diff --git a/.gitignore b/.gitignore index 06a56dd9..2d4a619d 100644 --- a/.gitignore +++ b/.gitignore @@ -26,6 +26,12 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST +scripts/MRI_ingest +scripts/Exaspim_ingest/original_spec_files +scripts/Exaspim_ingest/ExM Sample Tracking.xlsx +scripts/Exaspim_ingest/output +scripts/Exaspim_ingest/original_plus_materials +scripts/Exaspim_ingest/tars_info # PyInstaller # Usually these files are written by a python script from a template @@ -137,3 +143,6 @@ dmypy.json # MacOs **/.DS_Store + +# MRI stuff +scripts/MRI_ingest/MRI_files/* diff --git a/scripts/Exaspim_ingest/AIND_AntibodyMasterList.xlsx b/scripts/Exaspim_ingest/AIND_AntibodyMasterList.xlsx new file mode 100644 index 00000000..9ceec933 Binary files /dev/null and b/scripts/Exaspim_ingest/AIND_AntibodyMasterList.xlsx differ diff --git a/scripts/Exaspim_ingest/ExM Sample Tracking.xlsx b/scripts/Exaspim_ingest/ExM Sample Tracking.xlsx new file mode 100644 index 00000000..4bf8e954 Binary files /dev/null and b/scripts/Exaspim_ingest/ExM Sample Tracking.xlsx differ diff --git a/scripts/Exaspim_ingest/Mouse Tracker - Molecular Anatomy.xlsx b/scripts/Exaspim_ingest/Mouse Tracker - Molecular Anatomy.xlsx new file mode 100644 index 00000000..9b7eda6f Binary files /dev/null and b/scripts/Exaspim_ingest/Mouse Tracker - Molecular Anatomy.xlsx differ diff --git a/scripts/Exaspim_ingest/Mouse Tracker - RO injections.xlsx b/scripts/Exaspim_ingest/Mouse Tracker - RO injections.xlsx new file mode 100644 index 00000000..abb6a0ba Binary files /dev/null and b/scripts/Exaspim_ingest/Mouse Tracker - RO injections.xlsx differ diff --git a/scripts/Exaspim_ingest/ingest_exaspim.ipynb b/scripts/Exaspim_ingest/ingest_exaspim.ipynb new file mode 100644 index 00000000..f24ee2e5 --- /dev/null +++ b/scripts/Exaspim_ingest/ingest_exaspim.ipynb @@ -0,0 +1,598 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " Name Target Fluorophore \\\n", + "0 NaN Primaries NaN \n", + "1 NaN PRIMARY CONJUGATED NaN \n", + "2 Rabbit anti-GFP AF 488 Anti-GFP AlexaFluor 488 \n", + "3 Rabbit Anti-GFP AF 488 Anti-GFP AlexaFluor 488 \n", + "4 X Anti-tdT AF 568 Anti-tdT AlexaFluor 568 \n", + ".. ... ... ... \n", + "124 NaN Anti-Rabbit IgG (H+L) NaN \n", + "125 NaN Anti-Chicken IgY (H+L) NaN \n", + "126 NaN NaN NaN \n", + "127 NaN Anti-chicken IgY (H+L) NaN \n", + "128 Rabbit Anti-GFP Anti-GFP NaN \n", + "\n", + " Host Species Clone Company Catalog# RRID Lot# \\\n", + "0 NaN NaN NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN NaN NaN \n", + "2 Rabbit Polyclonal Invitrogen A-21311 AB_221477 2406548 \n", + "3 Rabbit Polyclonal Invitrogen A-21311 AB_221477 2413728 \n", + "4 X NaN Janelia NaN NaN NaN \n", + ".. ... ... ... ... ... ... \n", + "124 Donkey NaN Invitrogen A-21206 NaN 2330673 \n", + "125 Goat NaN Invitrogen A-21449 NaN 2420700 \n", + "126 Goat NaN Invitrogen A-11041 NaN 1622573 \n", + "127 Goat NaN Invitrogen A-11041 NaN 2335730 \n", + "128 Rabbit Polyclonal Abcam AB290 AB_303395 1037873-6 \n", + "\n", + " Amount Concentration # of vials Location Dilution \\\n", + "0 NaN NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN NaN \n", + "2 100 uL 2 mg/mL 1.0 4C NaN \n", + "3 100 uL 2 mg/mL 1.0 4C NaN \n", + "4 NaN 0.315ug/ul 1.0 -20C NaN \n", + ".. ... ... ... ... ... \n", + "124 500 uL (2 mg/mL) NaN NaN NaN NaN \n", + "125 500 uL (2 mg/mL) NaN NaN NaN NaN \n", + "126 500 uL NaN NaN NaN NaN \n", + "127 500 uL NaN NaN NaN NaN \n", + "128 50ul (0mg/ml) NaN 1.0 4C NaN \n", + "\n", + " Notes \n", + "0 NaN \n", + "1 NaN \n", + "2 primary conjugate \n", + "3 primary conjugate \n", + "4 Primary Conjugate From janelia. \"house-made\" \n", + ".. ... \n", + "124 NaN \n", + "125 NaN \n", + "126 NaN \n", + "127 NaN \n", + "128 Concentration : 5mg/mL \n", + "\n", + "[129 rows x 15 columns]\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\openpyxl\\styles\\stylesheet.py:226: UserWarning: Workbook contains no default style, apply openpyxl's default\n", + " warn(\"Workbook contains no default style, apply openpyxl's default\")\n", + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\openpyxl\\styles\\stylesheet.py:226: UserWarning: Workbook contains no default style, apply openpyxl's default\n", + " warn(\"Workbook contains no default style, apply openpyxl's default\")\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "import requests\n", + "import json\n", + "\n", + "from datetime import datetime\n", + "import glob\n", + "from enum import Enum\n", + "from pathlib import Path\n", + "\n", + "from aind_data_schema.core.procedures import SpecimenProcedure, ImmunolabelClass, HCRSeries, Antibody, Procedures\n", + "\n", + "from aind_data_schema_models.specimen_procedure_types import SpecimenProcedureType\n", + "\n", + "\n", + "from aind_data_schema_models.organizations import Organization\n", + "\n", + "from aind_data_schema_models.pid_names import PIDName\n", + "\n", + "from aind_data_schema_models.registry import Registry\n", + "\n", + "\n", + "sample_sheet = pd.read_excel(\"./ExM Sample Tracking.xlsx\", sheet_name=\"ExM Sample Tracking\", header=[0], converters={})\n", + "\n", + "antibody_sheet = pd.read_excel(\"./AIND_AntibodyMasterList.xlsx\", sheet_name=\"AIND_AntibodyMasterList\", header=[0], converters={})\n", + "print(antibody_sheet)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Index(['Auto', 'TRUE Priority', 'Submitted Priority', '#', 'External Sample',\n", + " 'Status', 'Processing Lead', 'Sample', 'Genotype', 'Label',\n", + " 'Age of Injection', 'tTA Virus Dose', 'DCM Delipidation Start',\n", + " 'DCM Delipidation End', 'SBiP Delipidation Start',\n", + " 'SBiP Delipidation End', 'Immuno: Primary Ab Start Date',\n", + " 'Immuno: Primary Antibody1',\n", + " 'Mass of Primary Antibody1 used per Brain (ug)',\n", + " 'Primary Antibody1 Catalog #', 'Primary Antibody1 Lot #',\n", + " 'Immuno: Primary Antibody2',\n", + " 'Mass of Primary Antibody2 used per Brain (ug)',\n", + " 'Primary Antibody2 Catalog #', 'Primary Antibody2 Lot #',\n", + " 'Immuno: Primary Antibody3',\n", + " 'Mass of Primary Antibody3 used per Brain (ug)',\n", + " 'Primary Antibody3 Catalog #', 'Primary Antibody3 Lot #',\n", + " 'Primary Antibody RRID', 'Immuno: Secondary Ab Start Date',\n", + " 'Immuno: Secondary Antibody1',\n", + " 'Mass of Secondary Antibody used per Brain (ug)',\n", + " 'Secondary Antibody Catalog #', 'Secondary Antibody Lot #',\n", + " 'Immuno: Secondary Antibody2',\n", + " 'Mass of Secondary Antibody2 used per Brain (ug)',\n", + " 'Secondary Antibody2 Catalog #', 'Secondary Antibody2 Lot #',\n", + " 'Immuno: Secondary Antibody3',\n", + " 'Mass of Secondary Antibody3 used per Brain (ug)',\n", + " 'Secondary Antibody3 Catalog #', 'Secondary Antibody3 Lot #',\n", + " 'Secondary Antibody RRID', 'Fluorophore1', 'Fluorophore2',\n", + " 'Fluorophore3', 'FluorophoreT', 'Gelation: MBS Start',\n", + " 'Gelation: MBS End', 'Gelation: AcX Start', 'Gelation: AcX End',\n", + " 'Gelation: PBS Wash Start', 'Gelation: PBS Wash End',\n", + " 'Gelation: Stock X + VA-044 Equilibration Start',\n", + " 'Gelation: Stock X + VA-044 Equilibration End',\n", + " 'Gelation + ProK RT Start', 'Gelation + ProK RT End',\n", + " 'Duration (days)', 'Gelation + Add'l ProK 37C Start',\n", + " 'Gelation + Add'l ProK 37C End',\n", + " 'Duration (days) Gelation + Add'l ProK 37C', 'PBS Wash Start',\n", + " 'PBS Wash End', 'Date of Storage in PBS Az 0.05% @4C',\n", + " 'Expansion Start Date', 'Expansion End Date', 'Notes', 'Notes II',\n", + " 'Notes III', 'Column34'],\n", + " dtype='object')\n" + ] + } + ], + "source": [ + "with pd.option_context(\"display.multi_sparse\", False):\n", + " print(sample_sheet.columns)\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "subj_procedures = {}\n", + "\n", + "download_files = False\n", + "\n", + "\n", + "if download_files:\n", + " for row_idx, row in sample_sheet.iterrows(): \n", + "\n", + " sample_id = str(row['Sample'])\n", + " print(sample_id)\n", + " \n", + " if len(sample_id) != 6:\n", + " continue\n", + "\n", + " # INFO: This originally loaded in the procedures files, but is not necessary at this moment since i have them saved. Prior block now loads these files into same structure.