Corrected a failing case. Reverted to mzml2isa-qt compliant ISA forma…

…tting for usermeta.

mzml2isa/__init__.py

@@ -40,5 +40,5 @@
 
 __credits__ = 'Thomas Lawson, Martin Larralde, Reza Salek, Ken Haug, Christoph Steinbeck'
 
-__version__ = '0.4.11'
+__version__ = '0.4.12'
 

mzml2isa/default/i_imzML.txt

@@ -5,57 +5,57 @@ Term Source Version	"28"	"2"	"568"	"14"	"18"	"40"	"19"	"2"	"42"	"22"	"86"	"29"	"
 Term Source Description	"National Cancer Institute Thesaurus"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Human Disease Ontology"	"SysMO JERM Ontology of Systems Biology for Micro-Organisms"	"Chemical Methods Ontology"	"National Cancer Institute Thesaurus"	"BioAssay Ontology"	"Cell Culture Ontology"	"Units of Measurement Ontology"	"Ontology for Biomedical Investigations"	"Mass Spectrometry Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Publishing Status Ontology"	"Publishing Roles Ontology"	"Computer Retrieval of Information on Scientific Projects Thesaurus"	"PSI Molecular Interactions"  Imaging Mass Spectrometry Ontology
 INVESTIGATION
 Investigation Identifier	"{Study Identifier}"
-Investigation Title	"Investigation"
-Investigation Description	""
-Investigation Submission Date	""
-Investigation Public Release Date	""
+Investigation Title	"{investigation[title]}"
+Investigation Description	"{investigation[description]}"
+Investigation Submission Date	"{investigation[submission_date]}"
+Investigation Public Release Date	"{investigation[release_date]}"
 Comment [Created With configuration]	""
 Comment [Last Opened With Configuration]	""
-Comment [Created With Converter]	"{Converter}{Converter version}"
+Comment [Created With Tool]	"{Converter}{Converter version}"
 INVESTIGATION PUBLICATIONS
-Investigation PubMed ID	""
-Investigation Publication DOI	""
-Investigation Publication Author List	""
-Investigation Publication Title	""
-Investigation Publication Status	""
-Investigation Publication Status Term Accession Number	""
-Investigation Publication Status Term Source REF	""
+Investigation PubMed ID	"{investigation_publication[pubmed]}"
+Investigation Publication DOI	"{investigation_publication[doi]}"
+Investigation Publication Author List	"{investigation_publication[author_list]}"
+Investigation Publication Title	"{investigation_publication[title]}"
+Investigation Publication Status	"{investigation_publication[status][value]}"
+Investigation Publication Status Term Accession Number	"{investigation_publication[status][accession]}"
+Investigation Publication Status Term Source REF	"{investigation_publication[status][ref]}"
 INVESTIGATION CONTACTS
-Investigation Person Last Name	""
-Investigation Person First Name	""
-Investigation Person Mid Initials	""
-Investigation Person Email	""
-Investigation Person Phone	""
-Investigation Person Fax	""
-Investigation Person Address	""
-Investigation Person Affiliation	""
-Investigation Person Roles	""
-Investigation Person Roles Term Accession Number	""
-Investigation Person Roles Term Source REF	""
+Investigation Person Last Name	"{investigation_contact[last_name]}"
+Investigation Person First Name	"{investigation_contact[first_name]}"
+Investigation Person Mid Initials	"{investigation_contact[mid]}"
+Investigation Person Email	"{investigation_contact[email]}"
+Investigation Person Phone	"{investigation_contact[phone]}"
+Investigation Person Fax	"{investigation_contact[fax]}"
+Investigation Person Address	"{investigation_contact[adress]}"
+Investigation Person Affiliation	"{investigation_contact[affiliation]}"
+Investigation Person Roles	"{investigation_contact[roles][value]}"
+Investigation Person Roles Term Accession Number	"{investigation_contact[roles][accession]}"
+Investigation Person Roles Term Source REF	"{investigation_contact[roles][ref]}"
 STUDY
 Study Identifier	"{Study Identifier}"
-Study Title	""
-Study Description	""
-Study Submission Date	""
-Study Public Release Date	""
+Study Title	"{study[title]}"
+Study Description	"{study[description]}"
+Study Submission Date	"{study[submission_date]}"
+Study Public Release Date	"{study[release_date]}"
 Study File Name	"{Study file name}"
 STUDY DESIGN DESCRIPTORS
-Study Design Type	""
-Study Design Type Term Accession Number	""
-Study Design Type Term Source REF	""
+Study Design Type	"{study_design[type][value]}"
+Study Design Type Term Accession Number	"{study_design[type][accession]}"
+Study Design Type Term Source REF	"{study_design[type][ref]}"
