From 470a7e08b6b7268122081327096573269f06623c Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Thu, 11 Apr 2024 15:39:07 +0200
Subject: [PATCH] minor update to workflows

---
 environment.yml                 |  3 +++
 pyscal_rdf/workflow/pyiron.py   |  2 +-
 pyscal_rdf/workflow/workflow.py | 30 +++++++++++++++++++++++++++---
 3 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/environment.yml b/environment.yml
index 32ab4ae..e6ca18c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,3 +16,6 @@ dependencies:
   - owlready2
   - plotly
   - ipywidgets
+  - sqlalchemy
+  - pip:
+    - "git+https://github.com/RDFLib/rdflib-sqlalchemy.git@develop"
diff --git a/pyscal_rdf/workflow/pyiron.py b/pyscal_rdf/workflow/pyiron.py
index 13ad67a..d1cf6f8 100644
--- a/pyscal_rdf/workflow/pyiron.py
+++ b/pyscal_rdf/workflow/pyiron.py
@@ -17,7 +17,7 @@ def _check_if_job_is_valid(job):
         raise TypeError('These type of pyiron Job is not currently supported')
 
 
-def _add_structures(kg, job):
+def _add_structures(job):
     initial_pyiron_structure = job.structure
     final_pyiron_structure = job.get_structure(frame=-1)
     initial_pyscal_structure =  System.read.ase(initial_pyiron_structure)
diff --git a/pyscal_rdf/workflow/workflow.py b/pyscal_rdf/workflow/workflow.py
index 936af82..1e29788 100644
--- a/pyscal_rdf/workflow/workflow.py
+++ b/pyscal_rdf/workflow/workflow.py
@@ -1,13 +1,22 @@
 """
 Workflows aspects for non-automated annotation of structures.
 
+This consists of a workflow class which implements the necessary methods to serialise triples as needed.
+Custom workflow solutions can be implemented. An example available here is pyiron.
+The custom workflow env should implement the following functions:
+
+_check_if_job_is_valid
+_add_structure
+_identify_method
+extract_calculated_properties
+inform_graph
+
+See pyscal_rdf.workflow.pyiron for more details
 """
 
 from pyscal_rdf.structure import System
 from rdflib import Graph, Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef, FOAF, SKOS, DCTERMS
 
-import pyscal_rdf.workflow.pyiron as pi
-
 import warnings
 import numpy as np
 import os
@@ -15,14 +24,29 @@
 import ast
 import uuid
 
+#Move imports to another file
 PROV = Namespace("http://www.w3.org/ns/prov#")
 CMSO = Namespace("http://purls.helmholtz-metadaten.de/cmso/")
 PODO = Namespace("http://purls.helmholtz-metadaten.de/podo/")
 ASO = Namespace("http://purls.helmholtz-metadaten.de/aso/")
 
+#custom imports as needed
+import pyscal_rdf.workflow.pyiron as pi
+
+
 class Workflow:
     def __init__(self, kg, 
         environment='pyiron'):
+        """
+        Initialize the workflow environment
+
+        Parameters
+        ----------
+        kg: pyscal-rdf KnowledgeGraph
+        environment: string
+            the workflow environment. This is used to import the necessary functions.
+
+        """
         self.kg = kg
         if environment == 'pyiron':
             self.wenv = pi
@@ -31,7 +55,7 @@ def __init__(self, kg,
 
     def _prepare_job(self, workflow_object):
         self.wenv._check_if_job_is_valid(workflow_object)
-        parent_structure, parent_sample, structure, sample = self.wenv._add_structures(self.kg, workflow_object)
+        parent_structure, parent_sample, structure, sample = self.wenv._add_structures(workflow_object)
         method_dict = self.wenv._identify_method(workflow_object)
 
         if (structure is None) and (sample is None):