\n", + " request = requests.get(f\"http://aind-metadata-service-dev/procedures/{sample_id}\")\n", + " #TODO: check for invalid/missing models\n", + "\n", + " if request.status_code == 404 or request.status_code == 500:\n", + " print(f\"{sample_id} model not found {request.status_code}\")\n", + "\n", + " continue\n", + "\n", + " print(f\"code: {request.status_code}\")\n", + "\n", + " \n", + " item = request.json()\n", + " # print(item['message'])\n", + " if not item or not item['data']:\n", + " continue\n", + "\n", + " if item['message'] == 'Valid Model.':\n", + " with open(f'./original_spec_files/{sample_id}.json', 'w') as outfile:\n", + " json.dump(item['data'], outfile)\n", + " else:\n", + " with open(f'./original_spec_files/{sample_id}_invalid.json', 'w') as outfile:\n", + " json.dump(item['data'], outfile)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import List\n", + "\n", + "\n", + "class SpecMaker():\n", + " def __init__(self, experimenter, sample_id, existing_procedure:dict=None) -> None:\n", + " self.experimenter = experimenter\n", + " self.sample_id = sample_id\n", + " self.existing_procedure = existing_procedure\n", + " \n", + " def make_spec_procedure(self, start, end, procedure_type, procedure_name, notes=None, protocol_id=[\"unknown\"], reagent=[], antibodies:List[Antibody]=None, hcr_series:HCRSeries=None):\n", + " print(start, end, self.sample_id, procedure_type, procedure_name, notes, protocol_id, antibodies)\n", + " \n", + " if pd.isna(end):\n", + " end = start\n", + " return SpecimenProcedure(\n", + " procedure_type=procedure_type,\n", + " procedure_name=procedure_name,\n", + " specimen_id=self.sample_id,\n", + " start_date=start,\n", + " end_date=end,\n", + " experimenter_full_name=self.experimenter,\n", + " protocol_id=protocol_id,\n", + " reagents=reagent,\n", + " hcr_series=hcr_series,\n", + " antibodies=antibodies,\n", + " notes=notes,\n", + " )\n", + " \n", + " def load_spec_models(self, spec_models):\n", + " print(f'EXISTING PROCEDURE: {self.existing_procedure}')\n", + " print(f'SPEC MODELS: {spec_models}')\n", + " if len(self.existing_procedure.specimen_procedures) < 1:\n", + " self.existing_procedure.specimen_procedures = spec_models\n", + " else:\n", + " for model in spec_models:\n", + " self.existing_procedure.specimen_procedures.append(model)\n", + "\n", + " def make_procedures(self, path, spec_models):\n", + "\n", + " Procedures.model_construct(\n", + " subject_id=self.sample_id,\n", + " subject_procedures=self.existing_procedure,\n", + " specimen_procedures=spec_models,\n", + " notes=\"test build model\"\n", + " ).write_standard_file(\n", + " output_directory=path,\n", + " prefix=self.sample_id\n", + " )\n", + "\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pydantic\\main.py:352: UserWarning: Pydantic serializer warnings:\n", + " Expected `Union[Surgery, TrainingProtocol, WaterRestriction, definition-ref]` but got `dict` - serialized value may not be as expected\n", + " return self.__pydantic_serializer__.to_json(\n", + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pydantic\\main.py:352: UserWarning: Pydantic serializer warnings:\n", + " Expected `Union[Surgery, TrainingProtocol, WaterRestriction, definition-ref]` but got `dict` - serialized value may not be as expected\n", + " Expected `Union[Surgery, TrainingProtocol, WaterRestriction, definition-ref]` but got `dict` - serialized value may not be as expected\n", + " return self.__pydantic_serializer__.to_json(\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '576404', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2021-11-10 00:00:00 2021-12-03 00:00:00 576404 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2021-10-01 00:00:00 2021-10-11 00:00:00 576404 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2021-10-25 00:00:00 2021-11-03 00:00:00 576404 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '609105', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609105'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609105'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-05-05 00:00:00 2022-06-02 00:00:00 609105 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-01-21 00:00:00 2022-02-02 00:00:00 609105 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-02-03 00:00:00 2022-02-15 00:00:00 609105 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '609107', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609107'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609107'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-07-21 00:00:00 2022-08-18 00:00:00 609107 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-04-12 00:00:00 2022-04-29 00:00:00 609107 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-05-05 00:00:00 2022-05-14 00:00:00 609107 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '609281', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-05', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609281'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-01-05', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609281'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-07-21 00:00:00 2022-08-18 00:00:00 609281 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-04-12 00:00:00 2022-04-29 00:00:00 609281 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-05-05 00:00:00 2022-05-14 00:00:00 609281 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '614978', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-16', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['614978'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-16', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['614978'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-07-21 00:00:00 2022-08-18 00:00:00 614978 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-04-12 00:00:00 2022-04-29 00:00:00 614978 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-05-05 00:00:00 2022-05-14 00:00:00 614978 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '614980', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-16', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['614980'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-16', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['614980'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-07-21 00:00:00 2022-08-18 00:00:00 614980 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-04-12 00:00:00 2022-04-29 00:00:00 614980 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-05-05 00:00:00 2022-05-14 00:00:00 614980 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '615296', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-18', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['615296'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-01-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-02-18', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['615296'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-07-21 00:00:00 2022-08-18 00:00:00 615296 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-04-12 00:00:00 2022-04-29 00:00:00 615296 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-05-05 00:00:00 2022-05-14 00:00:00 615296 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '603033', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-06-16 00:00:00 2022-07-15 00:00:00 603033 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2021-12-26 00:00:00 2022-01-05 00:00:00 603033 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-01-05 00:00:00 2022-01-14 00:00:00 603033 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '618584', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-02-11', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-03-18', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['618584'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-02-11', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': None, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-03-18', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['618584'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-09-23 