 STUDY PUBLICATIONS
-Study PubMed ID	""
-Study Publication DOI	""
-Study Publication Author List	""
-Study Publication Title	""
-Study Publication Status	""
-Study Publication Status Term Accession Number	""
-Study Publication Status Term Source REF	""
+Study PubMed ID	"{study_publication[pubmed]}"
+Study Publication DOI	"{study_publication[doi]}"
+Study Publication Author List	"{study_publication[author_list]}"
+Study Publication Title	"{study_publication[title]}"
+Study Publication Status	"{study_publication[status][value]}"
+Study Publication Status Term Accession Number	"{study_publication[status][accession]}"
+Study Publication Status Term Source REF	"{study_publication[status][ref]}"
 STUDY FACTORS
-Study Factor Name	""
-Study Factor Type	""
-Study Factor Type Term Accession Number	""
-Study Factor Type Term Source REF	""
+Study Factor Name	"{study_factor[name]}"
+Study Factor Type	"{study_factor[type][value]}"
+Study Factor Type Term Accession Number	"{study_factor[type][accession]}"
+Study Factor Type Term Source REF	"{study_factor[type][ref]}"
 STUDY ASSAYS
 Study Assay File Name	"{Assay file name}"
 Study Assay Measurement Type	"metabolite profiling"
@@ -64,13 +64,13 @@ Study Assay Measurement Type Term Source REF	"OBI"
 Study Assay Technology Type	"mass spectrometry"
 Study Assay Technology Type Term Accession Number	"http://purl.obolibrary.org/obo/OBI_0000470"
 Study Assay Technology Type Term Source REF	"OBI"
-Study Assay Technology Platform	"Exactive"
+Study Assay Technology Platform	"{Platform[name]}"
 STUDY PROTOCOLS
 Study Protocol Name	"Sample collection"	"Preparation"	"Mass spectrometry"	"Histology"	"Data transformation"	"Metabolite identification"
 Study Protocol Type	"Sample collection"	"Preparation"	"Mass spectrometry"	"Histology"	"Data transformation"	"Metabolite identification"
 Study Protocol Type Term Accession Number	"http://purl.bioontology.org/ontology/CSP/4009-0034"	"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25625"	"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17156"	"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16681"	"http://purl.obolibrary.org/obo/OBI_0200000"	"http://purl.obolibrary.org/obo/MI_2131"
 Study Protocol Type Term Source REF	"CSP"	"NCIT"	"NCIT"	"NCIT"	"OBI"	"MI"
-Study Protocol Description	""	""	""	""	""	""
+Study Protocol Description  	"{description[sample_collect]}" 	"{description[preparation]}" 	"{description[mass_spec]}" 	"{description[histology]}"  	"{description[data_trans]}" 	"{description[metabo_id]}"
 Study Protocol URI	""	""	""	""	""	""
 Study Protocol Version	""	""	""	""	""	""
 Study Protocol Parameters Name	""	"Sample mounting;Sample preservation;Sectioning instrument;Section thickness"	"Scan polarity;Mass analyzer;Ion source;Instrument;Scan m/z range;Spatial resolution;Solvent"	"Stain;High-res image;Low-res image"	"Data transformation software;Data transformation software version"	""
@@ -79,16 +79,16 @@ Study Protocol Parameters Name Term Source REF	""	";;;"	";;;;;;"	";;"	""	""
 Study Protocol Components Name	""	""	""	""	""	""
 Study Protocol Components Type	""	""	""	""	""	""
 Study Protocol Components Type Term Accession Number	""	""	""	""	""	""
-Study Protocol Components Type Term Source REF	""	""	""	""	""	""
+Study Protocol Components Type Term Source REF 	""	""	""	""	""	""
 STUDY CONTACTS
-Study Person Last Name	"McKenzie"	"Takats"
-Study Person First Name	"James"	"Zoltan"
-Study Person Mid Initials	"S"	""
-Study Person Email	"j.mckenzie@imperial.ac.uk"	"z.takats@imperial.ac.uk"
-Study Person Phone	""	""
-Study Person Fax	""	""
-Study Person Address	""	""
-Study Person Affiliation	"Imperial College, London"	"Imperial College, London"
-Study Person Roles	"Data curator"	"Principal investigator"
-Study Person Roles Term Accession Number	""	""
-Study Person Roles Term Source REF	""	""
+Study Person Last Name	"{study_contact[last_name]}"
+Study Person First Name	"{study_contact[first_name]}"
+Study Person Mid Initials	"{study_contact[mid]}"
+Study Person Email	"{study_contact[email]}"
+Study Person Phone	"{study_contact[phone]}"
+Study Person Fax	"{study_contact[fax]}"
+Study Person Address	"{study_contact[adress]}"
+Study Person Affiliation	"{study_contact[affiliation]}"
+Study Person Roles	"{study_contact[roles][value]}"
+Study Person Roles Term Accession Number	"{study_contact[roles][accession]}"
+Study Person Roles Term Source REF 	"{study_contact[roles][ref]}"

