Major Model Refactoring 2.0.0 (#160)

* Task/cv review (#153)

* changed data use enums to upper snake case

* updated case/control CV

* fix spelling

* updated storage enum

* updated study_type CV

* updated artifacts; fixed error

* added study type enums, generated artifacts

* reviewed properties; updated artifacts (#154)

* reviewed properties; updated artifacts

* implemented requested changes; updated artifacts

* Task/refactor modular model (#155)

* updated sample class

* updated individual class

* Deprecated reference_genome and reference_chromosome

* deprecated karyotype enum

* file entity update

* file update: lane nr

* analysis class update

* experiment class update

* clean up

* updated scripts; generated artifacts

* fixed missing sequencing_lane_id slot

* xlsx check

* minor fixes, description updates

* updated spreadsheet_conf; generated artifacts

* description update; sheet order update; generated artifacts

* updated "inlined" flag; generated artifacts

* "inlined" flag update

* supporting file anchor entity

* pseudofile declaration

* research data file -> multivalued

* slot update: ontology term/id, file anchors updated

* added 'ega_accession' slot for mappable classes

* bug fix, generated artifacts

* bug fix; generated artifacts

* supporting_file class update, CV update, added parameter and software versions

* supporting file update, CV update; generated artifacts

* bug fix, generated artifacts

* renamed to ExperimentMethod, description fixes; generated artifacts

* description updates; generated artifacts

* version update to 1.2.0

* generated artifacts

---------

Co-authored-by: anandhi-iyappan <anandhi.iyappan@embl.de>

* Fix/linkages (#157)

* added dataset - study link; experiment description fix

* ega_accession link fix

* file - analysis - analysis method linkage and cardinality; generated artifacts

* revision: analysis-research_data_file linkage; generated artifacts

* updated docs

* er update

* updated slot definitions for parameter and software version

* Update src/schema/submission.yaml

Co-authored-by: Leon Kuchenbecker <leon.kuchenbecker@uni-tuebingen.de>

* Update src/schema/submission.yaml

Co-authored-by: Leon Kuchenbecker <leon.kuchenbecker@uni-tuebingen.de>

* updated descriptions

---------

Co-authored-by: sbilge <bilge.sueruen@uni-tuebingen.de>
Co-authored-by: Leon Kuchenbecker <leon.kuchenbecker@uni-tuebingen.de>

* added integer range for replicate slots and boolean range for pseudof… (#158)

* added integer range for replicate slots and boolean range for pseudofile slot

* generated artifacts

* Fix/slot fixes (#159)

* set "required" flag to "true" in Submission class

* slot update / deprecation of unused slots

* ontology term and id separation

* delete size, checksum and checksum_type

---------

Co-authored-by: sbilge <bilge.sueruen@uni-tuebingen.de>

---------

Co-authored-by: Karoline Mauer <105430060+mauerk@users.noreply.github.com>
Co-authored-by: anandhi-iyappan <anandhi.iyappan@embl.de>
Co-authored-by: sbilge <bilge.sueruen@uni-tuebingen.de>

Author: 4 people

.erdiagrams.yaml

@@ -4,39 +4,53 @@
   model: submission.yaml
   tree_root: true
   include_attributes: false
-- title: Sample, Biospecimen, & Individual
-  description: Focusses on the relation between Sample, Biospecimen, and Individual.
+- title: Sample & Individual
+  description: Focusses on the relation between Sample and Individual.
   model: submission.yaml
-  classes: ["Sample", "Biospecimen", "Individual"]
+  classes: ["Sample", "Individual"]
   tree_root: false
   include_attributes: false
 - title: Experiment, Sample, & File
   description: Focusses on the relation between Experiment, Sample, and File.
   model: submission.yaml
-  classes: ["SequencingExperiment", "Sample", "File", "SequencingProcess"]
+  classes:
+    [
+      "Experiment",
+      "Sample",
+      "ResearchDataFile",
+      "ExperimentMethod",
+      "ExperimentMethodSupportingFile",
+    ]
   tree_root: false
   include_attributes: false
-- title: Study, Condition, & Sample
-  description: Focusses on the relation between Study, Condition, and Sample.
-  model: submission.yaml
-  classes: ["Study", "Condition", "Sample"]
-  tree_root: false
-  include_attributes: false
-- title: Sample, Biospecimen, & Individual (with attributes)
+# - title: Study & Sample
+#   description: Focusses on the relation between Study, Condition, and Sample.
+#   model: submission.yaml
+#   classes: ["Study", "Sample"]
+#   tree_root: false
+#   include_attributes: false
+- title: Sample & Individual (with attributes)
   description: Focusses on the details of the relation between Sample, Biospecimen, and Individual.
   model: submission.yaml
-  classes: ["Sample", "Biospecimen", "Individual"]
+  classes: ["Sample", "Individual"]
   tree_root: false
   include_attributes: true
 - title: Experiment, Sample, & File (with attributes)
   description: Focusses on the relation between Experiment, Sample, and File.
   model: submission.yaml
-  classes: ["SequencingExperiment", "Sample", "File", "SequencingProcess"]
-  tree_root: false
-  include_attributes: true
-- title: Study, Condition, & Sample (with attributes)
-  description: Focusses on the relation between Study, Condition, and Sample.
-  model: submission.yaml
-  classes: ["Study", "Condition", "Sample"]
+  classes:
+    [
+      "Experiment",
+      "Sample",
+      "ResearchDataFile",
+      "ExperimentMethod",
+      "ExperimentMethodSupportingFile",
+    ]
   tree_root: false
   include_attributes: true
+# - title: Study & Sample (with attributes)
+#   description: Focusses on the relation between Study, Condition, and Sample.
+#   model: submission.yaml
+#   classes: ["Study", "Sample"]
+#   tree_root: false
+#   include_attributes: true