00:00:00 2022-10-26 00:00:00 618584 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-06-10 00:00:00 2022-06-23 00:00:00 618584 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-06-27 00:00:00 2022-07-14 00:00:00 618584 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '620631', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-04-01', 'experimenter_full_name': '13040', 'iacuc_protocol': '2104', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['620631'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-04-01', 'experimenter_full_name': '13040', 'iacuc_protocol': '2104', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['620631'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-11-08 00:00:00 2022-12-07 00:00:00 620631 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-06-21 00:00:00 2022-06-30 00:00:00 620631 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-07-06 00:00:00 2022-07-12 00:00:00 620631 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '620629', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-04-01', 'experimenter_full_name': '13040', 'iacuc_protocol': '2104', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['620629'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-04-01', 'experimenter_full_name': '13040', 'iacuc_protocol': '2104', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['620629'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2022-11-09 00:00:00 2022-12-01 00:00:00 620629 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-06-21 00:00:00 2022-06-30 00:00:00 620629 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-07-06 00:00:00 2022-07-12 00:00:00 620629 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "OG FILE: {'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '648860', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2022-09-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': {'virus_tars_id': 'AiV300024', 'plasmid_tars_alias': None, 'prep_lot_number': 'VT3214g', 'prep_date': '2023-02-04', 'prep_type': 'Purified', 'prep_protocol': 'SOP#VC003'}, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}]}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-10-31', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['648860'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "ORIGINAL SUBJ PROCEDURES: [{'procedure_type': 'Surgery', 'start_date': '2022-09-26', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None, 'injection_materials': [{'material_type': 'Virus', 'name': 'AAV-PHP-eB_Syn-Flex TRE-2tTA', 'tars_identifiers': {'virus_tars_id': 'AiV300024', 'plasmid_tars_alias': None, 'prep_lot_number': 'VT3214g', 'prep_date': '2023-02-04', 'prep_type': 'Purified', 'prep_protocol': 'SOP#VC003'}, 'addgene_id': None, 'titer': 30000000000, 'titer_unit': 'gc/mL'}], 'protocol_id': 'unknown'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}, {'procedure_type': 'Surgery', 'start_date': '2022-10-31', 'experimenter_full_name': '13040', 'iacuc_protocol': '2109', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['648860'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}]\n", + "2023-02-01 00:00:00 2023-02-27 00:00:00 648860 SpecimenProcedureType.GELATION Gelation None ['dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1'] None\n", + "2022-11-07 00:00:00 2022-11-17 00:00:00 648860 SpecimenProcedureType.DELIPIDATION DCM Delipidation None ['dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1'] None\n", + "2022-11-22 00:00:00 2022-12-06 00:00:00 648860 SpecimenProcedureType.DELIPIDATION SBiP Delipidation None ['dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1'] None\n", + "[Antibody(name='Goat Anti-tDT', source=Other(name='Other', abbreviation=None, registry=None, registry_identifier=None), rrid=None, lot_number='unknown', expiration_date=None, immunolabel_class='Primary', fluorophore=None, mass=Decimal('10.0'), mass_unit=, notes=None)]\n", + "2022-12-19 00:00:00 2022-12-19 00:00:00 648860 SpecimenProcedureType.IMMUNOLABELING Primary Antibody Immunolabeling None ['dx.doi.org/10.17504/protocols.io.ewov1okwylr2/v1'] [Antibody(name='Goat Anti-tDT', source=Other(name='Other', abbreviation=None, registry=None, registry_identifier=None), rrid=None, lot_number='unknown', expiration_date=None, immunolabel_class='Primary', fluorophore=None, mass=Decimal('10.0'), mass_unit=, notes=None)]\n" + ] + }, + { + "ename": "KeyError", + "evalue": "'Mass of Secondary Antibody1 used per Brain (ug)'", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3802\u001b[0m, in \u001b[0;36mIndex.get_loc\u001b[1;34m(self, key, method, tolerance)\u001b[0m\n\u001b[0;32m 3801\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m-> 3802\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_engine\u001b[38;5;241m.\u001b[39mget_loc(casted_key)\n\u001b[0;32m 3803\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\_libs\\index.pyx:138\u001b[0m, in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\_libs\\index.pyx:165\u001b[0m, in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mpandas\\_libs\\hashtable_class_helper.pxi:5745\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mpandas\\_libs\\hashtable_class_helper.pxi:5753\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[1;34m()\u001b[0m\n", + "\u001b[1;31mKeyError\u001b[0m: 'Mass of Secondary Antibody1 used per Brain (ug)'", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[5], line 115\u001b[0m\n\u001b[0;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m pd\u001b[38;5;241m.\u001b[39misna(immuno_antibody):\n\u001b[0;32m 113\u001b[0m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[1;32m--> 115\u001b[0m immuno_mass \u001b[38;5;241m=\u001b[39m row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mMass of \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mwhich\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Antibody\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m used per Brain (ug)\u001b[39m\u001b[38;5;124m'\u001b[39m]\n\u001b[0;32m 116\u001b[0m immuno_catalogue \u001b[38;5;241m=\u001b[39m row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mwhich\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Antibody\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Catalog #\u001b[39m\u001b[38;5;124m'\u001b[39m]\n\u001b[0;32m 117\u001b[0m immuno_lot \u001b[38;5;241m=\u001b[39m row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mwhich\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Antibody\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Lot #\u001b[39m\u001b[38;5;124m'\u001b[39m]\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\series.py:981\u001b[0m, in \u001b[0;36mSeries.__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m 978\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_values[key]\n\u001b[0;32m 980\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m key_is_scalar:\n\u001b[1;32m--> 981\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_value(key)\n\u001b[0;32m 983\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_hashable(key):\n\u001b[0;32m 984\u001b[0m \u001b[38;5;66;03m# Otherwise index.get_value will raise InvalidIndexError\u001b[39;00m\n\u001b[0;32m 985\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m 986\u001b[0m \u001b[38;5;66;03m# For labels that don't resolve as scalars like tuples and frozensets\u001b[39;00m\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\series.py:1089\u001b[0m, in \u001b[0;36mSeries._get_value\u001b[1;34m(self, label, takeable)\u001b[0m\n\u001b[0;32m 1086\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_values[label]\n\u001b[0;32m 1088\u001b[0m \u001b[38;5;66;03m# Similar to Index.get_value, but we do not fall back to positional\u001b[39;00m\n\u001b[1;32m-> 1089\u001b[0m loc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mindex\u001b[38;5;241m.\u001b[39mget_loc(label)\n\u001b[0;32m 1090\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mindex\u001b[38;5;241m.