test: add reference to test data

data/ex/data.zarr/.zmetadata

@@ -5,66 +5,62 @@
         },
         "ex/.zattrs": {
             "@type": "MODO",
-            "creation_date": "2024-01-03T00:00:00",
-            "has_assay": [
-                "demo-assay"
-            ],
-            "last_update_date": "2024-01-04T00:00:00"
+            "creation_date": "2024-01-17T00:00:00",
+            "description": "Example modo for tests",
+            "last_update_date": "2024-01-17T00:00:00",
+            "name": "Example"
         },
         "ex/.zgroup": {
             "zarr_format": 2
         },
-        "ex/demo-assay/.zattrs": {
+        "ex/assay1/.zattrs": {
             "@type": "Assay",
-            "description": "Fake dataset used for tests.",
+            "description": "Example assay for tests",
             "has_data": [
-                "demo1",
-                "demo1",
-                "demo2"
+                "ex/assay1/demo1"
+            ],
+            "has_sample": [
+                "ex/assay1/sample1"
             ],
-            "name": "E. coli dummy WGS",
+            "name": "Assay 1",
             "omics_type": [
                 "GENOMICS"
             ]
         },
-        "ex/demo-assay/.zgroup": {
+        "ex/assay1/.zgroup": {
             "zarr_format": 2
         },
-        "ex/demo-assay/demo1/.zattrs": {
-            "@type": "AlignmentSet",
+        "ex/assay1/demo1/.zattrs": {
+            "@type": "DataEntity",
             "data_format": "CRAM",
             "data_path": "demo1.cram",
-            "description": "E. coli wgs",
-            "has_sample": [
-                "bac1"
+            "description": "Demo CRAM file for tests.",
+            "has_reference": [
+                "ex/assay1/demo1/reference1"
             ],
-            "name": "demo 1"
+            "name": "Demo 1"
         },
-        "ex/demo-assay/demo1/.zgroup": {
+        "ex/assay1/demo1/.zgroup": {
             "zarr_format": 2
         },
-        "ex/demo-assay/demo1/bac1/.zattrs": {
-            "@type": "Sample",
-            "collector": [
-                "SDSC"
-            ],
-            "description": "A bacterial sample",
-            "name": "bac 1",
-            "taxon_id": [
-                562
-            ]
+        "ex/assay1/demo1/reference1/.zattrs": {
+            "@type": "ReferenceGenome",
+            "data_path": "reference.fa",
+            "name": "reference 1"
         },
-        "ex/demo-assay/demo1/bac1/.zgroup": {
+        "ex/assay1/demo1/reference1/.zgroup": {
             "zarr_format": 2
         },
-        "ex/demo-assay/demo2/.zattrs": {
-            "@type": "AlignmentSet",
-            "data_format": "CRAM",
-            "data_path": "demo2.cram",
-            "description": "E. coli wgs resequencing",
-            "name": "demo 2"
+        "ex/assay1/sample1/.zattrs": {
+            "@type": "Sample",
+            "collector": [
+                "Foo university"
+            ],
+            "description": "A dummy sample for tests.",
+            "name": "Sample 1",
+            "sex": "Male"
         },
-        "ex/demo-assay/demo2/.zgroup": {
+        "ex/assay1/sample1/.zgroup": {
             "zarr_format": 2
         }
     },

data/ex/data.zarr/ex/.zattrs

@@ -1,8 +1,7 @@
 {
     "@type": "MODO",
-    "has_assay": [
-        "demo-assay"
-    ],
-    "creation_date": "2024-01-03T00:00:00",
-    "last_update_date": "2024-01-04T00:00:00"
+    "creation_date": "2024-01-17T00:00:00",
+    "description": "Example modo for tests",
+    "last_update_date": "2024-01-17T00:00:00",
+    "name": "Example"
 }

data/ex/data.zarr/ex/assay1/.zattrs

@@ -0,0 +1,14 @@
+{
+    "@type": "Assay",
+    "description": "Example assay for tests",
+    "has_data": [
+        "ex/assay1/demo1"
+    ],
+    "has_sample": [
+        "ex/assay1/sample1"
+    ],
+    "name": "Assay 1",
+    "omics_type": [
+        "GENOMICS"
+    ]
+}

data/ex/data.zarr/ex/assay1/demo1/.zattrs

@@ -0,0 +1,10 @@
+{
+    "@type": "DataEntity",
+    "data_format": "CRAM",
+    "data_path": "demo1.cram",
+    "description": "Demo CRAM file for tests.",
+    "has_reference": [
+        "ex/assay1/demo1/reference1"
+    ],
+    "name": "Demo 1"
+}

