feature: generalized get_raw_doc function

cutlass/Project.py

@@ -24,6 +24,7 @@ class Project(Base):
         namespace (str): The namespace this class will use in OSDF.
     """
     namespace = "ihmp"
+    osdf_node_type = "project"
 
     def __init__(self):
         """
@@ -384,7 +385,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': Project.namespace,
-            'node_type': 'project',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'name': self._name,
                 'mixs': self._mixs,

cutlass/Sample.py

@@ -24,6 +24,7 @@ class Sample(Base):
         namespace (str): The namespace this class will use in OSDF.
     """
     namespace = "ihmp"
+    osdf_node_type = "sample"
 
     def __init__(self):
         """
@@ -384,7 +385,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': Sample.namespace,
-            'node_type': 'sample',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'fma_body_site': self._fma_body_site,
                 'mixs': self._mixs,

cutlass/SixteenSDnaPrep.py

@@ -24,6 +24,7 @@ class SixteenSDnaPrep(Base):
         namespace (str): The namespace this class will use in the OSDF instance
     """
     namespace = "ihmp"
+    osdf_node_type = "16s_dna_prep"
 
     date_format = '%Y-%m-%d'
 
@@ -440,7 +441,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': SixteenSDnaPrep.namespace,
-            'node_type': '16s_dna_prep',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'comment': self._comment,
                 'lib_layout': self._lib_layout,

cutlass/SixteenSRawSeqSet.py

@@ -26,6 +26,7 @@ class SixteenSRawSeqSet(Base):
         namespace (str): The namespace this class will use in the OSDF instance
     """
     namespace = "ihmp"
+    osdf_node_type = "16s_raw_seq_set"
 
     aspera_server = "aspera.ihmpdcc.org"
 
@@ -468,7 +469,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': SixteenSRawSeqSet.namespace,
-            'node_type': '16s_raw_seq_set',
+            'node_type': self.osdf_node_type,
             'meta': {
                 "checksums": self._checksums,
                 "comment": self._comment,

cutlass/SixteenSTrimmedSeqSet.py

@@ -23,6 +23,7 @@ class SixteenSTrimmedSeqSet(Base):
         namespace (str): The namespace this class will use in the OSDF instance
     """
     namespace = "ihmp"
+    osdf_node_type = "16s_trimmed_seq_set"
 
     def __init__(self):
         """
@@ -390,7 +391,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': SixteenSTrimmedSeqSet.namespace,
-            'node_type': '16s_trimmed_seq_set',
+            'node_type': self.osdf_node_type,
             'meta': {
                 "checksums": self._checksums,
                 "comment": self._comment,

cutlass/Study.py

@@ -22,6 +22,7 @@ class Study(Base):
         namespace (str): The namespace this class will use in OSDF.
     """
     namespace = "ihmp"
+    osdf_node_type = "study"
 
     def __init__(self):
         """
@@ -268,7 +269,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': Study.namespace,
-            'node_type': 'study',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'name': self._name,
                 'description': self._description,

cutlass/Subject.py

@@ -22,6 +22,7 @@ class Subject(Base):
         namespace (str): The namespace this class will use in the OSDF instance
     """
     namespace = "ihmp"
+    osdf_node_type = "subject"
 
     valid_races = ( "african_american", "american_indian_or_alaska_native",
                     "asian", "caucasian", "hispanic_or_latino", "native_hawaiian",
@@ -215,7 +216,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': Subject.namespace,
-            'node_type': 'subject',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'gender': self._gender,
                 'rand_subject_id': self._rand_subject_id,

cutlass/Visit.py

@@ -23,6 +23,7 @@ class Visit(Base):
         namespace (str): The namespace this class will use in OSDF.
     """
     namespace = "ihmp"
+    osdf_node_type = "visit"
 
     date_format = '%Y-%m-%d'
 
@@ -230,7 +231,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': Visit.namespace,
-            'node_type': 'visit',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'visit_number': self._visit_number,
                 'date': self._date,

cutlass/WgsDnaPrep.py

@@ -24,6 +24,7 @@ class WgsDnaPrep(Base):
         namespace (str): The namespace this class will use in OSDF.
     """
     namespace = "ihmp"
+    osdf_node_type = "wgs_dna_prep"
 
     def __init__(self):
         """
@@ -437,7 +438,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': WgsDnaPrep.namespace,
-            'node_type': 'wgs_dna_prep',
+            'node_type': self.osdf_node_type,
             'meta': {
                 'comment': self._comment,
                 'lib_layout': self._lib_layout,

cutlass/WgsRawSeqSet.py

@@ -24,6 +24,7 @@ class WgsRawSeqSet(Base):
         namespace (str): The namespace this class will use in the OSDF instance
     """
     namespace = "ihmp"
+    osdf_node_type = "wgs_raw_seq_set"
 
     aspera_server = "aspera.ihmpdcc.org"
 
@@ -450,7 +451,7 @@ def _get_raw_doc(self):
             },
             'linkage': self._links,
             'ns': WgsRawSeqSet.namespace,
-            'node_type': 'wgs_raw_seq_set',
+            'node_type': self.osdf_node_type,
             'meta': {
                 "checksums": self._checksums,
                 "comment": self._comment,

cutlass/__init__.py

@@ -13,3 +13,23 @@
 from .mixs import MIXS, MixsException
 from .mims import MIMS, MimsException
 from .mimarks import MIMARKS, MimarksException
+
+_node_type_idx = {
+                  Project.osdf_node_type : Project.load_project,
+                    Study.osdf_node_type : Study.load_study,
+                    Visit.osdf_node_type : Visit.load_visit,
+                   Sample.osdf_node_type : Sample.load_sample,
+                  Subject.osdf_node_type : Subject.load_subject,
+          SixteenSDnaPrep.osdf_node_type : SixteenSDnaPrep.load_sixteenSDnaPrep,
+               WgsDnaPrep.osdf_node_type : WgsDnaPrep.load_wgsDnaPrep,
+        SixteenSRawSeqSet.osdf_node_type : SixteenSRawSeqSet.load_sixteenSRawSeqSet,
+             WgsRawSeqSet.osdf_node_type : WgsRawSeqSet.load_wgsRawSeqSet,
+    SixteenSTrimmedSeqSet.osdf_node_type : SixteenSTrimmedSeqSet.load_sixteenSTrimmedSeqSet,
+}
+
+def load(node_id):
+    doc = iHMPSession.get_session().get_osdf().get_node(node_id)
+    load_func = _node_type_idx.get(doc['node_type'], None)
+    if load_func is None:
+        raise ValueError("Unknown node type: "+nodetype)
+    return load_func(doc)