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fixes for issue #65 issue #72 and issue #73 which involves removing l…
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…egacy code, unused tests, removing usage of type as a variable
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@coleslaw481
coleslaw481 committed Feb 12, 2020
1 parent d9d76f2 commit 22ab26a
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26 changes: 26 additions & 0 deletions HISTORY.rst
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Expand Up @@ -2,6 +2,32 @@
History
=======

4.0.0a1 (2020-02-12)
---------------------

**Note this release contains breaking changes**

* Remove ``add_edge()`` and ``add_node()`` since they always raise Warning
`Issue #47 <https://github.com/ndexbio/ndex2-client/issues/47>`_

* Remove ``NiceCXNetwork.get_edge_attribute_object()`` since it always raises Warning
`Issue #48 <https://github.com/ndexbio/ndex2-client/issues/48>`_

* ``NiceCXNetwork.get_node_attribute_objects()`` incorrectly raises Warning bug
`Issue #49 <https://github.com/ndexbio/ndex2-client/issues/49>`_

* Convert all print calls to use logging framework
`Issue #63 <https://github.com/ndexbio/ndex2-client/issues/63>`_

* In ``NiceCXNetwork`` remove ``get_edge_attribute_objects()`` since it always raises Warning (which is incorrect behavior anyways)
`Issue #67 <https://github.com/ndexbio/ndex2-client/issues/67>`_

* Remove deprecated methods from ``NiceCXNetwork``
`Issue #68 <https://github.com/ndexbio/ndex2-client/issues/68>`_

* Remove forced setting of localhost url if ``localhost`` in host name in Ndex2 client constructor bug
`Issue #69 <https://github.com/ndexbio/ndex2-client/issues/69>`_

3.3.1 (2019-09-23)
-------------------

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32 changes: 16 additions & 16 deletions ndex2/__init__.py
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Expand Up @@ -8,7 +8,7 @@
import json
import base64
import numpy as np
from ndex2cx.nice_cx_builder import NiceCXBuilder
from ndex2.nice_cx_builder import NiceCXBuilder


logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -216,7 +216,7 @@ def create_nice_cx_from_networkx(G):
# node_id = niceCxBuilder.add_node(name=d.get('name'),represents=d.get('name'), map_node_ids=True)
#else:
if isinstance(n, int):
node_id = niceCxBuilder.add_node(name=n,represents=d.get('represents'), id=n, map_node_ids=True)
node_id = niceCxBuilder.add_node(name=n, represents=d.get('represents'), node_id=n, map_node_ids=True)
else:
node_id = niceCxBuilder.add_node(name=n, represents=d.get('represents'), map_node_ids=True)

Expand All @@ -230,7 +230,7 @@ def create_nice_cx_from_networkx(G):
use_this_value = [use_this_value]
attr_type = 'list_of_string'
if use_this_value is not None:
niceCxBuilder.add_node_attribute(node_id, k, use_this_value, type=attr_type)
niceCxBuilder.add_node_attribute(node_id, k, use_this_value, attribute_type=attr_type)

index = 0
for u, v, d in G.edges(data=True):
Expand All @@ -243,10 +243,10 @@ def create_nice_cx_from_networkx(G):
interaction = d.get('interaction')

if isinstance(u, int):
niceCxBuilder.add_edge(source=u, target=v, interaction=interaction, id=index)
niceCxBuilder.add_edge(source=u, target=v, interaction=interaction, edge_id=index)
else:
niceCxBuilder.add_edge(source=niceCxBuilder.node_id_lookup.get(u), target=niceCxBuilder.node_id_lookup.get(v),
interaction=interaction, id=index)
interaction=interaction, edge_id=index)

# ==============================
# ADD EDGE ATTRIBUTES
Expand All @@ -260,7 +260,7 @@ def create_nice_cx_from_networkx(G):
attr_type = 'list_of_string'

if use_this_value is not None:
niceCxBuilder.add_edge_attribute(property_of=index, name=k, values=use_this_value, type=attr_type)
niceCxBuilder.add_edge_attribute(property_of=index, name=k, values=use_this_value, attribute_type=attr_type)

index += 1

Expand Down Expand Up @@ -461,7 +461,7 @@ def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
else:
use_this_interaction = 'interacts-with'

niceCxBuilder.add_edge(id=index, source=source_node_id, target=target_node_id, interaction=use_this_interaction)
niceCxBuilder.add_edge(edge_id=index, source=source_node_id, target=target_node_id, interaction=use_this_interaction)

