Merge branch 'master' into develop

docs/creation.rst

@@ -75,7 +75,7 @@ one Study section structured as defined by the
 `ISA-Tab Specification <http://isa-specs.readthedocs.io/en/latest/isatab.html>`_.
 
 .. hint:: Remember that when you ``dump()`` ISA content, you do it on the ``Investigation`` object. This means any
-``Study`` and ``Assay`` objects and content must be attached to the ``Investigation`` for it to be serialized out.
+   ``Study`` and ``Assay`` objects and content must be attached to the ``Investigation`` for it to be serialized out.
 
 Different classes in ``isatools.model.v1`` have class constructors and instance variables that roughly map to the
 ISA Abstract Model. For full details of how to instantiate model classes, access and manipulate ISA data as objects,

isatools/io/isatab_parser.py

@@ -227,25 +227,20 @@ def __init__(self, base_file):
                                          "Comment", "Label", "Material Type", "Factor Value"),
                            "node": ("Sample Name", "Source Name", "Image File",
                                     "Raw Data File", "Derived Data File", "Acquisition Parameter Data File",
-                                    "Extract Name", "Labeled Extract Name"),
+                                    "Extract Name", "Labeled Extract Name", "Array Data File",
+                                    "Raw Spectral Data File", "Protein Assignment File", "Peptide Assignment File",
+                                    "Post Translational Modification Assignment File", "Derived Spectral Data File",
+                                    "Derived Array Data File"),
                            "node_assay": ("Assay Name", "Data Transformation Name",
                                           "Normalization Name"),
                            "processing": "Protocol REF",
                            "parameter": ("Parameter Value", "Array Design REF")
                            }
-        self._synonyms = {"Array Data File": "Raw Data File",
-                          "Free Induction Decay Data File": "Raw Data File",
-                          "Derived Array Data File" : "Derived Data File",
+        self._synonyms = {
                           "Hybridization Assay Name": "Assay Name",
                           "Scan Name": "Assay Name",
-                          "Array Data Matrix File": "Derived Data File",
-                          "Derived Array Data Matrix File": "Derived Data File",
-                          "Raw Spectral Data File": "Raw Data File",
-                          "Derived Spectral Data File": "Derived Data File",
-                          "MS Assay Name": "Assay Name",
-                          "Protein Assignment File": "Derived Data File",
-                          "Peptide Assignment File": "Derived Data File",
-                          "Post Translational Modification Assignment File": "Derived Data File"}
+                          "MS Assay Name": "Assay Name"
+        }
 
     def parse(self, rec):
         """Retrieve row data from files associated with the ISATabRecord.
@@ -620,30 +615,45 @@ def _swap_synonyms(self, header):
     def _build_node_index(self, type, name):
         if type=="Source Name":
             return "source-"+name
+        elif type == "Sample Name":
+            return "sample-"+name
+        elif type == "Extract Name":
+            return "extract-"+name
+        elif type == "Labeled Extract Name":
+            return "labeledextract-"+name
+        elif type == "Raw Data File":
+            return "rawdatafile-"+name
+        elif type=="Derived Data File":
+            return "deriveddatafile-"+name
+        elif type=="Acquisition Parameter Data File":
+            return "acquisitionparameterfile-"+name
+        elif type=="Image File":
+            return "imagefile-"+name
+        elif type == "Array Data File":
+            return "arraydatafile-" + name
+        elif type == "Array Data Matrix File":
+            return "arraydatamatrixfile-" + name
+        elif type == "Derived Array Data Matrix File":
+            return "derivedarraydatamatrixfile-" + name
+        elif type == "Raw Spectral Data File":
+            return "rawspectraldatafile-" + name
+        elif type == "Derived Array Data Matrix File":
+            return "derivedarraydatamatrixfile-" + name
+        elif type == "Protein Assignment File":
+            return "proteinassignmentfile-" + name
+        elif type == "Peptide Assignment File":
+            return "peptideassignmentfile-" + name
+        elif type == "Post Translational Modification Assignment File":
+            return "posttranslationalmodificationassignmentfile-" + name
+        elif type == "Free Induction Decay Data File":
+            return "freeinductiondecaydatafile-" + name
+        elif type == "Derived Array Data File":
+            return "derivedarraydatafile-" + name
+        elif type == "Derived Spectral Data File":
+            return "derivedspectraldatafile-" + name
         else:
-            if type == "Sample Name":
-                return "sample-"+name
-            else:
-                if type == "Extract Name":
-                    return "extract-"+name
-                else:
-                    if type == "Labeled Extract Name":
-                        return "labeledextract-"+name
-                    else:
-                        if type == "Raw Data File":
-                            return "rawdatafile-"+name
-                        else:
-                            if type=="Derived Data File":
-                                return "deriveddatafile-"+name
-                            else:
-                                if type=="Acquisition Parameter Data File":
-                                    return "acquisitionparameterfile-"+name
-                                else:
-                                     if type=="Image File":
-                                        return "imagefile-"+name
-                                     else:
-                                        "ERROR - Type not being considered! ", type
-                                        return name
+            print("ERROR - Type not being considered! ", type)
+            return name
 
 
 _record_str = \

isatools/isajson.py

@@ -44,23 +44,6 @@ def get_roles(j):
                 roles.append(role)
         return roles
 
-    def _build_assay_graph(process_sequence=list()):
-        G = nx.DiGraph()
-        for process in process_sequence:
-            if process.next_process is not None or len(process.outputs) > 0:  # first check if there"s some valid outputs to connect
-                if len(process.outputs) > 0:
-                    for output in [n for n in process.outputs if not isinstance(n, DataFile)]:
-                        G.add_edge(process, output)
-                else:  # otherwise just connect the process to the next one
-                    G.add_edge(process, process.next_process)
-            if process.prev_process is not None or len(process.inputs) > 0:
-                if len(process.inputs) > 0:
-                    for input_ in process.inputs:
-                        G.add_edge(input_, process)
-                else:
-                    G.add_edge(process.prev_process, process)
-        return G
-
     def get_jvalue(dict, key):
         if key in dict.keys():
             return dict[key]
@@ -1760,7 +1743,8 @@ def get_data_file(o):
                 {
                     "@id": id_gen(o),
                     "name": o.filename,
-                    "type": o.label
+                    "type": o.label,
+                    "comments": get_comments(o.comments)
                 }
             )