BS_u40_Pe_u41__sequence"/>
+    <sbol:displayId>mKate2__u38__BS_u40_Pe_u41__sequence</sbol:displayId>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:elements>atggtgtctaagggcgaagagctgattaaggagaacatgcacatgaagctgtacatggagggcaccgtgaacaaccaccacttcaagtgcacatccgagggcgaaggcaagccctacgagggcacccagaccatgagaatcaaggtggtcgagggcggccctctccccttcgccttcgacatcctggctaccagcttcatgtacggcagcaaaaccttcatcaaccacacccagggcatccccgacttctttaagcagtccttccctgaggtaagtgtgctcgcttcggcagcacatatactatgttgaatgaggcttcagtactttacagaatcgttgcctgcacatcttggaaacacttgctgggattacttcttcagggacttcttaacccaacagaaggctcgagaaggtatattgctgttgacagtgagcgccgcttgaagtctttaattaaatagtgaagccacagatgtatttaattaaagacttcaagcggtgcctactgcctcggacttcaaggggctagaattcaaggggctactttaggagcaattatcttgtttactaaaactgaataccttgctatctctttgatacatttttacaaagctgaattaaaatggtataaattaaatcacttttttcaattgtactaacttcgagtcttctttttttttttcacagggcttcacatgggagagagtcaccacatacgaagacgggggcgtgctgaccgctacccaggacaccagcctccaggacggctgcctcatctacaacgtcaagatcagaggggtgaacttcccatccaacggccctgtgatgcagaagaaaacactcggctgggaggcctccaccgagatgctgtaccccgctgacggcggcctggaaggcagaagcgacatggccctgaagctcgtgggcgggggccacctgatctgcaacttgaagaccacatacagatccaagaaacccgctaagaacctcaagatgcccggcgtctactatgtggacagaagactggaaagaatcaaggaggccgacaaagagacctacgtcgagcagcacgaggtggctgtggccagatactgcgacctccctagcaaactggggcacaaacttaattgataaacataggatggcaagatcctggtatcggtctgcgagcaccgcttgaagtctttaattaaatacgcaccgcttgaagtctttaattaaatacgcaccgcttgaagtctttaattaaatacctcgagcctctggccacatcggttcctgcggtaagcgggactctggggttcgaaatgaccgaccaagcgacgcccaacctgccatcacgagatttcgattccaccgccgccttctatgaaaggttgggcttcggaatcgttttccgggacgccggctggatgatcctccagcgcggggatctcatgctggagttcttcgcccaccctagggggaggctaactgaaacacggaaggagacaataccggaaggaacccgcgctatgacggcaataaaaagacagaataaaacgcacggtgttgggtcgtttgttcataaacgcggggttcggtcccagggctggcactctgtcgataccccaccgagacgccattggggccaatacgcccgcgtttcttccttttccccaccccaccccccaagttcgggtgaaggcccagggctcgcagccaacgtcggggcggcaggccctgccataggcaccgcttgaagtctttaattaaatacgcaccgcttgaagtctttaattaaatacgcaccgcttgaagtctttaattaaatac</sbol:elements>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="http://examples.org/SSX1_sequence/1">
+    <sbol:displayId>SSX1_sequence</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/SSX1_sequence"/>
+    <sbol:elements>cggccgccctgcagggtagccagatcatggctcactgcaacctcgtactcctgggctcaagctatcctcctacctcagcctcctgagtaacggactacaggcacaccaccccacctcgctaattttatttattttttttgtagagaaaagagacagggtattgctctgttgcccagggtggggtgcagtggcatgatcatggctcactgcaacctctgcctcccaggttcaagtgatcctccagctgtggcctccctaagtgctgggattacaaccgtgagccgccgcaccggcccaaatttcttacgtcactacagagttcctaggaaaaaatcccatacctgaaaaagatagaaactgacaggaaggatttgagatgatgacctgcttcatatacactccttattaaaactggataacaatgcaccaccgaggaggtggggagggataggaaaaatgaaaagagaaaatcagcgcatgcgtactctgatttgggaagactccaaagagaaaatcagagcatgcgtactctgaacttggagtagccaatcccaggggatgctttaggcgggaaagtcagagtttctgcctccattttgagaaggttctgtccctagagcctagactgatagaccccacatcagcttggcttgtcccgcctactgttctgacttctgattggccagatggagttcactaactgccctgattggtccatcatcctggagcaatgacattgcagaatattttctcctcctccagccacactttgtcaccaactgctgccaactcgccaccactgctgccgacctcgcaaccactgctttgtctctggcgcgcc</sbol:elements>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="http://examples.org/ECFP__u38__BS_u40_B_u41__sequence/1">
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:displayId>ECFP__u38__BS_u40_B_u41__sequence</sbol:displayId>
+    <sbol:version>1</sbol:version>
+    <sbol:elements>ccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagatagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagcttgtaagcgggactctggggttgaattcggatccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagatagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagcttgtaagcgggactctggggttaaagcaaattaaaaacaggatgaaaaagactgattggctcttcctcaatgcttgtgtgggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaacgccatcagcgacaacgtctatatcaccgccgacaagcagaagaacggcatcaaggccaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccaagctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggcatggacgagctgtacaagtaaggatccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagatagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaagctagccgcttgaaggaataattaaa</sbol:elements>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/ECFP__u38__BS_u40_B_u41__sequence"/>
+  </sbol:Sequence>
+  <sbol:Sequence rdf:about="http://examples.org/MAFK_sequence/1">
+    <sbol:displayId>MAFK_sequence</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://examples.org/MAFK_sequence"/>
+    <sbol:elements>tgctgagtcagcaagatgctgagtcagcatcgtgctgagtcagcagactgctgagtcagcactatgctgagtcagcaacttgctgagtcagcatgctgctgagtcagcagtatgctgagtcagca</sbol:elements>
+    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
+    <sbol:version>1</sbol:version>
+  </sbol:Sequence>
+</rdf:RDF>

requirements.txt

@@ -7,4 +7,4 @@ sbol3==1.0.1
 tyto==1.2
 urllib3==1.26.5
 validators==0.18.2
-excel_sbol_utils==1.0.42
+excel_sbol_utils==1.0.43