# ==============================
# ADD SOURCE NODE ATTRIBUTES
Expand All @@ -487,7 +487,7 @@ def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
if sp == 'citation' and not isinstance(row[sp], list):
row[sp] = [row[sp]]
attr_type = 'list_of_string'
niceCxBuilder.add_node_attribute(source_node_id, sp, str(row[sp]), type=attr_type)
niceCxBuilder.add_node_attribute(source_node_id, sp, str(row[sp]), attribute_type=attr_type)

# ==============================
# ADD TARGET NODE ATTRIBUTES
Expand All @@ -513,7 +513,7 @@ def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
if tp == 'citation' and not isinstance(row[tp], list):
row[tp] = [row[tp]]
attr_type = 'list_of_string'
niceCxBuilder.add_node_attribute(target_node_id, tp, str(row[tp]), type=attr_type)
niceCxBuilder.add_node_attribute(target_node_id, tp, str(row[tp]), attribute_type=attr_type)

# ==============================
# ADD EDGE ATTRIBUTES
Expand All @@ -536,7 +536,7 @@ def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
row[ep] = [row[ep]]
attr_type = 'list_of_string'

niceCxBuilder.add_edge_attribute(property_of=index, name=ep, values=row[ep], type=attr_type)
niceCxBuilder.add_edge_attribute(property_of=index, name=ep, values=row[ep], attribute_type=attr_type)

else:
for index, row in df.iterrows():
Expand All @@ -551,9 +551,9 @@ def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
# ADD EDGES
# =============
if len(row) > 2:
niceCxBuilder.add_edge(id=index, source=source_node_id, target=target_node_id, interaction=row[2])
niceCxBuilder.add_edge(edge_id=index, source=source_node_id, target=target_node_id, interaction=row[2])
else:
niceCxBuilder.add_edge(id=index, source=source_node_id, target=target_node_id, interaction='interacts-with')
niceCxBuilder.add_edge(edge_id=index, source=source_node_id, target=target_node_id, interaction='interacts-with')

return niceCxBuilder.get_nice_cx() # my_nicecx

Expand Down Expand Up @@ -617,7 +617,7 @@ def create_nice_cx_from_server(server, username=None, password=None, uuid=None):
objects = my_nicecx.get_aspect(uuid, 'nodes', server, username, password)
for node_item in objects:
niceCxBuilder._add_node_from_fragment(node_item)
#niceCxBuilder.add_node(node_item.get('n'), node_item.get('r'), id=node_item.get('@id'))
#niceCxBuilder.add_node(node_item.get('n'), node_item.get('r'), node_id=node_item.get('@id'))

# ===================
# EDGES
Expand All @@ -628,7 +628,7 @@ def create_nice_cx_from_server(server, username=None, password=None, uuid=None):
niceCxBuilder._add_edge_from_fragment(edge_item)

#niceCxBuilder.add_edge(source=edge_item.get('s'), target=edge_item.get('t'),
# interaction=edge_item.get('i'), id=edge_item.get('@id'))
# interaction=edge_item.get('i'), edge_id=edge_item.get('@id'))

# ===================
# NODE ATTRIBUTES
Expand All @@ -638,7 +638,7 @@ def create_nice_cx_from_server(server, username=None, password=None, uuid=None):
for att in objects:
niceCxBuilder._add_node_attribute_from_fragment(att)

#niceCxBuilder.add_node_attribute(att.get('po'), att.get('n'), att.get('v'), type=att.get('d'))
#niceCxBuilder.add_node_attribute(att.get('po'), att.get('n'), att.get('v'), attribute_type=att.get('d'))

# ===================
# EDGE ATTRIBUTES
Expand All @@ -649,7 +649,7 @@ def create_nice_cx_from_server(server, username=None, password=None, uuid=None):
niceCxBuilder._add_edge_attribute_from_fragment(att)

#niceCxBuilder.add_edge_attribute(property_of=att.get('po'), name=att.get('n'),
# values=att.get('v'), type=att.get('d'))
# values=att.get('v'), attribute_type=att.get('d'))

# ===================
# CITATIONS
Expand Down

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