support track_order on dataset attributes

h5pyd/_hl/attrs.py

@@ -452,7 +452,7 @@ def __len__(self):
     def __iter__(self):
         """ Iterate over the names of attributes. """
         if self._objdb_attributes is not None:
-            if self._parent._track_order:
+            if self._parent.track_order:
                 attrs = sorted(self._objdb_attributes.items(), key=lambda x: x[1]['created'])
             else:
                 attrs = sorted(self._objdb_attributes.items())
@@ -469,7 +469,7 @@ def __iter__(self):
             req = self._req_prefix
             # backup over the trailing slash in req
             req = req[:-1]
-            rsp = self._parent.GET(req, params={"CreateOrder": "1" if self._parent._track_order else "0"})
+            rsp = self._parent.GET(req, params={"CreateOrder": "1" if self._parent.track_order else "0"})
             attributes = rsp['attributes']
 
             attrlist = []
@@ -505,7 +505,7 @@ def __repr__(self):
     def __reversed__(self):
         """ Iterate over the names of attributes in reverse order. """
         if self._objdb_attributes is not None:
-            if self._parent._track_order:
+            if self._parent.track_order:
                 attrs = sorted(self._objdb_attributes.items(), key=lambda x: x[1]['created'])
             else:
                 attrs = sorted(self._objdb_attributes.items())
@@ -522,7 +522,7 @@ def __reversed__(self):
             req = self._req_prefix
             # backup over the trailing slash in req
             req = req[:-1]
-            rsp = self._parent.GET(req, params={"CreateOrder": "1" if self._parent._track_order else "0"})
+            rsp = self._parent.GET(req, params={"CreateOrder": "1" if self._parent.track_order else "0"})
             attributes = rsp['attributes']
 
             attrlist = []

h5pyd/_hl/base.py

@@ -948,6 +948,10 @@ def modified(self):
         """Last modified time as a datetime object"""
         return self.id._modified
 
+    @property
+    def track_order(self):
+        return self._track_order
+
     def verifyCert(self):
         # default to validate CERT for https requests, unless
         # the H5PYD_VERIFY_CERT environment variable is set and True
@@ -1072,7 +1076,7 @@ def DELETE(self, req, params=None):
         if rsp.status_code != 200:
             raise IOError(rsp.reason)
 
-    def __init__(self, oid, file=None):
+    def __init__(self, oid, file=None, track_order=None):
         """ Setup this object, given its low-level identifier """
         self._id = oid
         self.log = self._id.http_conn.logging
@@ -1092,6 +1096,24 @@ def __init__(self, oid, file=None):
         else:
             pass
 
+        if track_order is None:
+            # set order based on group creation props
+            obj_json = self.id.obj_json
+            if "creationProperties" in obj_json:
+                cpl = obj_json["creationProperties"]
+            else:
+                cpl = {}
+            if "CreateOrder" in cpl:
+                createOrder = cpl["CreateOrder"]
+                if not createOrder or createOrder == "0":
+                    self._track_order = False
+                else:
+                    self._track_order = True
+            else:
+                self._track_order = False
+        else:
+            self._track_order = track_order
+
     def __hash__(self):
         return hash(self.id.id)
 

h5pyd/_hl/dataset.py

@@ -31,6 +31,7 @@
 from . import selections as sel
 from .datatype import Datatype
 from .h5type import getTypeItem, createDataType, check_dtype, special_dtype, getItemSize
+from .. import config
 
 _LEGACY_GZIP_COMPRESSION_VALS = frozenset(range(10))
 VERBOSE_REFRESH_TIME = 1.0  # 1 second
@@ -77,6 +78,7 @@ def make_new_dset(
     compression_opts=None,
     fillvalue=None,
     scaleoffset=None,
+    track_order=None,
     track_times=None,
     initializer=None,
     initializer_opts=None
@@ -88,6 +90,7 @@ def make_new_dset(
 
     # fill in fields for the body of the POST request as we got
     body = {}
+    cfg = config.get_config()
 
     # Convert data to a C-contiguous ndarray
     if data is not None and not isinstance(data, Empty):
@@ -249,17 +252,14 @@ def make_new_dset(
 
             dcpl["fillValue"] = fillvalue
 
+    if track_order or cfg.track_order:
+        dcpl["CreateOrder"] = 1
+
     if chunks and isinstance(chunks, dict):
         dcpl["layout"] = chunks
 
     body["creationProperties"] = dcpl
 
-    """
-    if track_times in (True, False):
-        dcpl.set_obj_track_times(track_times)
-    elif track_times is not None:
-        raise TypeError("track_times must be either True or False")
-    """
     if maxshape is not None and len(maxshape) > 0:
         if shape is not None:
             maxshape = tuple(m if m is not None else 0 for m in maxshape)
@@ -291,7 +291,7 @@ def make_new_dset(
 
     if data is not None:
         # init data
-        dset = Dataset(dset_id)
+        dset = Dataset(dset_id, track_order=(track_order or cfg.track_order))
         dset[...] = data
 
     return dset_id
@@ -763,12 +763,12 @@ def allocated_size(self):
         self._getVerboseInfo()
         return self._allocated_size
 
