upgrading github action to clear error message

ISA-tools · Oct 23, 2023 · b265303 · b265303
1 parent a2a5a98
commit b265303
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Showing 2 changed files with 17 additions and 11 deletions.
diff --git a/.github/workflows/buildandtestpython.yml b/.github/workflows/buildandtestpython.yml
@@ -13,9 +13,9 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Download Test Data

diff --git a/isatools/isatab/dump/write.py b/isatools/isatab/dump/write.py
@@ -62,8 +62,9 @@ def flatten(current_list):
         log.warning(s_graph.nodes())
 
         sample_in_path_count = 0
+        protocol_in_path_count = 0
         longest_path = _longest_path_and_attrs(paths, s_graph.indexes)
-
+        
         for node_index in longest_path:
             node = s_graph.indexes[node_index]
             if isinstance(node, Source):
@@ -76,8 +77,9 @@ def flatten(current_list):
                     map(lambda x: get_comment_column(
                         olabel, x), node.comments))
             elif isinstance(node, Process):
-                olabel = "Protocol REF.{}".format(node.executes_protocol.name)
+                olabel = "Protocol REF.{}".format(protocol_in_path_count)
                 columns.append(olabel)
+                protocol_in_path_count += 1
                 if node.executes_protocol.name not in protnames.keys():
                     protnames[node.executes_protocol.name] = protrefcount
                     protrefcount += 1
@@ -104,6 +106,7 @@ def flatten(current_list):
                 columns += flatten(map(lambda x: get_fv_columns(olabel, x),
                                        node.factor_values))
 
+
         omap = get_object_column_map(columns, columns)
         # load into dictionary
         df_dict = dict(map(lambda k: (k, []), flatten(omap)))
@@ -113,6 +116,7 @@ def flatten(current_list):
                 df_dict[k].extend([""])
 
             sample_in_path_count = 0
+            protocol_in_path_count = 0
             for node_index in path_:
                 node = s_graph.indexes[node_index]
                 if isinstance(node, Source):
@@ -129,8 +133,8 @@ def flatten(current_list):
                         df_dict[colabel][-1] = co.value
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                    protocol_in_path_count += 1
                     df_dict[olabel][-1] = node.executes_protocol.name
                     for pv in node.parameter_values:
                         pvlabel = "{0}.Parameter Value[{1}]".format(
@@ -263,6 +267,8 @@ def flatten(current_list):
             if _longest_path_and_attrs(paths, a_graph.indexes) is None:
                 raise IOError(
                     "Could not find any valid end-to-end paths in assay graph")
+
+            protocol_in_path_count = 0
             for node_index in _longest_path_and_attrs(paths, a_graph.indexes):
                 node = a_graph.indexes[node_index]
                 if isinstance(node, Sample):
@@ -279,9 +285,9 @@ def flatten(current_list):
                                 node.factor_values))
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
                     columns.append(olabel)
+                    protocol_in_path_count += 1
                     if node.executes_protocol.name not in protnames.keys():
                         protnames[node.executes_protocol.name] = protrefcount
                         protrefcount += 1
@@ -338,12 +344,12 @@ def pbar(x):
                 for k in df_dict.keys():  # add a row per path
                     df_dict[k].extend([""])
 
+                protocol_in_path_count = 0
                 for node_index in path_:
                     node = a_graph.indexes[node_index]
                     if isinstance(node, Process):
-                        olabel = "Protocol REF.{}".format(
-                            node.executes_protocol.name
-                        )
+                        olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                        protocol_in_path_count += 1
                         df_dict[olabel][-1] = node.executes_protocol.name
                         if node.executes_protocol.protocol_type:
                             oname_label = get_column_header(