data/ex/data.zarr/ex/assay1/demo1/reference1/.zattrs

@@ -0,0 +1,5 @@
+{
+    "@type": "ReferenceGenome",
+    "data_path": "reference.fa",
+    "name": "reference 1"
+}

data/ex/data.zarr/ex/assay1/sample1/.zattrs

@@ -0,0 +1,9 @@
+{
+    "@type": "Sample",
+    "collector": [
+        "Foo university"
+    ],
+    "description": "A dummy sample for tests.",
+    "name": "Sample 1",
+    "sex": "Male"
+}

data/ex/reference.fa

@@ -0,0 +1,100 @@
+>BA000007.3 Escherichia coli O157:H7 str. Sakai DNA, part of genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGCTTCTGAACTG
+GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
+AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCACCACCATCACC
+ATTACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCT
+TTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACG
+TTTTCTGCGGGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAA
+TCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGT
+ATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGCCGGGATTCCCGCTGGCGCAATTGAAAACTTTCGTCGACCA
+GGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTAGGGCAGTGCCCGGATAGCATTAACGCTGCGCTGA
+TTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGAT
+CCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGC
+AAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTACTTG
+GACGCAACGGTTCCGACTACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTT
+GACGGGGTATATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAATCGATGTCCTACCAGGAAGCGATGGA
+GCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTA
+AAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGTCGTGATGAAGACGAATTACCGGTCAAGGGCATT
+TCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGAATGGTCGGCATGGCGGCGCGCGTCTT
+TGCTGCAATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTC
+CGCAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCG
+CTGGCGGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATT
+CTTTGCCGCGCTGGCCCGCGCCAATATCAACATTGTCGCTATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGG
+TAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTT
+GTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGTTGAAGAATAAACATAT
+CGACTTACGTGTCTGCGGTGTTGCTAACTCGAAGGCTCTGCTCACCAATGTGCATGGCCTAAATCTGGAAAACTGGCAGG
+AAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCG
+GTCATTGTTGACTGCACCTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCAC
+GCCGAACAAAAAGGCCAACACCTCGTCGATGGATTACTACCATCTGTTGCGTCATGCGGCTGAAAAATCGCGGCGTAAAT
+TCCTCTATGACACCAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCTGGTGATGAATTG
+ATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGC
+GACTACGCTGGCGCGGGAAATGGGTTATACCGAACCGGATCCGCGAGATGATCTTTCTGGTATGGATGTAGCGCGTAAAC
+TATTAATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTT
+AACGCTGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAGCTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGC
+CCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGG
+ATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTTTATAGCCACTATTATCAGCCGCTGCCG
+TTGGTGCTGCGCGGATATGGTGCGGGCAATGACGTTACCGCTGCCGGTGTCTTTGCCGATCTGCTACGTACCCTCTCATG
+GAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGG
+GCGGCGGTGACACCCGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGTCGGCAGAGACATTCAGTCTCAACAA
+CCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGG
+AGCTGGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGT
+TCGGTGGTCGCGGCTCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACCCGTTTGCTGGCTTTGATGGG
+CGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGA
+TCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAA
+GTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACACTTGGC
+AGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCAGAACCCTACC
+GTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGC
+TCCGGCCCGACCTTGTTTGCTCTGTGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCT
+GCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCT
+ACAATCTTAAAGATCACAATGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTT
+TTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAA
+GATCCTCTCGGCGTTTATTGGTGATGAAATCCCGCAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGG
+CTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGC
+GGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGCGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATAC
+CGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTTTATCCACGAGGCAAAATCAGTC
+CACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAG
+GCGCTGGTGAAGCAGGCGTTTGATGATGAAGAGCTGAAAGTGGCGCTGGGGTTAAACTCAGCTAACTCGATTAACATTAG
+CCGGTTGCTGGCGCAGATTTGCTACTACTTTGAAGCAGTTGCGCAGCTGCCGCAGGAAGCGCGCAACCAGCTGGTTGTCT
+CGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATT
+GCTGCGACCAACGTGAACGATACCGTGCCACGTTTCCTGCATGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTT
+ATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGA
+AAGAGCTGGGTTATGCCGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCG
+GAGCCGCACGCTGCCGTAGCGTATCGTGCGCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGC
+GCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTG
+CCGATTTACCCTTGCTTTCGCATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAACAT
+CTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTGTGAAGAAAATATGGAGAGAAACGACA
+GGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGCTCTCATCGC
+GTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCA
+CTTTCCCTGGTTCTGGTCGCTCCCATGGCAACGCAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGG
+CGATCGTGATAATCGCGGTTATTACTGGGATGGCGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGC
+GAGGCAATCGCTGGCACCCACACGGACCGCCGCCACCGCCGCGTCACCATAAGAAAGCTCATCATGATCATCACGGCGGT
+CATGGTCCAGGCAAACATCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCG
+CGTCTTATCAGGCCTACGTGAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCA
+TCCGGCATTGACTACAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAAGCTTCATCAAAG
+AAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAGACC
+GCGTGCTTTCTTAGCGTAGAAGCTGATTATCTTAAATTTGCCGTTCTTCTCATCGAGGAACACCGGCTTGATAATCTCGG
+CATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCG
+AGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGAT
+CCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCT
+GTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATC
+GCCTGGCGGGCATTCTCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCTGCCAGTTTGTCGCT
+GATACGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCTTCATGGATCAACTGCTGGGAATTGTCTAACAGCT
+CCGGCAGTGTATATCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCC
+AGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAAAGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGAAAC
+ATCATCCCACGCGTCCCGAGAAAGCTGGCGACCGATATCCGGATAACGCAACGGATCAAACACCGGGCGCACGCCGAGTT
+TACGCTGGCGTAGATAATCACTGGCAATGGTATGAACCACAGGCGAGAGCAGTAATATGGCAGTCAAATTGGTAATAGCC
+ATGCAGGCCATTATGATATCTGCCAGTTGCCACATCAGCGGAAGACTTAGCAAGGTGCCGCCGATGACCGTTGCGAAGGT
+GCAGATCCGCAAACACCAGATCGCTTTAGGGTTGTTCAGGCGTAAAAAGAAGAGATTGTTTTCGGCATAAATGTAGTTGG
+CAACGATGGAGCTGAAGGCAAACAGAATAACCACGAGGGTAACAAATTCAGCACCCCAGGAACCCATTAGCACCCGCATC
+GCCTTCTGGATAAGCTGAATACCTTCCAGCGGCATGTAGGTTGTGCCGTTACCCGCCAGTAATATCAGCATGGCGCTTGC
+CGTACAGATGACCAGGGTGTCGATAAAAATGCCAATCATCTGGACAATTCCTTGCGCTGCCGGATGCGGAGGCCAGGACG
+CCGCTGCCGCTGCCGCGTTTGGCGTCGACCCCATTCCCGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATC
+GCCTGGCTTAAGGTATATCCCGCCGCGCCGCCTGCCGCTTCCTGCCAGCCAAAAGCACTCTCAAAAATAGACCAAATGAC
+GTGGGGAAGTTGCCCGATATTTATTACGCAAATCACCAGGCTGGTCAGTACCCAGATTATCGCCATCAACGGGACAAACC
+CCTGCATGAGCCGGGCGACGCCATGAAGACCGCGAATGATTGCCAGCAGAGCAAAGACAGCAAGAATAATGCCTGTCACC
+AGCGGGGGAAAATCAAAAGAAAAACTCAGAGCTCGGGCAACAGCGTTTGCCTGAACTCCGCTGAAAATTATGCCGTAGGC
+GATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCAC
+GAAACTGCCCATTGACGTCACGTTCTTTATAAAGTTGTGCAAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAAC
+GCGGCAACCCACATCCAAAAGACGGCTCCAGGTCCACCGGCGGTAATAGCCAGCGCAACGCCGGCCAGGTTGCCGCTACC
+CACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTTAAGAC
+TTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGG

modo/api.py

@@ -174,6 +174,10 @@ def add_element(
             parent_path = next(self.archive.groups())[0]
         else:
             parent_path = part_of
+
+        element_path = parent_path + "/" + element.id
+
+        if part_of is not None:
             parent_type = getattr(
                 model,
                 self.metadata[parent_path]["@type"],
@@ -187,7 +191,7 @@ def add_element(
             # has_part is multivalued
             if has_prop not in self.archive[part_of].attrs:
                 self.archive[part_of].attrs[has_prop] = []
-            self.archive[part_of].attrs[has_prop] += [element.id]
+            self.archive[part_of].attrs[has_prop] += [element_path]
 
         # Add element to metadata
         parent_group = self.archive[parent_path]