From f07fe616cfdad95597690d039c26e9d9ba8b5b90 Mon Sep 17 00:00:00 2001
From: haeussma <83341109+haeussma@users.noreply.github.com>
Date: Fri, 27 Sep 2024 19:02:46 +0200
Subject: [PATCH] rerun tests

---
 docs/examples/SAHH_kinetics.ipynb           |   42 +-
 docs/examples/data/enzymeml_TmSAHH_SAH.json | 1676 +++++++++----------
 2 files changed, 852 insertions(+), 866 deletions(-)

diff --git a/docs/examples/SAHH_kinetics.ipynb b/docs/examples/SAHH_kinetics.ipynb
index ac55366..032f852 100644
--- a/docs/examples/SAHH_kinetics.ipynb
+++ b/docs/examples/SAHH_kinetics.ipynb
@@ -92,20 +92,6 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [],
-   "source": [
-    "from mtphandler.molecule import Protein\n",
-    "\n",
-    "my_variant = Protein(\n",
-    "    id=\"L191G\",\n",
-    "    name=\"L191G\",\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -144500,7 +144486,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144542,7 +144528,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144586,19 +144572,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
-       "<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
+       "<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
        "</pre>\n"
       ],
       "text/plain": [
-       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n",
-       "\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
+       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\n",
+       "\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
       ]
      },
      "metadata": {},
@@ -144634,7 +144620,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -144874,7 +144860,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -144914,7 +144900,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -147682,7 +147668,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147717,7 +147703,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -147748,7 +147734,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -147807,7 +147793,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json
index 9847b80..1c191ca 100644
--- a/docs/examples/data/enzymeml_TmSAHH_SAH.json
+++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json
@@ -18,7 +18,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "enzml:BaseUnit/5e0b185b-48eb-4282-8b06-365f5daf0665",
+                        "ld_id": "enzml:BaseUnit/085c0609-ab77-4c89-9686-e00e2628535c",
                         "ld_type": [
                             "enzml:BaseUnit"
                         ],
@@ -29,7 +29,7 @@
                         }
                     }
                 ],
-                "ld_id": "enzml:UnitDefinition/8e86dd4e-c6dd-4def-a82a-0326aea97524",
+                "ld_id": "enzml:UnitDefinition/380763e6-e15c-4f8e-b8a0-4a286d0da22d",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -40,7 +40,7 @@
                 }
             },
             "constant": true,
-            "ld_id": "enzml:Vessel/dddda8f2-2c71-4b4e-9721-0727fba436f6",
+            "ld_id": "enzml:Vessel/42805267-b5a9-4bfe-b348-061d4f044a46",
             "ld_type": [
                 "enzml:Vessel",
                 "OBO:OBI_0400081"
@@ -69,7 +69,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/46f25b1c-6827-4996-bdc6-aa5a1c1013aa",
+            "ld_id": "enzml:Protein/efc8d1cb-4880-4115-9980-f0ae647afa2b",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -107,7 +107,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/e7555c43-6761-4551-a3eb-3f2d091335dc",
+            "ld_id": "enzml:Protein/84b031d1-b665-4d92-b783-c50f39095dd7",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -145,7 +145,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/13580886-c6ec-404c-af88-b1dca28f9ced",
+            "ld_id": "enzml:Protein/2d55f1d7-2376-4fc1-b65e-0261440fc0c4",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -183,7 +183,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/0d401d19-df8b-4695-96f9-9f68e54d5867",
+            "ld_id": "enzml:Protein/abbc1199-549a-4ebb-8040-1873c6ea95f0",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -223,7 +223,7 @@
             "inchi": null,
             "inchikey": null,
             "references": [],
-            "ld_id": "enzml:SmallMolecule/742602e5-b8f4-42a8-bfdb-150595b822ab",
+            "ld_id": "enzml:SmallMolecule/f5ddc0d9-cfb3-44ec-876e-17a4eeec3def",
             "ld_type": [
                 "enzml:SmallMolecule"
             ],
@@ -425,7 +425,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -438,7 +438,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/55582c11-57ea-4f12-b140-1b520d243ce2",
+                                "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -468,7 +468,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/20988505-e1dc-4fee-9baa-edf58a9b95c7",
+                                "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -486,7 +486,93 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/5ff53c97-5633-4515-9781-05bce920409b",
+                    "ld_id": "enzml:MeasurementData/2d97c741-c14f-49cd-a02f-84a032d483e0",