\u001b[39m_get_values_for_loc(\u001b[38;5;28mself\u001b[39m, loc, label)\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3804\u001b[0m, in \u001b[0;36mIndex.get_loc\u001b[1;34m(self, key, method, tolerance)\u001b[0m\n\u001b[0;32m 3802\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_engine\u001b[38;5;241m.\u001b[39mget_loc(casted_key)\n\u001b[0;32m 3803\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n\u001b[1;32m-> 3804\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01merr\u001b[39;00m\n\u001b[0;32m 3805\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[0;32m 3806\u001b[0m \u001b[38;5;66;03m# If we have a listlike key, _check_indexing_error will raise\u001b[39;00m\n\u001b[0;32m 3807\u001b[0m \u001b[38;5;66;03m# InvalidIndexError. Otherwise we fall through and re-raise\u001b[39;00m\n\u001b[0;32m 3808\u001b[0m \u001b[38;5;66;03m# the TypeError.\u001b[39;00m\n\u001b[0;32m 3809\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_indexing_error(key)\n", + "\u001b[1;31mKeyError\u001b[0m: 'Mass of Secondary Antibody1 used per Brain (ug)'" + ] + } + ], + "source": [ + "from aind_data_schema.core.procedures import SpecimenProcedure, SpecimenProcedureType, ImmunolabelClass, HCRSeries, Antibody, Procedures, Surgery\n", + "\n", + "missing_companies = []\n", + "\n", + "for row_idx, row in sample_sheet.iterrows():\n", + "\n", + " items = []\n", + "\n", + " new_procedures = []\n", + "\n", + " # general info\n", + " processor = row['Processing Lead']\n", + " sample_id = str(row['Sample'])\n", + " genotype = row['Genotype']\n", + " label = row['Label']\n", + " inj_age = row['Age of Injection']\n", + " tta_virus_dose = row['tTA Virus Dose']\n", + "\n", + "\n", + " if len(sample_id) != 6:\n", + " continue \n", + "\n", + " try:\n", + " with open(f'./original_plus_materials/{sample_id}_procedures.json', 'r') as infile:\n", + " data = json.load(infile)\n", + "\n", + " print(\"OG FILE: \", data)\n", + "\n", + " if str(data.get('subject_id', None)) != sample_id:\n", + " print(f\"subject_id mismatch: {data.get('subject_id', None)} != {sample_id}.\")\n", + "\n", + " original_subj_procedures = []\n", + " for item in data.get('subject_procedures', []):\n", + " if 'protocol_id' not in item.keys():\n", + " item['protocol_id'] = \"unknown\"\n", + " \n", + " for procedure in item['procedures']:\n", + " if 'protocol_id' not in procedure.keys():\n", + " procedure['protocol_id'] = \"unknown\"\n", + "\n", + " original_subj_procedures.append(item)\n", + "\n", + " except FileNotFoundError:\n", + " original_subj_procedures = []\n", + "\n", + " print(\"ORIGINAL SUBJ PROCEDURES: \", original_subj_procedures)\n", + "\n", + " spec_maker = SpecMaker(processor, sample_id, original_subj_procedures)\n", + "\n", + " \n", + " gelation_start = row['Gelation: MBS Start']\n", + " gelation_end = row['PBS Wash End']\n", + "\n", + " if not pd.isna(gelation_start):\n", + " new_procedures.append(\n", + " spec_maker.make_spec_procedure(\n", + " start=gelation_start, \n", + " end=gelation_end, \n", + " procedure_type=SpecimenProcedureType.GELATION, \n", + " procedure_name=\"Gelation\",\n", + " protocol_id=[\"dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1\"],\n", + " reagent=[],\n", + " )\n", + " )\n", + "\n", + " # delipidation\n", + " dcm_delip_start = row['DCM Delipidation Start']\n", + " dcm_delip_end = row['DCM Delipidation End']\n", + "\n", + " if not pd.isna(dcm_delip_start):\n", + " new_procedures.append(\n", + " spec_maker.make_spec_procedure(\n", + " start=dcm_delip_start, \n", + " end=dcm_delip_end, \n", + " procedure_type=SpecimenProcedureType.DELIPIDATION, \n", + " procedure_name=\"DCM Delipidation\",\n", + " protocol_id=[\"dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1\"],\n", + " reagent=[],\n", + " )\n", + " )\n", + "\n", + "\n", + " sbip_delip_start = row['SBiP Delipidation Start']\n", + " sbip_delip_end = row['SBiP Delipidation End']\n", + "\n", + " if not pd.isna(sbip_delip_start):\n", + " new_procedures.append(\n", + " spec_maker.make_spec_procedure(\n", + " start=sbip_delip_start, \n", + " end=sbip_delip_end, \n", + " procedure_type=SpecimenProcedureType.DELIPIDATION, \n", + " procedure_name=\"SBiP Delipidation\",\n", + " protocol_id=[\"dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1\"],\n", + " reagent=[],\n", + " )\n", + " )\n", + "\n", + " immuno_primary_start = row[f'Immuno: Primary Ab Start Date']\n", + "\n", + " antibody_courses = {}\n", + "\n", + " \n", + " \n", + " for which in ['Primary', 'Secondary']:\n", + " antibodies = []\n", + " start_date = row[f'Immuno: {which} Ab Start Date']\n", + " if pd.isna(start_date):\n", + " continue\n", + " for i in range(1, 4):\n", + " immuno_antibody = row[f'Immuno: {which} Antibody{i}']\n", + "\n", + " if pd.isna(immuno_antibody):\n", + " continue\n", + "\n", + " immuno_mass = row[f'Mass of {which} Antibody{i} used per Brain (ug)']\n", + " immuno_catalogue = row[f'{which} Antibody{i} Catalog #']\n", + " immuno_lot = row[f'{which} Antibody{i} Lot #']\n", + " fluorophore = None\n", + "\n", + " if which == 'Secondary':\n", + " fluorophore = row[f'Fluorophore{i}']\n", + "\n", + " if not pd.isna(immuno_lot) and immuno_lot in antibody_sheet['Lot#'].tolist():\n", + "\n", + " info_row = antibody_sheet.loc[antibody_sheet['Lot#'] == immuno_lot]\n", + "\n", + " try:\n", + " source = Organization.from_abbreviation(info_row['Company'].values[0])\n", + " except KeyError:\n", + " mapping = {\n", + " \"Jackson Immuno\": Organization.JAX,\n", + " \"Sicgen\": Organization.OTHER,\n", + " \"Thermo Fisher\": Organization.THERMOFISHER,\n", + " \"Invitrogen\": Organization.THERMOFISHER,\n", + " \"Abcam\": Organization.ABCAM,\n", + " }\n", + " missing_companies.append(info_row['Company'].values[0])\n", + " source = mapping[info_row['Company'].values[0]]\n", + "\n", + " rrid = info_row['RRID'].values[0]\n", + " if pd.isna(rrid):\n", + " rrid = None\n", + " else:\n", + " rrid = PIDName(\n", + " name=info_row['Name'].values[0],\n", + " registry= Registry.RRID,\n", + " registry_identifier=rrid\n", + " )\n", + " else:\n", + " immuno_lot = 'unknown'\n", + " source = Organization.OTHER\n", + " rrid = None\n", + "\n", + " # look up: source, RRID, concentration from aind_antibody masterlist\n", + " \n", + " if not pd.isna(fluorophore):\n", + " fluorophore = fluorophore.replace('AF', 'Alexa Fluor')\n", + " if pd.isna(fluorophore) or fluorophore == \"n/a\":\n", + " fluorophore = None\n", + "\n", + " if pd.isna(immuno_mass):\n", + " continue\n", + " \n", + " antibodies.append(\n", + " Antibody(\n", + " name=immuno_antibody,\n", + " source=source,\n", + " rrid=rrid,\n", + " lot_number=str(immuno_lot),\n", + " immunolabel_class=which,\n", + " fluorophore=fluorophore,\n", + " mass=immuno_mass,\n", + " )\n", + " )\n", + " \n", + " if len(antibodies) < 1:\n", + " continue\n", + "\n", + " print(antibodies)\n", + "\n", + " new_procedures.append(\n", + " spec_maker.make_spec_procedure(\n", + " start=start_date, \n", + " end=start_date, \n", + " procedure_type=SpecimenProcedureType.IMMUNOLABELING, \n", + " procedure_name=f\"{which} Antibody Immunolabeling\",\n", + " protocol_id=[\"dx.doi.org/10.17504/protocols.io.ewov1okwylr2/v1\"],\n", + " reagent=[],\n", + " antibodies=antibodies,\n", + " )\n", + " )\n", + "\n", + "\n", + " # spec_maker.load_spec_models(new_procedures)\n", + " spec_maker.make_procedures(Path(\"output\"), new_procedures)\n", + " \n", + "print(set(missing_companies))\n", + "\n", + "\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ainds", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.5" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/scripts/Exaspim_ingest/ingest_exaspim_materials.ipynb b/scripts/Exaspim_ingest/ingest_exaspim_materials.ipynb new file mode 100644 index 00000000..eaef0049 --- /dev/null +++ b/scripts/Exaspim_ingest/ingest_exaspim_materials.ipynb @@ -0,0 +1,538 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\openpyxl\\styles\\stylesheet.py:226: UserWarning: Workbook contains no default style, apply openpyxl's