Add example for #185

.gitignore

@@ -63,7 +63,7 @@ target/
 
 
 .DS_Store
-reated by https://www.gitignore.io
+## Created by https://www.gitignore.io
 
 ### PyCharm ###
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm

isatools/examples/i_investigation.txt

@@ -0,0 +1,95 @@
+ONTOLOGY SOURCE REFERENCE
+Term Source Name
+Term Source File
+Term Source Version
+Term Source Description
+INVESTIGATION
+Investigation Identifier	"investigation"
+Investigation Title
+Investigation Description
+Investigation Submission Date
+Investigation Public Release Date
+Comment[Created With Configuration]
+Comment[Last Opened With Configuration]
+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 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
+STUDY
+Study Identifier	"study"
+Study Title
+Study Description
+Comment[Study Grant Number]
+Comment[Study Funding Agency]
+Study Submission Date
+Study Public Release Date
+Study File Name
+STUDY DESIGN DESCRIPTORS
+Study Design Type
+Study Design Type Term Accession Number
+Study Design Type Term Source 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 FACTORS
+Study Factor Name
+Study Factor Type
+Study Factor Type Term Accession Number
+Study Factor Type Term Source REF
+STUDY ASSAYS
+Study Assay File Name
+Study Assay Measurement Type
+Study Assay Measurement Type Term Accession Number
+Study Assay Measurement Type Term Source REF
+Study Assay Technology Type
+Study Assay Technology Type Term Accession Number
+Study Assay Technology Type Term Source REF
+Study Assay Technology Platform
+STUDY PROTOCOLS
+Study Protocol Name
+Study Protocol Type
+Study Protocol Type Term Accession Number
+Study Protocol Type Term Source REF
+Study Protocol Description
+Study Protocol URI
+Study Protocol Version
+Study Protocol Parameters Name
+Study Protocol Parameters Name Term Accession Number
+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 CONTACTS
+Study Person Last Name
+Study Person First Name
+Study Person Mid Initials
+Study Person Email
+Study Person Phone
+Study Person Fax
+Study Person Address
+Study Person Affiliation
+Study Person Roles
+Study Person Roles Term Accession Number
+Study Person Roles Term Source REF

isatools/examples/modifyInvestigationOnly.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+from isatools.isatab import load, dumps
+from isatools.model.v1 import *
+
+
+def modify_investigation():
+    """Load, edit, and dump an ISA-Tab 1.0 descriptor."""
+
+    # Load an existing ISA-Tab investigation file. In this example, we load an unpopulated i_investigation.txt file
+
+    with open('i_investigation.txt') as fp:
+        investigation = load(fp, skip_load_tables=True)
+
+        investigation.identifier = "i1"
+        investigation.title = "My Simple ISA Investigation"
+        investigation.description = "We could alternatively use the class constructor's parameters to set some default " \
+                                    "values at the time of creation, however we want to demonstrate how to use the " \
+                                    "object's instance variables to set values."
+        investigation.submission_date = "2016-11-03"
+        investigation.public_release_date = "2016-11-03"
+
+        obi = OntologySource(name='OBI', description="Ontology for Biomedical Investigations")
+        investigation.ontology_source_references.append(obi)
+
+        study = Study(filename="s_study.txt")
+        study.identifier = "s1"
+        study.title = "My ISA Study"
+        study.description = "Like with the Investigation, we could use the class constructor to set some default values, " \
+                            "but have chosen to demonstrate in this example the use of instance variables to set initial " \
+                            "values."
+        study.submission_date = "2016-11-03"
+        study.public_release_date = "2016-11-03"
+
+        intervention_design = OntologyAnnotation(term_source=obi)
+        intervention_design.term = "intervention design"
+        intervention_design.term_accession = "http://purl.obolibrary.org/obo/OBI_0000115"
+        study.design_descriptors.append(intervention_design)
+
+        contact = Person(first_name="Alice", last_name="Robertson", affiliation="University of Life", roles=[OntologyAnnotation(term='submitter')])
+        study.contacts.append(contact)
+        publication = Publication(title="Experiments with Elephants", author_list="A. Robertson, B. Robertson")
+        publication.pubmed_id = "12345678"
+        publication.status = OntologyAnnotation(term="published")
+        study.publications.append(publication)
+
+        investigation.studies[0] = study  # replace the existing content with the new study we just created above
+
+    return dumps(investigation, skip_dump_tables=True)  # dumps() writes out the ISA as a string representation of the ISA-Tab
+
+if __name__ == '__main__':
+    print(modify_investigation())  # print the result to stdout

isatools/isatab.py

@@ -2752,14 +2752,14 @@ def batch_validate(tab_dir_list):
     return batch_report
 
 
-def dumps(isa_obj):
+def dumps(isa_obj, skip_dump_tables=False):
     import tempfile
     import shutil
     tmp = None
     output = str()
     try:
         tmp = tempfile.mkdtemp()
-        dump(isa_obj=isa_obj, output_path=tmp)
+        dump(isa_obj=isa_obj, output_path=tmp, skip_dump_tables=skip_dump_tables)
         with open(os.path.join(tmp, 'i_investigation.txt'), 'r') as i_fp:
             output += os.path.join(tmp, 'i_investigation.txt') + '\n'
             output += i_fp.read()