minor updates to metadata parsing

ResearchObject · Apr 14, 2022 · 299f6f4 · 299f6f4
1 parent 81b1e1e
commit 299f6f4
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Showing 2 changed files with 26 additions and 9 deletions.
diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py
@@ -16,7 +16,7 @@
 
 from prov.identifier import Identifier
 from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity
-from tools.load_ga_export import load_ga_history_export, GalaxyJob
+from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset
 from ast import literal_eval
 import os
 
@@ -109,14 +109,30 @@ def __init__(
         # move to separate function
         metadata_export = load_ga_history_export(ga_export)
         self.generate_prov_doc()
-        self.jobs = []
+
+        self.datasets = {}
         # print(metadata_export["jobs_attrs"][0]["params"])
-        for job in metadata_export["jobs_attrs"]:
+        for i,dataset in enumerate(metadata_export["datasets_attrs"]):
+            datasets_attrs = GalaxyDataset()
+            datasets_attrs.parse_ga_dataset_attrs(dataset)
+            print(i)
+            print(datasets_attrs.attributes['encoded_id'])
+            self.datasets[datasets_attrs.attributes['encoded_id']] = datasets_attrs.attributes
+            # self.declare_process(ds_attrs.attributes)
+
+        self.jobs = {}
+        for i,job in enumerate(metadata_export["jobs_attrs"]):
             job_attrs = GalaxyJob()
             job_attrs.parse_ga_jobs_attrs(job)
-            self.jobs.append(job_attrs.attributes)
+            print(i)
+            print(job_attrs.attributes.keys())
+            # for k,v in job_attrs.attributes['parameters'].items():
+            #     print(k, "      :     ",v)
+            self.jobs[job_attrs.attributes['encoded_id']] = job_attrs.attributes
             self.declare_process(job_attrs.attributes)
 
+        # print(self.jobs[0]['inputs'])
+
     def __str__(self) -> str:
         """Represent this Provenvance profile as a string."""
         return "ProvenanceProfile <{}>".format(
@@ -223,7 +239,8 @@ def declare_process(
         # cmd = ga_export_jobs_attrs["command_line"]
         process_name = ga_export_jobs_attrs["tool_id"]
         # tool_version = ga_export_jobs_attrs["tool_version"]
-        prov_label = "Run of ga_export/jobs_attrs.txt#" + process_name
+        # TODO: insert workflow id 
+        prov_label = "Run of workflow_id_placeholder" + process_name
         start_time = ga_export_jobs_attrs["create_time"]
         end_time = ga_export_jobs_attrs["update_time"]
 

diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py
@@ -48,21 +48,21 @@ def parse_ga_jobs_attrs(self, job_attrs):
 
 class GalaxyDataset(Dict):
 
-    def __init__(self, ga_export_dataset_attrs):
+    def __init__(self):
         """
         Initialize the GalaxyDataset object.
         """
         self.attributes = {}
         self.attributes["metadata"] = {}
 
-    def parse_ga_dataset_attrs(self, job_attrs):
+    def parse_ga_dataset_attrs(self, dataset_attrs):
 
-        for key, value in job_attrs.items():
+        for key, value in dataset_attrs.items():
             if not isinstance(value, dict):
                 self.attributes[key] = value
             else:
                 if len(value) == 0:
                     pass
                 else:
                     if "metadata" in key:
-                        self.attributes["metadata"].update(job_attrs[key])
+                        self.attributes["metadata"].update(dataset_attrs[key])