default\n", + " warn(\"Workbook contains no default style, apply openpyxl's default\")\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "import requests\n", + "import json\n", + "\n", + "from datetime import datetime\n", + "import glob\n", + "from enum import Enum\n", + "from pathlib import Path\n", + "\n", + "from aind_data_schema.core.procedures import SpecimenProcedure, ImmunolabelClass, HCRSeries, Antibody, Procedures, ViralMaterial, TarsVirusIdentifiers\n", + "\n", + "from aind_data_schema_models.specimen_procedure_types import SpecimenProcedureType\n", + "\n", + "from aind_data_schema_models.organizations import Organization\n", + "\n", + "from aind_data_schema_models.pid_names import PIDName\n", + "\n", + "from aind_data_schema_models.registry import Registry\n", + "\n", + "import logging\n", + "\n", + "\n", + "\n", + "materials_sheet = pd.read_excel(\"./Mouse Tracker - Molecular Anatomy.xlsx\", sheet_name=\"Mouse Tracker - Molecular Anato\", header=[0], converters={})\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "log_file_name = \"./logging/log_\" + datetime.now().strftime(\"%Y%m%d_%H%M%S\") + \".log\"\n", + "logger = logging.getLogger()\n", + "logger.setLevel(logging.DEBUG)\n", + "# create file handler which logs even debug messages\n", + "fh = logging.FileHandler(log_file_name, \"w\", \"utf-8\")\n", + "fh.setLevel(logging.DEBUG)\n", + "\n", + "# create formatter and add it to the handlers\n", + "formatter = logging.Formatter(\"%(asctime)s - %(name)s - %(levelname)s - %(message)s\")\n", + "fh.setFormatter(formatter)\n", + "# add the handlers to logger\n", + "logger.addHandler(fh)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{}\n" + ] + } + ], + "source": [ + "subj_procedures = {}\n", + "\n", + "download_files = False\n", + "\n", + "files = glob.glob(\"./original_spec_files/*.json\")\n", + "\n", + "\n", + "tars_models = {}\n", + "\n", + "if download_files:\n", + " for file in files: \n", + " print(file)\n", + " subj_id = file.split(\"\\\\\")[-1].split(\"_\")[0].split(\".\")[0]\n", + " print(subj_id)\n", + " if int(subj_id) not in materials_sheet[\"Mouse ID\"].tolist():\n", + " print(\"not found\")\n", + " continue\n", + "\n", + " subj_row = materials_sheet.loc[materials_sheet[\"Mouse ID\"] == int(subj_id)]\n", + " \n", + " if len(subj_id) != 6:\n", + " continue\n", + "\n", + " for virus_number in [1,2,3]:\n", + " item = None\n", + " tars_id = subj_row[f\"Virus{virus_number} ID\"].values[0]\n", + " logging.info(f\"Processing {tars_id} for {subj_id}\")\n", + " print(tars_id)\n", + "\n", + " if pd.isna(tars_id):\n", + " continue\n", + "\n", + " if tars_id not in tars_models.keys():\n", + " request = requests.get(f\"http://aind-metadata-service/tars_injection_materials/{tars_id}\")\n", + " else:\n", + " continue\n", + "\n", + " if request.status_code == 404 or request.status_code == 500:\n", + " print(f\"{tars_id} model not found\")\n", + " continue\n", + "\n", + " print(f\"code: {request.status_code}\")\n", + "\n", + " \n", + " item = request.json()\n", + "\n", + " if not item or not item['data']:\n", + " continue\n", + "\n", + " if item['message'] == 'Valid Model.':\n", + " logging.info(f\"Valid model for {tars_id}: {item['data']}\")\n", + " tars_models[tars_id] = item['data']\n", + " else:\n", + " print(f\"invalid model for {tars_id}\")\n", + " print(item['message'])\n", + "\n", + "print(tars_models)\n", + "\n", + "for key, value in tars_models.items():\n", + " logging.info(f\"Writing {key} for {value}\")\n", + " with open(f'./tars_info/{key}.json', 'w') as outfile:\n", + " json.dump(value, outfile)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "tars_files = glob.glob(\"./tars_info/*.json\")\n", + "tars_models = {}\n", + "for file in tars_files:\n", + " logging.info(f\"Reading file {file}\")\n", + " with open(file) as json_file:\n", + " data = json.load(json_file)\n", + " tars_models[str(data['tars_identifiers'][\"prep_lot_number\"])] = data\n" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "sanity_checks = []\n", + "\n", + "def get_inj_material(subj_id, virus_number):\n", + " print(materials_sheet[\"Mouse ID\"].tolist())\n", + " print(type(subj_id))\n", + " print(type(materials_sheet[\"Mouse ID\"].tolist()[0]))\n", + " if int(subj_id) not in materials_sheet[\"Mouse ID\"].tolist():\n", + " logging.info(f\"Subject {subj_id} not found in materials sheet\")\n", + " return []\n", + " \n", + " materials = []\n", + "\n", + " subj_row = materials_sheet.loc[materials_sheet[\"Mouse ID\"] == int(subj_id)]\n", + " logging.info(f\"subj_row: {subj_row}\")\n", + "\n", + " virus = subj_row[f\"Virus{virus_number}\"].values[0]\n", + " logging.info(f\"virus{virus_number}: {virus}\")\n", + " if pd.isna(virus):\n", + " logging.info(f\"virus{virus_number} is NA\")\n", + " return None\n", + "\n", + " virus_id = subj_row[f\"Virus{virus_number} ID\" ].values[0] # use this to look up TARS info\n", + "\n", + " titer = subj_row[f\"Virus{virus_number} Stock Titer (GC/mL)\"].values[0]\n", + " dose = float(subj_row[f\"Virus{virus_number} Dose (GC/mouse)\"].values[0])\n", + " volume = subj_row[f\"Virus{virus_number} Volume Injected\"].values[0]\n", + " mix_volume = subj_row[f\"Virus Mix Volume injected\"].values[0]\n", + " if pd.isna(mix_volume):\n", + " mix_volume = .1\n", + " else:\n", + " if isinstance(mix_volume, str):\n", + " mix_volume = float(mix_volume.split(\"u\")[0])\n", + " else:\n", + " mix_volume = float(mix_volume)\n", + " mix_volume = mix_volume*.0001\n", + " logging.info(f\"titer: {titer}\")\n", + " logging.info(f\"mix vol: {mix_volume}\")\n", + "\n", + " if not pd.isna(mix_volume):\n", + " logging.info(\"FOUND MIX VOL: \" + str(mix_volume))\n", + " else:\n", + " return None\n", + "\n", + "\n", + " try:\n", + " logging.info(f\"titer: {titer}, dose: {dose}, volume: {volume}, mix volume: {mix_volume}\")\n", + " \n", + " mix_titer = None\n", + " if not pd.isna(mix_volume):\n", + " \n", + " logging.info(\"mix volume is not NA\")\n", + " mix_titer = int(dose/(mix_volume))\n", + " logging.info(f\"mix titer: {mix_titer}\")\n", + " \n", + " if mix_titer is not None:\n", + " logging.info(\"using mixed titer\")\n", + " titer = mix_titer\n", + " else:\n", + " logging.info(\"using original titer\")\n", + "\n", + " except:\n", + " logging.info(\"something missing\")\n", + "\n", + "\n", + " if pd.isna(titer): # actually, do the calculation for everything\n", + " logging.info(\"titer is NA\")\n", + " \n", + " \n", + " if pd.isna(volume):\n", + " logging.error(f\"Volume is NA for material {virus_number} : {subj_id}, {virus}\")\n", + " return None\n", + " \n", + "\n", + " if isinstance(volume, str):\n", + " volume = float(volume.split(\"u\")[0])\n", + " logging.info(f\"dose: {dose}, volume: {volume}\")\n", + "\n", + " titer = int(dose/(volume*.001))\n", + " else:\n", + " try:\n", + " titer = float(titer)\n", + " except:\n", + " logging.error(f\"titer cannot be converted to float: {titer}\")\n", + " return None\n", + "\n", + " # do some checks to see how accurate titer is to dose/volume\n", + " \n", + " tars = None\n", + " logging.info(f\"virus_id: {virus_id}\")\n", + " logging.info(f\"tars_models: {tars_models.keys()}\")\n", + " if str(virus_id) in tars_models.keys():\n", + " logging.info(f\"found tars for {virus_id}\")\n", + " tars = TarsVirusIdentifiers.model_validate(tars_models[virus_id][\"tars_identifiers\"])\n", + " logging.info(f\"tars for {subj_id}: {tars}\")\n", + "\n", + " logging.info(f\"titer: {titer}, dose: {dose}, volume: {volume}\")\n", + " new_material = ViralMaterial(\n", + " name=virus,\n", + " titer=titer,\n", + " tars_identifiers=tars, \n", + " )\n", + "\n", + " logging.info(f\"new material: {new_material}\")\n", + "\n", + " logging.info(f\"finished virus {virus_number}\")\n", + "\n", + " return new_material\n" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1\n", + "2\n" + ] + } + ], + "source": [ + "from decimal import Decimal\n", + "from math import isclose\n", + "\n", + "def find_which_injection(subj_id, coordinates):\n", + " subj_row = materials_sheet.loc[materials_sheet[\"Mouse