fix add_default_workflow (#3446)

* fix add_default_workflow

* fix get_merging_scheme_from_job

* gp_params is not None

* str(y.id)

Author: antgonza

qiita_db/archive.py

@@ -116,6 +116,7 @@ def get_merging_scheme_from_job(cls, job):
             acmd = job.command
             parent = job.input_artifacts[0]
             parent_pparameters = parent.processing_parameters
+            phms = None
             if parent_pparameters is None:
                 parent_cmd_name = None
                 parent_parameters = None
@@ -125,12 +126,26 @@ def get_merging_scheme_from_job(cls, job):
                 parent_cmd_name = pcmd.name
                 parent_parameters = parent_pparameters.values
                 parent_merging_scheme = pcmd.merging_scheme
-
-            return qdb.util.human_merging_scheme(
+                if not parent_merging_scheme['ignore_parent_command']:
+                    gp = parent.parents[0]
+                    gp_params = gp.processing_parameters
+                    if gp_params is not None:
+                        gp_cmd = gp_params.command
+                        phms = qdb.util.human_merging_scheme(
+                            parent_cmd_name, parent_merging_scheme,
+                            gp_cmd.name, gp_cmd.merging_scheme,
+                            parent_parameters, [], gp_params.values)
+
+            hms = qdb.util.human_merging_scheme(
                 acmd.name, acmd.merging_scheme,
                 parent_cmd_name, parent_merging_scheme,
                 job.parameters.values, [], parent_parameters)
 
+            if phms is not None:
+                hms = qdb.util.merge_overlapping_strings(hms, phms)
+
+            return hms
+
     @classmethod
     def retrieve_feature_values(cls, archive_merging_scheme=None,
                                 features=None):

qiita_db/metadata_template/prep_template.py

@@ -808,14 +808,24 @@ def _get_node_info(workflow, node):
 
             parent_cmd_name = None
             parent_merging_scheme = None
+            phms = None
             if pcmd is not None:
                 parent_cmd_name = pcmd.name
                 parent_merging_scheme = pcmd.merging_scheme
+                if not parent_merging_scheme['ignore_parent_command']:
+                    phms = _get_node_info(workflow, parent)
 
-            return qdb.util.human_merging_scheme(
+            hms = qdb.util.human_merging_scheme(
                 ccmd.name, ccmd.merging_scheme, parent_cmd_name,
                 parent_merging_scheme, cparams, [], pparams)
 
+            # if the parent should not ignore its parent command, then we need
+            # to merge the previous result with the new one
+            if phms is not None:
+                hms = qdb.util.merge_overlapping_strings(hms, phms)
+
+            return hms
+
         def _get_predecessors(workflow, node):
             # recursive method to get predecessors of a given node
             pred = []
@@ -871,7 +881,7 @@ def _get_predecessors(workflow, node):
                          'artifact transformation']
         merging_schemes = {
             qdb.archive.Archive.get_merging_scheme_from_job(j): {
-                x: y.id for x, y in j.outputs.items()}
+                x: str(y.id) for x, y in j.outputs.items()}
             # we are going to select only the jobs that were a 'success', that
             # are not 'hidden' and that have an output - jobs that are not
             # hidden and a successs but that do not have outputs are jobs which
@@ -989,7 +999,7 @@ def _get_predecessors(workflow, node):
                     init_artifacts = {
                         wkartifact_type: f'{starting_job.id}:'}
                 else:
-                    init_artifacts = {wkartifact_type: self.artifact.id}
+                    init_artifacts = {wkartifact_type: str(self.artifact.id)}
 
             cmds_to_create.reverse()
             current_job = None

qiita_db/util.py

@@ -2955,3 +2955,25 @@ def merge_rows(rows):
                 row['node_model']]
             qdb.sql_connection.TRN.add(sql, sql_args=to_insert)
             qdb.sql_connection.TRN.execute()
+
+
+def merge_overlapping_strings(str1, str2):
+    """Helper function to merge 2 overlapping strings
+
+    Parameters
+    ----------
+    str1: str
+        Initial string
+    str2: str
+        End string
+
+    Returns
+    ----------
+    str
+        The merged strings
+    """
+    overlap = ""
+    for i in range(1, min(len(str1), len(str2)) + 1):
+        if str1.endswith(str2[:i]):
+            overlap = str2[:i]
+    return str1 + str2[len(overlap):]