Update Assay and Investigation File, add corresponding files

arc-validate-results.xml

+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="arc-validate"><testcase name="[ Critical; Filesystem; DataPathNames; Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E2" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; Sample2_714ca2b7-22b7-4f69-b83d-9165f624da25.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E3" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; Sample3_66fac760-acc7-4ed4-ba21-2cb67fa36e4d.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E4" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; Sample4_cba5f40c-fc05-44d6-a589-b0e3dafaeefe.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E5" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; Sample5_84c37b60-2342-4226-a36c-4b8dfe84ebe9.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E6" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; Sample6_208df064-4b1c-4da0-a1f8-6412e1fb2284.png ]" time="0.009"><failure message="Actual entity is not present: /arc/studies/experiment1_material/isa.study.xlsx in Worksheet Some(process_2) at Cell: E7" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.009"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B2" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.009"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B3" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.009"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B4" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.009"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B5" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B6" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B7" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; extractionProtocol.txt ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Extraction) at Cell: B8" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample1.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H2" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample2.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H3" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample3.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H4" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample4.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H5" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample5.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H6" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample6.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H7" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; sample7.raw ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Protein Measurement) at Cell: H8" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E2" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E3" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E4" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E5" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E6" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E7" /></testcase><testcase name="[ Critical; Filesystem; DataPathNames; proteomics_results.csv ]" time="0.000"><failure message="Actual entity is not present: /arc/assays/measurement1/isa.assay.xlsx in Worksheet Some(Computational Proteome Analysis) at Cell: E8" /></testcase><testcase name="[ Critical; ISA; Semantic; Investigation; Description ]" time="0.021" /><testcase name="[ Critical; ISA; Semantic; Investigation; Title ]" time="0.021" /><testcase name="[ Critical; ISA; Semantic; Investigation; Contacts ]" time="0.020" /><testcase name="[ Critical; ISA; Semantic; Investigation; Studies; experiment1_material ]" time="0.010" /><testcase name="[ Critical; Filesystem; arcFolder ]" time="0.003" /><testcase name="[ Critical; Filesystem; InvestigationFile ]" time="0.003" /><testcase name="[ Critical; Filesystem; StudiesFolder ]" time="0.003" /><testcase name="[ Critical; Filesystem; AssaysFolder ]" time="0.003" /><testcase name="[ Critical; Filesystem; Git; gitFolder ]" time="0.003" /><testcase name="[ Critical; Filesystem; Studies; experiment1_material ]" time="0.003" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person1 [Timo Mühlhaus]; First name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person1 [Timo Mühlhaus]; Last name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person1 [Timo Mühlhaus]; Email address ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person1 [Timo Mühlhaus]; Affiliation ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person2 [Christoph Garth]; First name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person2 [Christoph Garth]; Last name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person2 [Christoph Garth]; Email address ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person2 [Christoph Garth]; Affiliation ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person3 [Oliver Maus]; First name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person3 [Oliver Maus]; Last name ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person3 [Oliver Maus]; Email address ]" time="0.000" /><testcase name="[ Critical; ISA; Semantic; Investigation; Person; Person3 [Oliver Maus]; Affiliation ]" time="0.000" /></testsuite></testsuites>
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assays/measurement1/protocols/extractionProtocol.txt

+- centrifuge again
+- discard the supernate
+- solve the pellet in buffer chemical X
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