ID\"] == int(subj_id)]\n", + "\n", + " for val in range(1,4):\n", + " coord = {}\n", + " coord['ap'] = subj_row[f\"Virus{val} AP (mm)\"].values[0]\n", + " coord['ml'] = subj_row[f\"Virus{val} ML (mm)\"].values[0]\n", + " coord['dv'] = subj_row[f\"Virus{val} DV (mm)\"].values[0]\n", + "\n", + " if None in coord.values() or '?' in coord.values() or 'n/a' in coord.values():\n", + " logging.error(f\"Missing coordinates for {subj_id} {val}\")\n", + " continue\n", + "\n", + " logging.info(f\"coord: {coord}\")\n", + " flag = True\n", + " for key, value in coordinates.items():\n", + " logging.info(f\"coord {coord[key]} vs {value}\")\n", + " if 'L' in str(coord[key]) or 'R' in str(coord[key]) or '+' in str(coord[key]):\n", + " continue\n", + " if not isclose(coord[key], value):\n", + " logging.info(f\"coord {coord[key]} does not match {value}\")\n", + " logging.info(f\"{type(coord[key])} vs {type(value)}\")\n", + " flag = False\n", + "\n", + " if flag:\n", + " return val\n", + " \n", + " return None\n", + "\n", + "\n", + "coordinates1 = {\n", + " \"ap\": -1.6,\n", + " \"ml\": -.4,\n", + " \"dv\": 3.3\n", + "}\n", + "\n", + "coords2 = {\n", + " \"ap\": -3.3,\n", + " \"ml\": .43,\n", + " \"dv\": 4.4\n", + "}\n", + "\n", + "print(find_which_injection('709393', coordinates1))\n", + "print(find_which_injection('709393', coords2))" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "3\n" + ] + } + ], + "source": [ + "def find_which_ro(subj_id):\n", + " subj_row = materials_sheet.loc[materials_sheet[\"Mouse ID\"] == int(subj_id)]\n", + "\n", + " for val in range(1,4):\n", + " if subj_row[f\"Virus{val} Injection Type\"].values[0] == \"RO\":\n", + " return val\n", + "\n", + " return None\n", + "\n", + "print(find_which_ro('709393'))" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '576404', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "describedBy='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py' schema_version='0.13.3' subject_id='576404' subject_procedures=[{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}] specimen_procedures=[] notes=None\n", + "{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}\n", + "{'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '576404', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}], 'specimen_procedures': [], 'notes': None}\n", + "describedBy='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py' schema_version='0.13.3' subject_id='576404' subject_procedures=[{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}] specimen_procedures=[] notes=None\n", + "{'procedure_type': 'Surgery', 'start_date': '2021-07-12', 'experimenter_full_name': '28908', 'iacuc_protocol': '1806', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['576404'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}\n", + "{'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '603033', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}], 'specimen_procedures': [], 'notes': None}\n", + "describedBy='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py' schema_version='0.13.3' subject_id='603033' subject_procedures=[{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}] specimen_procedures=[] notes=None\n", + "{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None, 'protocol_id': 'dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1'}\n", + "{'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '603033', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}], 'specimen_procedures': [], 'notes': None}\n", + "describedBy='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py' schema_version='0.13.3' subject_id='603033' subject_procedures=[{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}] specimen_procedures=[] notes=None\n", + "{'procedure_type': 'Surgery', 'start_date': '2021-11-19', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['603033'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}\n", + "{'describedBy': 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py', 'schema_version': '0.13.3', 'subject_id': '609105', 'subject_procedures': [{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None}], 'notes': None}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609105'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}], 'specimen_procedures': [], 'notes': None}\n", + "describedBy='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py' schema_version='0.13.3' subject_id='609105' subject_procedures=[{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None}], 'notes': None}, {'procedure_type': 'Surgery', 'start_date': '2022-01-06', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'procedure_type': 'Perfusion', 'output_specimen_ids': ['609105'], 'protocol_id': 'dx.doi.org/10.17504/protocols.io.bg5vjy66'}], 'notes': None}] specimen_procedures=[] notes=None\n", + "{'procedure_type': 'Surgery', 'start_date': '2021-12-09', 'experimenter_full_name': '13040', 'iacuc_protocol': '2107', 'animal_weight_prior': None, 'animal_weight_post': None, 'weight_unit': 'gram', 'anaesthesia': None, 'workstation_id': None, 'procedures': [{'recovery_time': None, 'recovery_time_unit': 'minute', 'injection_duration': None, 'injection_duration_unit': 'minute', 'instrument_id': None, 'procedure_type': 'Retro-orbital injection', 'injection_volume': None, 'injection_volume_unit': 'microliter', 'injection_eye': None}], 'notes': None}\n", + "['Template', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Chat-IRES-Cre;Slc6a3-T2A-FlpO(ND)', 670784, 670784, 676411, 676410, 676407, 676403, 691966, 691965, 694593, 694590, 694589, 694588, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'ePet-Cre', 650008, 650009, 650010, 650011, 667241, 667242, 667244, 669528, 669530, 669533, 673887, 673893, 673894, 673896, 677995, 677993, 677992, 697837, 697836, nan, 'Slc6a4-Cre', 652779, 652781, 669973, 669974, 669977, 673286, 673288, 673289, 684436, 684434, 685592, 685590, 685586, 704473, 704471, 704470, 704469, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'xx', nan, 'Sert-FlpO', 678601, 678600, 678599, 678991, 678988, 678987, 686488, 686485, 686486, 686487, 686484, 686483, 703261, 703260, 703259, 703258, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Dbh-Cre', 648434, 648435, 648436, 651305, 684101, 684100, 685222, 685221, 708490, 708482, 708489, 708481, 717615, 717614, 717612, 721328, 717613, 721330, 721331, 721332, 722845, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Dbh-Cre; Ai166', 651324, 651327, 664953, 664956, 664957, 664958, 669461, 669462, 669790, 669793, 686714, 684924, 684920, 685244, 685242, 685241, 692426, 692425, 692423, 692870, 692869, 692867, 697573, 697572, 697571, 697569, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Dbh-Cre; DAT-Flp', 671476, 671477, 684932, 684931, 684929, 692376, 692371, 692368, 705056, 705052, nan, 'Dbh-Cre; Sert-Flp', 670808, 670809, 670812, 670813, 682904, 682903, 682900, 682852, 693733, 693732, 693729, 701928, 701927, 701926, 701924, 702924, 702920, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Hdc-Cre', 667857, 667858, 667860, 668956, 668957, 668962, 674681, 674682, 674684, 679201, 679200, 679199, nan, 'Hdc-Cre_IM1; Ai166', 668294, 668295, 668296, 668297, 674884, 674886, 681687, 681686, 681690, 681692, 695660, 695660, 695658, 695657, 697890, 697889, 697887, 697886, nan, 'Cart-IRES2-Cre-neo', 652440, 652441, 652445, 652446, 653980, 653981, 653983, 653984, 660949, 660950, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Kara notified to stop breeding 2/28/23', nan, nan, nan, nan, nan, nan, nan, 'Calb2-CreERT2;Ai166', 603033, 603034, 603036, 603037, 603039, 603040, 605952, 605955, 608895, 608896, 608900, 608901, 611326, 611328, 611329, 611330, 611333, 611334, 611646, 614952, 614956, 616568, 619050, 619051, 620629, 620630, 620631, 620633, 620639, 620640, 620642, 620643, 626319, 626679, 626681, 627947, 627949, 627950, 634172, 634173, 650817, 650818, 650819, 658733, 658734, 658735, 660625, 660627, 660629, 660630, 668384, 668385, 668386, 668556, 668557, 668558, 668559, 671997, 673993, 673994, 673996, 673998, 674000, 674093, 682218, 