+                    "ld_type": [
+                        "enzml:MeasurementData"
+                    ],
+                    "ld_context": {
+                        "enzml": "http://www.enzymeml.org/v2/",
+                        "schema": "https://schema.org/",
+                        "OBO": "http://purl.obolibrary.org/obo/",
+                        "species_id": {
+                            "@type": "@id"
+                        }
+                    }
+                },
+                {
+                    "species_id": "BUFFER",
+                    "initial": 50.0,
+                    "data_unit": {
+                        "id": null,
+                        "name": "umol / l",
+                        "base_units": [
+                            {
+                                "kind": "mole",
+                                "exponent": 1,
+                                "multiplier": null,
+                                "scale": -6.0,
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            },
+                            {
+                                "kind": "litre",
+                                "exponent": -1,
+                                "multiplier": null,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000064",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
+                    "prepared": 50.0,
+                    "data": [],
+                    "time": [],
+                    "time_unit": {
+                        "id": null,
+                        "name": "s",
+                        "base_units": [
+                            {
+                                "kind": "second",
+                                "exponent": 1,
+                                "multiplier": 60.0,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000031",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "is_simulated": false,
+                    "ld_id": "enzml:MeasurementData/487ebfd9-6d55-4f0e-897c-d211a2f6dae9",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -511,7 +597,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -524,7 +610,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/55582c11-57ea-4f12-b140-1b520d243ce2",
+                                "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -1998,7 +2084,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/20988505-e1dc-4fee-9baa-edf58a9b95c7",
+                                "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2016,7 +2102,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/61561a0e-c353-4bb6-8ce7-12afe4323dab",
+                    "ld_id": "enzml:MeasurementData/97d7bf19-8513-4730-a815-2a84b8ea2625",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -2028,10 +2114,61 @@
                             "@type": "@id"
                         }
                     }
+                }
+            ],
+            "group_id": "",
+            "ph": 7.4,
+            "temperature": 37.04466019417476,
+            "temperature_unit": {
+                "id": null,
+                "name": "Celsius",
+                "base_units": [
+                    {
+                        "kind": "celsius",
+                        "exponent": 1,
+                        "multiplier": null,
+                        "scale": 1.0,
+                        "ld_id": "md:BaseUnit/d0bcada3-1c11-4e8f-aa1e-aebc218f6be5",
+                        "ld_type": [
+                            "md:BaseUnit"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    }
+                ],
+                "ld_id": "md:UnitDefinition/6ac5c79a-36fd-4f2c-acba-6ac83b58fdba",
+                "ld_type": [
+                    "OBO:UO_0000000"
+                ],
+                "ld_context": {
+                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                }
+            },
+            "ld_id": "enzml:Measurement/cb1495b3-cd84-4c00-ac7c-4c79c9aa7619",
+            "ld_type": [
+                "enzml:Measurement"
+            ],
+            "ld_context": {
+                "enzml": "http://www.enzymeml.org/v2/",
+                "schema": "https://schema.org/",
+                "OBO": "http://purl.obolibrary.org/obo/",
+                "id": {
+                    "@id": "schema:identifier",
+                    "@type": "@id"
                 },
+                "group_id": {
+                    "@type": "@id"
+                }
+            }
+        },
+        {
+            "id": "F8",
+            "name": "photometric measurement",
+            "species_data": [
                 {
-                    "species_id": "BUFFER",
-                    "initial": 50.0,
+                    "species_id": "Hyc",
+                    "initial": 0.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -2041,7 +2178,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -2054,7 +2191,7 @@
                                 "exponent": -1,
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