mzml2isa/default/i_mzML.txt

@@ -5,57 +5,57 @@ Term Source Version	"103"	"2"	"4"	"132"	"26"	"16"	"40"	"43"	"25"	""	""	""	""
 Term Source Description	"Mass Spectrometry Ontology"	"Cigarette Smoke Exposure Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Chemical Methods Ontology"	"National Cancer Institute Thesaurus"	"Units of Measurement Ontology"	"Ontology for Biomedical Investigations"	"Publishing Status Ontology"	"Publishing Roles Ontology"	"PSI Molecular Interactions"	"Computer Retrieval of Information on Scientific Projects Thesaurus"
 INVESTIGATION
 Investigation Identifier	"{Study Identifier}"
-Investigation Title	"{Investigation[title]}"
-Investigation Description	"{Investigation[description]}"
-Investigation Submission Date	"{Investigation[submission_date]}"
-Investigation Public Release Date	"{Investigation[release_date]}"
+Investigation Title	"{investigation[title]}"
+Investigation Description	"{investigation[description]}"
+Investigation Submission Date	"{investigation[submission_date]}"
+Investigation Public Release Date	"{investigation[release_date]}"
 Comment [Created With Configuration]	""
 Comment [Last Opened With Configuration]	""
 Comment [Created With Converter]	"{Converter} {Converter version}"
 INVESTIGATION PUBLICATIONS
-Investigation PubMed ID	"{Investigation publication[pubmed]}"
-Investigation Publication DOI	"{Investigation publication[doi]}"
-Investigation Publication Author List	"{Investigation publication[author_list]}"
-Investigation Publication Title	"{Investigation publication[title]}"
-Investigation Publication Status	"{Investigation publication[status][value]}"
-Investigation Publication Status Term Accession Number	"{Investigation publication[status][accession]}"
-Investigation Publication Status Term Source REF	"{Investigation publication[status][ref]}"
+Investigation PubMed ID	"{investigation_publication[pubmed]}"
+Investigation Publication DOI	"{investigation_publication[doi]}"
+Investigation Publication Author List	"{investigation_publication[author_list]}"
+Investigation Publication Title	"{investigation_publication[title]}"
+Investigation Publication Status	"{investigation_publication[status][value]}"
+Investigation Publication Status Term Accession Number	"{investigation_publication[status][accession]}"
+Investigation Publication Status Term Source REF	"{investigation_publication[status][ref]}"
 INVESTIGATION CONTACTS
-Investigation Person Last Name	"{Investigation contact[last_name]}"
-Investigation Person First Name	"{Investigation contact[first_name]}"
-Investigation Person Mid Initials	"{Investigation contact[mid]}"
-Investigation Person Email	"{Investigation contact[email]}"
-Investigation Person Phone	"{Investigation contact[phone]}"
-Investigation Person Fax	"{Investigation contact[fax]}"
-Investigation Person Address	"{Investigation contact[adress]}"
-Investigation Person Affiliation	"{Investigation contact[affiliation]}"
-Investigation Person Roles	"{Investigation contact[roles][value]}"
-Investigation Person Roles Term Accession Number	"{Investigation contact[roles][accession]}"
-Investigation Person Roles Term Source REF	"{Investigation contact[roles][ref]}"
+Investigation Person Last Name	"{investigation_contact[last_name]}"
+Investigation Person First Name	"{investigation_contact[first_name]}"
+Investigation Person Mid Initials	"{investigation_contact[mid]}"
+Investigation Person Email	"{investigation_contact[email]}"
+Investigation Person Phone	"{investigation_contact[phone]}"
+Investigation Person Fax	"{investigation_contact[fax]}"
+Investigation Person Address	"{investigation_contact[adress]}"
+Investigation Person Affiliation	"{investigation_contact[affiliation]}"
+Investigation Person Roles	"{investigation_contact[roles][value]}"
+Investigation Person Roles Term Accession Number	"{investigation_contact[roles][accession]}"