682217, 682216, 682215, 682214, 682210, 682205, 687346, 683441, 686040, 686039, nan, 'Slc17a6-IRES-Cre', 603308, 603310, 603311, 609281, 609283, 609285, 609286, 609105, 609106, 609107, 613810, 613813, 613814, 613817, 614978, 614979, 614980, 615296, 615299, 618583, 618584, 618586, 618589, 625096, 637432, 637436, 637439, 638331, 638332, 654302, 654304, 654306, 654308, 654309, 654310, 673157, 673158, 673160, 673161, 673163, 678794, 678797, 689898, 689897, 689896, 689895, 689893, 696800, 696140, 696139, 706300, 706301, 706302, 706434, 706435, 724752, 724753, 625097, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Slc17a7-IRES2-Cre;Ai223', 685376, 685372, 695307, 695305, 705159, 705160, 705161, 705162, 705163, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Penk1-IRES-Cre', 667154, 667156, 670944, 674740, 674741, 674742, 674743, 674744, 683787, 683788, 683789, 683790, 683791, 683792, 670948, 'Gal-Cre_KI187', 648079, 648077, 653153, 653158, 653159, 653162, 659142, 659144, 659145, 659146, 663394, 663395, 709848, 709849, 709850, 709851, 709852, 720164, 720165, 720166, nan, 'Ntrk1_IRES-Cre', 651895, 651897, 651899, 651900, 651901, 652228, 655145, 655146, 655147, 655148, 662960, 662965, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Notified Kara to stop breeding', nan, nan, nan, 'Necab1-IRES-Cre', 648858, 648860, 648861, 648862, 662770, 662774, 662775, 670934, 670936, 670938, 3163606, 3163608, 662771, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'notify Kara to pause breeding- remember to adjust titer ttA', nan, nan, nan, 'Slc6a5-Cre_KF109', 648695, 648696, 648697, 648698, 648699, 648700, 667352, 667353, 667354, 667355, 664549, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Notified Kara to pause but not eliminate this line until the last mouse is perfused ~ April 15th', nan, nan, nan, nan, nan, 'Slc17a8-iCre', 654727, 657676, 657677, 657679, 661293, 661299, 661300, 663413, 663412, 663410, 663409, 'Informed Kara to stop breeding after last perfusion Is complete', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Crh-IRES-Cre_BL', 664760, 664761, 664762, 665465, 665467, 665469, 665470, 678112, 678116, 686955, 686953, 686952, 686951, 686950, 686948, 686947, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Asked Sara to stop breeding 6/14/23', nan, 'Grp-IRES-Cre_KH288', 665081, 665082, 665083, 667267, 667996, 667997, 667998, 675057, 675058, 675059, 675060, 675061, 677572, 677574, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Pvalb-IRES-Cre', 670471, 676009, 676007, 704520, 704521, 704522, 704523, 721054, 721056, 721059, 734738, 'St18-T2A-Cre-B2', 516429, nan, nan, nan, 'Penk-IRES2-Cre-neo', 670339, 670344, 681465, 681469, nan, nan, nan, nan, nan, nan, 'Slc32a1-IRES-Cre', 701770, 701771, 701772, 701773, 701774, 709220, 709221, 709222, 709838, 709839, nan, 'C57BL6J + CN5146', 707208, 'Rorb-IRES2-Cre', 3163611, nan, nan, 'Ntsr1-Cre_GN220', 709011, 709013, 709014, 709016, 717983, 717984, 717981, 719180, 719179, nan, nan, 'Rbp4-Cre_KL100', 712226, 712228, 718162, 718163, 718166, 718168, 719744, 719747, 719749, '109_11', '109_03', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'C57BL6J + Thomas Jefferson rabies', 397, nan, nan, 'C57BL6J + AAVrg Cre + RO Supernova', 709393, 709394, 709203, 709204, 713600, 713601, 'C57BL6J + eHGT_607h', 708367, 708375, 708376, nan, nan, 'C57BL6J + MGT_E252', 674184, 674190, 675374, 708365, 708370, 708371, 'C57BL6J + MGT_E256', 708364, 708368, 708369, nan, nan, 'C57BL6J + MGT_E255', 674185, 674191, 675375, 708366, 708373, 708374, 'C57BL/6J + MGT_E241', 717442, 717443, 717444, 717445, nan, nan, nan, nan, 'C57BL/6J + MGT_E199', 715344, 715345, 715346, 715347, 'C57BL/6J + MGT_E265', 719651, 719652, 719653, 719654, nan, 737561, 737562, 737563, 737564, 'C57BL/6J + MGT_E253', 720811, 720812, 720813, 720814, nan, 729504, 729505, 729506, 729507, nan, 'C57BL/6J + MGT_E267', 721826, 721828, 721829, 721830, nan, 730901, 730902, 730903, 730904, 'C57BL/6J + Cre in ALM + GFP in Medulla', 703066, 703067, 703070, 703071, 'Lbhd2-Cre-ERT2', 236, 237, 238, 239, nan, nan, nan, nan, 'Slc17a7-IRES2-Cre', 730221, nan, 730223, nan, 730228, nan, 730229, nan, 739424, nan, 739429, nan, nan, nan, nan, nan, nan, nan, nan, 'C57BL/6J + CN_5129', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 'Syt17-Cre_NO14', 733838, nan, 733840, nan, 742007, nan, 742009, nan, nan, nan, nan, 'Htr2a-Cre_KM207', 733418, 733420, 737826, 738139, 737829, 737828, 738138]\n", + "\n", + "\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "c:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pydantic\\main.py:352: UserWarning: Pydantic serializer warnings:\n", + " Expected `Union[Surgery, TrainingProtocol, WaterRestriction, definition-ref]` but got `dict` - serialized value may not be as expected\n", + " return self.__pydantic_serializer__.to_json(\n" + ] + }, + { + "ename": "KeyError", + "evalue": "'Virus1 Volume Injected'", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3802\u001b[0m, in \u001b[0;36mIndex.get_loc\u001b[1;34m(self, key, method, tolerance)\u001b[0m\n\u001b[0;32m 3801\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m-> 3802\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_engine\u001b[38;5;241m.\u001b[39mget_loc(casted_key)\n\u001b[0;32m 3803\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\_libs\\index.pyx:138\u001b[0m, in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\_libs\\index.pyx:165\u001b[0m, in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mpandas\\_libs\\hashtable_class_helper.pxi:5745\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[1;34m()\u001b[0m\n", + "File \u001b[1;32mpandas\\_libs\\hashtable_class_helper.pxi:5753\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[1;34m()\u001b[0m\n", + "\u001b[1;31mKeyError\u001b[0m: 'Virus1 Volume Injected'", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[12], line 40\u001b[0m\n\u001b[0;32m 38\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m which:\n\u001b[0;32m 39\u001b[0m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[1;32m---> 40\u001b[0m material \u001b[38;5;241m=\u001b[39m get_inj_material(subj, which)\n\u001b[0;32m 42\u001b[0m logging\u001b[38;5;241m.\u001b[39minfo(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRO material for subject \u001b[39m\u001b[38;5;132;01m{\u001b[39;00msubj\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, inj \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mwhich\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmaterial\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m 44\u001b[0m subj_procedure[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minjection_materials\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m [material]\n", + "Cell \u001b[1;32mIn[9], line 26\u001b[0m, in \u001b[0;36mget_inj_material\u001b[1;34m(subj_id, virus_number)\u001b[0m\n\u001b[0;32m 24\u001b[0m titer \u001b[38;5;241m=\u001b[39m subj_row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVirus\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvirus_number\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Stock Titer (GC/mL)\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m 25\u001b[0m dose \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mfloat\u001b[39m(subj_row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVirus\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvirus_number\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Dose (GC/mouse)\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m])\n\u001b[1;32m---> 26\u001b[0m volume \u001b[38;5;241m=\u001b[39m subj_row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVirus\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvirus_number\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Volume Injected\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m 27\u001b[0m mix_volume \u001b[38;5;241m=\u001b[39m subj_row[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVirus Mix Volume injected\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m 28\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m pd\u001b[38;5;241m.