-    def __init__(self, bind, track_order=False):
+    def __init__(self, bind, track_order=None):
         """Create a new Dataset object by binding to a low-level DatasetID."""
 
         if not isinstance(bind, DatasetID):
             raise ValueError(f"{bind} is not a DatasetID")
-        HLObject.__init__(self, bind)
+        HLObject.__init__(self, bind, track_order=track_order)
 
         self._dcpl = self.id.dcpl_json
         self._filters = filters.get_filters(self._dcpl)
@@ -778,7 +778,14 @@ def __init__(self, bind, track_order=False):
         # make a numpy dtype out of the type json
         self._dtype = createDataType(self.id.type_json)
         self._item_size = getItemSize(self.id.type_json)
-        self._track_order = track_order
+        if track_order is None:
+            if "CreateOrder" in self._dcpl:
+                if not self._dcpl["CreateOrder"] or self._dcpl["CreateOrder"] == "0":
+                    self._track_order = False
+                else:
+                    self._track_order = True
+        else:
+            self._track_order = track_order
 
         self._shape = self.get_shape()
 

h5pyd/_hl/group.py

@@ -58,8 +58,8 @@ def __init__(self, bind, track_order=None, **kwargs):
 
         if not isinstance(bind, GroupID):
             raise ValueError(f"{bind} is not a GroupID")
-        HLObject.__init__(self, bind, **kwargs)
-
+        HLObject.__init__(self, bind, track_order=track_order, **kwargs)
+        """
         if track_order is None:
             # set order based on group creation props
             gcpl = self.id.gcpl_json
@@ -73,6 +73,7 @@ def __init__(self, bind, track_order=None, **kwargs):
                 self._track_order = False
         else:
             self._track_order = track_order
+        """
         self._req_prefix = "/groups/" + self.id.uuid
         self._link_db = {}  # cache for links
 
@@ -164,7 +165,7 @@ def _get_link_json(self, h5path):
             req = "/groups/" + parent_uuid + "/links/" + name
 
             try:
-                rsp_json = self.GET(req, params={"CreateOrder": "1" if self._track_order else "0"})
+                rsp_json = self.GET(req, params={"CreateOrder": "1" if self.track_order else "0"})
             except IOError:
                 raise KeyError("Unable to open object (Component not found)")
 
@@ -219,9 +220,9 @@ def _make_group(self, parent_id=None, parent_name=None, link=None, track_order=N
 
         group_json = rsp
         groupId = GroupID(self, group_json)
-        sub_group = Group(groupId)
-        if track_order or cfg.track_order:
-            sub_group._track_order = True
+
+        sub_group = Group(groupId, track_order=(track_order or cfg.track_order))
+
         if parent_name:
             if parent_name[-1] == '/':
                 parent_name = parent_name + link
@@ -355,6 +356,8 @@ def create_dataset(self, name, shape=None, dtype=None, data=None, **kwds):
             conjunction with the scale/offset filter.
         fillvalue
             (Scalar) Use this value for uninitialized parts of the dataset.
+        track_oder
+            (T/F) List attributes by creation_time if set
         track_times
             (T/F) Enable dataset creation timestamps.
         initializer
@@ -426,12 +429,17 @@ def create_dataset_like(self, name, other, **kwupdate):
                   'fillvalue'):
             kwupdate.setdefault(k, getattr(other, k))
         # TODO: more elegant way to pass these (dcpl to create_dataset?)
-        # TBD: track times and creation order not yet supported
-        """
-        dcpl = other.id.get_create_plist()
-        kwupdate.setdefault('track_times', dcpl.get_obj_track_times())
-        kwupdate.setdefault('track_order', dcpl.get_attr_creation_order() > 0)
-        """
+
+        dcpl_json = other.id.dcpl_json
+        track_order = None
+        if "CreateOrder" in dcpl_json:
+            createOrder = dcpl_json["CreateOrder"]
+            if not createOrder or createOrder == "0":
+                track_order = False
+            else:
+                track_order = True
+
+        kwupdate.setdefault('track_order', track_order)
 