+Investigation Person Roles Term Source REF	"{investigation_contact[roles][ref]}"
 STUDY
 Study Identifier	"{Study Identifier}"
-Study Title	"{Study[title]}"
-Study Description	"{Study[description]}"
-Study Submission Date	"{Study[submission_date]}"
-Study Public Release Date	"{Study[release_date]}"
+Study Title	"{study[title]}"
+Study Description	"{study[description]}"
+Study Submission Date	"{study[submission_date]}"
+Study Public Release Date	"{study[release_date]}"
 Study File Name	"{Study file name}"
 STUDY DESIGN DESCRIPTORS
-Study Design Type	"{Study design[type][value]}"
-Study Design Type Term Accession Number	"{Study design[type][accession]}"
-Study Design Type Term Source REF	"{Study design[type][ref]}"
+Study Design Type	"{study_design[type][value]}"
+Study Design Type Term Accession Number	"{study_design[type][accession]}"
+Study Design Type Term Source REF	"{study_design[type][ref]}"
 STUDY PUBLICATIONS
-Study PubMed ID	"{Study publication[pubmed]}"
-Study Publication DOI	"{Study publication[doi]}"
-Study Publication Author List	"{Study publication[author_list]}"
-Study Publication Title	"{Study publication[title]}"
-Study Publication Status	"{Study publication[status][value]}"
-Study Publication Status Term Accession Number	"{Study publication[status][accession]}"
-Study Publication Status Term Source REF	"{Study publication[status][ref]}"
+Study PubMed ID	"{study_publication[pubmed]}"
+Study Publication DOI	"{study_publication[doi]}"
+Study Publication Author List	"{study_publication[author_list]}"
+Study Publication Title	"{study_publication[title]}"
+Study Publication Status	"{study_publication[status][value]}"
+Study Publication Status Term Accession Number	"{study_publication[status][accession]}"
+Study Publication Status Term Source REF	"{study_publication[status][ref]}"
 STUDY FACTORS
-Study Factor Name	"{Study factor[name]}"
-Study Factor Type	"{Study factor[type][value]}"
-Study Factor Type Term Accession Number	"{Study factor[type][accession]}"
-Study Factor Type Term Source REF	"{Study factor[type][ref]}"
+Study Factor Name	"{study_factor[name]}"
+Study Factor Type	"{study_factor[type][value]}"
+Study Factor Type Term Accession Number	"{study_factor[type][accession]}"
+Study Factor Type Term Source REF	"{study_factor[type][ref]}"
 STUDY ASSAYS
 Study Assay File Name	"{{Written assays[{}]}}"
 Study Assay Measurement Type	"{{Measurement type[{}][name]}}"
@@ -81,14 +81,14 @@ Study Protocol Components Type	""	""	""	""	""	""
 Study Protocol Components Type Term Accession Number	""	""	""	""	""	""
 Study Protocol Components Type Term Source REF	""	""	""	""	""	""
 STUDY CONTACTS
-Study Person Last Name	"{Study contact[last_name]}"
-Study Person First Name	"{Study contact[first_name]}"
-Study Person Mid Initials	"{Study contact[mid]}"
-Study Person Email	"{Study contact[email]}"
-Study Person Phone	"{Study contact[phone]}"
-Study Person Fax	"{Study contact[fax]}"
-Study Person Address	"{Study contact[adress]}"
-Study Person Affiliation	"{Study contact[affiliation]}"
-Study Person Roles	"{Study contact[roles][value]}"
-Study Person Roles Term Accession Number	"{Study contact[roles][accession]}"
-Study Person Roles Term Source REF	"{Study contact[roles][ref]}"
+Study Person Last Name	"{{study_contact[{}][last_name]}}"
+Study Person First Name	"{{study_contact[{}][first_name]}"
+Study Person Mid Initials	"{{study_contact[{}][mid]}}"
+Study Person Email	"{{study_contact[{}][email]}}"
+Study Person Phone	"{{study_contact[{}][phone]}}"
+Study Person Fax	"{{study_contact[{}][fax]}}"
+Study Person Address	"{{study_contact[{}][adress]}}"
+Study Person Affiliation	"{{study_contact[{}][affiliation]}}"
+Study Person Roles	"{{study_contact[{}][roles][value]}}"
+Study Person Roles Term Accession Number	"{{study_contact[{}][roles][accession]}}"
+Study Person Roles Term Source REF 	"{{study_contact[{}][roles][ref]}}"

mzml2isa/default/s_imzML.txt

@@ -1,2 +1,3 @@
 "Source Name"	"Characteristics[Organism]"	"Term Source REF"	"Term Accession Number"	"Characteristics[Variant]"	"Term Source REF"	"Term Accession Number"	"Characteristics[Organism part]"	"Term Source REF"	"Term Accession Number"	"Protocol REF"	"Sample Name"
-""	"{Characteristics[Organism][value]}"	"{Characteristics[Organism][ref]}"	"{Characteristics[Organism][accession]}"	"{Characteristics[Variant][value]}"	"{Characteristics[Variant][ref]}"	"{Characteristics[Variant][accession]}"	"{Characteristics[Part][value]}"	"{Characteristics[Part][ref]}"	"{Characteristics[Part][accession]}"	"Sample collection"	"{Sample Name[value]}"
+""	"{characteristics[organism][value]}"	"{characteristics[organism][ref]}"	"{characteristics[organism][accession]}"	"{characteristics[organism_variant][value]}"	"{characteristics[organism_variant][ref]}"	"{characteristics[organism_variant][variant]}"	"{characteristics[organism_part][value]}"	"{characteristics[organism_part][ref]}"	"{characteristics[organism_part][accession]}"	"Sample collection"	"{Sample Name[value]}"
+

mzml2isa/default/s_mzML.txt

@@ -1,2 +1,2 @@
 "Source Name"	"Characteristics[Organism]"	"Term Source REF"	"Term Accession Number"	"Characteristics[Variant]"	"Term Source REF"	"Term Accession Number"	"Characteristics[Organism part]"	"Term Source REF"	"Term Accession Number"	"Protocol REF"	"Sample Name"
-""	"{Characteristics[Organism][value]}"	"{Characteristics[Organism][ref]}"	"{Characteristics[Organism][accession]}"	"{Characteristics[Variant][value]}"	"{Characteristics[Variant][ref]}"	"{Characteristics[Variant][accession]}"	"{Characteristics[Part][value]}"	"{Characteristics[Part][ref]}"	"{Characteristics[Part][accession]}"	"Sample collection"	"{Sample Name[value]}"
+""	"{characteristics[organism][value]}"	"{characteristics[organism][ref]}"	"{characteristics[organism][accession]}"	"{characteristics[organism_variant][value]}"	"{characteristics[organism_variant][ref]}"	"{characteristics[organism_variant][variant]}"	"{characteristics[organism_part][value]}"	"{characteristics[organism_part][ref]}"	"{characteristics[organism_part][accession]}"	"Sample collection"	"{Sample Name[value]}"

mzml2isa/isa.py

@@ -138,9 +138,6 @@ def create_investigation(self, metalist, datatype):
 
                         if label in chained:
 
-                            print(label)
-                            print(len(chained[label]))
-
                             for k in range(len(chained[label])):
                                 l = '\t'.join([l, value.format(k)])
                             l += '\n'