         # Special case: the maxshape property always exists, but if we pass it
         # to create_dataset, the new dataset will automatically get chunked
@@ -566,9 +574,10 @@ def getObjByUuid(self, uuid, collection_type=None, track_order=None):
             else:
                 raise IOError(f"Unexpected uuid: {uuid}")
         objdb = self.id.http_conn.getObjDb()
-        if objdb and uuid in objdb:
+        if objdb and uuid in objdb and False:
             # we should be able to construct an object from objdb json
             obj_json = objdb[uuid]
+            print('fetch from db')
         else:
             # will need to get JSON from server
             req = f"/{collection_type}/{uuid}"
@@ -583,11 +592,11 @@ def getObjByUuid(self, uuid, collection_type=None, track_order=None):
         elif collection_type == 'datatypes':
             tgt = Datatype(TypeID(self, obj_json))
         elif collection_type == 'datasets':
-            # create a Table if the daset is one dimensional and compound
+            # create a Table if the dataset is one dimensional and compound
             shape_json = obj_json["shape"]
             dtype_json = obj_json["type"]
             if "dims" in shape_json and len(shape_json["dims"]) == 1 and dtype_json["class"] == 'H5T_COMPOUND':
-                tgt = Table(DatasetID(self, obj_json))
+                tgt = Table(DatasetID(self, obj_json), track_order=track_order)
             else:
                 tgt = Dataset(DatasetID(self, obj_json), track_order=track_order)
         else:
@@ -700,6 +709,10 @@ def get(self, name, default=None, getclass=False, getlink=False, track_order=Non
             Return HardLink, SoftLink and ExternalLink classes.  Return
             "default" if nothing with that name exists.
 
+        "track_order" is (T/F):
+            List links and attributes by creation order if True, alphanumerically if False.
+            If None, the track_order used when creating the group will be used.
+
         "limit" is an integer:
             If "name" is None, this will return the first "limit" links in the group.
 
@@ -876,8 +889,8 @@ def __setitem__(self, name, obj):
             parent_uuid = link_json["id"]
             req = "/groups/" + parent_uuid
             params = {}
-            if self._track_order is not None:
-                params["CreateOrder"] = "1" if self._track_order else "0"
+            if self.track_order is not None:
+                params["CreateOrder"] = "1" if self.track_order else "0"
             group_json = self.GET(req, params=params)
             tgt = Group(GroupID(self, group_json))
             tgt[basename] = obj
@@ -977,8 +990,8 @@ def __len__(self):
 
         req = "/groups/" + self.id.uuid
         params = {}
-        if self._track_order is not None:
-            params["CreateOrder"] = "1" if self._track_order else "0"
+        if self.track_order is not None:
+            params["CreateOrder"] = "1" if self.track_order else "0"
         rsp_json = self.GET(req, params=params)
         return rsp_json['linkCount']
 
@@ -989,8 +1002,8 @@ def __iter__(self):
         if links is None:
             req = "/groups/" + self.id.uuid + "/links"
             params = {}
-            if self._track_order is not None:
-                params["CreateOrder"] = "1" if self._track_order else "0"
+            if self.track_order is not None:
+                params["CreateOrder"] = "1" if self.track_order else "0"
             rsp_json = self.GET(req, params=params)
             links = rsp_json['links']
 
@@ -1003,7 +1016,7 @@ def __iter__(self):
             for x in links:
                 yield x['title']
         else:
-            if self._track_order:
+            if self.track_order:
                 links = sorted(links.items(), key=lambda x: x[1]['created'])
             else:
                 links = sorted(links.items())
@@ -1217,8 +1230,8 @@ def visititems(self, func):
                     # request from server
                     req = "/groups/" + parent.id.uuid + "/links"
                     params = {}
-                    if self._track_order is not None:
-                        params["CreateOrder"] = "1" if self._track_order else "0"
+                    if self.track_order is not None:
+                        params["CreateOrder"] = "1" if self.track_order else "0"
                     rsp_json = self.GET(req, params=params)
                     links = rsp_json['links']
                 for link in links:
@@ -1270,7 +1283,7 @@ def __reversed__(self):
 
         if links is None:
             req = "/groups/" + self.id.uuid + "/links"
-            rsp_json = self.GET(req, params={"CreateOrder": "1" if self._track_order else "0"})
+            rsp_json = self.GET(req, params={"CreateOrder": "1" if self.track_order else "0"})
             links = rsp_json['links']
 
             # reset the link cache
@@ -1282,7 +1295,7 @@ def __reversed__(self):
             for x in reversed(links):
                 yield x['title']
         else:
-            if self._track_order:
+            if self.track_order:
                 links = sorted(links.items(), key=lambda x: x[1]['created'])
             else:
                 links = sorted(links.items())

h5pyd/_hl/table.py

@@ -82,13 +82,13 @@ class Table(Dataset):
     """
         Represents an HDF5 dataset
     """
-    def __init__(self, bind):
+    def __init__(self, bind, track_order=None):
         """ Create a new Table object by binding to a low-level DatasetID.
         """
 
         if not isinstance(bind, DatasetID):
             raise ValueError(f"{bind} is not a DatasetID")
-        Dataset.__init__(self, bind)
+        Dataset.__init__(self, bind, track_order=track_order)
 
         if len(self._dtype) < 1:
             raise ValueError("Table type must be compound")