\u001b[39misna(mix_volume):\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\frame.py:3807\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m 3805\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcolumns\u001b[38;5;241m.\u001b[39mnlevels \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m 3806\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_getitem_multilevel(key)\n\u001b[1;32m-> 3807\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcolumns\u001b[38;5;241m.\u001b[39mget_loc(key)\n\u001b[0;32m 3808\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_integer(indexer):\n\u001b[0;32m 3809\u001b[0m indexer \u001b[38;5;241m=\u001b[39m [indexer]\n", + "File \u001b[1;32mc:\\Users\\mae.moninghoff\\AppData\\Local\\miniconda3\\envs\\ainds\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3804\u001b[0m, in \u001b[0;36mIndex.get_loc\u001b[1;34m(self, key, method, tolerance)\u001b[0m\n\u001b[0;32m 3802\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_engine\u001b[38;5;241m.\u001b[39mget_loc(casted_key)\n\u001b[0;32m 3803\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n\u001b[1;32m-> 3804\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01merr\u001b[39;00m\n\u001b[0;32m 3805\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[0;32m 3806\u001b[0m \u001b[38;5;66;03m# If we have a listlike key, _check_indexing_error will raise\u001b[39;00m\n\u001b[0;32m 3807\u001b[0m \u001b[38;5;66;03m# InvalidIndexError. Otherwise we fall through and re-raise\u001b[39;00m\n\u001b[0;32m 3808\u001b[0m \u001b[38;5;66;03m# the TypeError.\u001b[39;00m\n\u001b[0;32m 3809\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_indexing_error(key)\n", + "\u001b[1;31mKeyError\u001b[0m: 'Virus1 Volume Injected'" + ] + } + ], + "source": [ + "files = glob.glob(\"./original_spec_files/*.json\")\n", + "\n", + "for file in files:\n", + " with open(file) as f:\n", + " data = json.load(f)\n", + " print(data)\n", + " original_procedure = Procedures.model_construct(**data)\n", + "\n", + " print(original_procedure)\n", + "\n", + " subj = original_procedure.subject_id\n", + "\n", + " logging.info(f\"Processing subject {subj}\")\n", + "\n", + " for surgery in original_procedure.subject_procedures:\n", + " print(surgery)\n", + " if \"protocol_id\" not in surgery.keys():\n", + " surgery[\"protocol_id\"] = \"dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1\"\n", + " logging.info(f\"adding surgery protocol id for subject {subj}\")\n", + " elif surgery[\"protocol_id\"] == \"unknown\":\n", + " logging.info(f\"replacing surgery protocol id for subject {subj}\")\n", + " surgery[\"protocol_id\"] = \"dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1\"\n", + " for subj_procedure in surgery[\"procedures\"]:\n", + " logging.info(f\"checking procedure {subj_procedure} for subject {subj}\")\n", + " if subj_procedure[\"procedure_type\"] == \"Perfusion\":\n", + " if \"protocol_id\" not in subj_procedure.keys():\n", + " logging.info(f\"adding perfusion protocol id for subject {subj}\")\n", + " subj_procedure[\"protocol_id\"] = \"dx.doi.org/10.17504/protocols.io.bg5vjy66\"\n", + " \n", + " elif subj_procedure[\"protocol_id\"] == \"unknown\":\n", + " logging.info(f\"replacing perfusion protocol id for subject {subj}\")\n", + " subj_procedure[\"protocol_id\"] = \"dx.doi.org/10.17504/protocols.io.bg5vjy66\"\n", + "\n", + " if subj_procedure[\"procedure_type\"] == \"Retro-orbital injection\":\n", + " logging.info(f\"checking retro-orbital injection for subject {subj}\")\n", + "\n", + " which = find_which_ro(subj)\n", + " if not which:\n", + " continue\n", + " material = get_inj_material(subj, which)\n", + "\n", + " logging.info(f\"RO material for subject {subj}, inj {which}: {material}\")\n", + "\n", + " subj_procedure[\"injection_materials\"] = [material]\n", + "\n", + " if subj_procedure[\"procedure_type\"] == \"Nanoject injection\":\n", + " coords = {}\n", + " coords['ap'] = Decimal(subj_procedure[\"injection_coordinate_ap\"])\n", + " coords['ml'] = Decimal(subj_procedure[\"injection_coordinate_ml\"])\n", + " coords['dv'] = Decimal(subj_procedure[\"injection_coordinate_depth\"][0])\n", + " logging.info(f\"coords: {coords}\")\n", + " which = find_which_injection(subj, coords)\n", + " if not which:\n", + " logging.error(f\"Could not find which injection for {subj} nanoject injection {coords}\")\n", + " continue\n", + " material = get_inj_material(subj, which)\n", + " logging.info(f\"Nanoject material for subject {subj}, inj {which}: {material}\")\n", + " subj_procedure[\"injection_materials\"] = [material]\n", + " \n", + " \n", + "\n", + " original_procedure.write_standard_file(\n", + " output_directory=Path(\"original_plus_materials\"),\n", + " prefix=subj\n", + " )\n", + "\n", + " \n", + "print(sanity_checks)\n", + "\n", + "\n", + " # titer = dose / volume, with volume in ml (gc/ml) (translate to ml)\n", + "\n", + " # perhaps put vehicle in notes field of surgery?\n", + "\n", + " # for value in [1,2,3]:\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ainds", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.5" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/scripts/Exaspim_ingest/original_plus_materials/576404_procedures.json b/scripts/Exaspim_ingest/original_plus_materials/576404_procedures.json new file mode 100644 index 00000000..dcecd33c --- /dev/null +++ b/scripts/Exaspim_ingest/original_plus_materials/576404_procedures.json @@ -0,0 +1,31 @@ +{ + "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py", + "schema_version": "0.13.3", + "subject_id": "576404", + "subject_procedures": [ + { + "procedure_type": "Surgery", + "start_date": "2021-07-12", + "experimenter_full_name": "28908", + "iacuc_protocol": "1806", + "animal_weight_prior": null, + "animal_weight_post": null, + "weight_unit": "gram", + "anaesthesia": null, + "workstation_id": null, + "procedures": [ + { + "procedure_type": "Perfusion", + "output_specimen_ids": [ + "576404" + ], + "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66" + } + ], + "notes": null, + "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1" + } + ], + "specimen_procedures": [], + "notes": null +} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/original_plus_materials/603033_procedures.json b/scripts/Exaspim_ingest/original_plus_materials/603033_procedures.json new file mode 100644 index 00000000..94924310 --- /dev/null +++ b/scripts/Exaspim_ingest/original_plus_materials/603033_procedures.json @@ -0,0 +1,31 @@ +{ + "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py", + "schema_version": "0.13.3", + "subject_id": "603033", + "subject_procedures": [ + { + "procedure_type": "Surgery", + "start_date": "2021-11-19", + "experimenter_full_name": "13040", + "iacuc_protocol": "2107", + "animal_weight_prior": null, + "animal_weight_post": null, + "weight_unit": "gram", + "anaesthesia": null, + "workstation_id": null, + "procedures": [ + { + "procedure_type": "Perfusion", + "output_specimen_ids": [ + "603033" + ], + "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66" + } + ], + "notes": null, + "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1" + } + ], + "specimen_procedures": [], + "notes": null +} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/original_plus_materials/609105_procedures.json b/scripts/Exaspim_ingest/original_plus_materials/609105_procedures.json new file mode 100644 index 00000000..6f006995 --- /dev/null +++ b/scripts/Exaspim_ingest/original_plus_materials/609105_procedures.json @@ -0,0 +1,67 @@ +{ + "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py", + "schema_version": "0.13.3", + "subject_id": "609105", + "subject_procedures": [ + { + "procedure_type": "Surgery", + "start_date": "2021-12-09", + "experimenter_full_name": "13040", + "iacuc_protocol": "2107", + "animal_weight_prior": null, + "animal_weight_post": null, + "weight_unit": "gram", + "anaesthesia": null, + "workstation_id": null, + "procedures": [ + { + "recovery_time": null, + "recovery_time_unit": "minute", + "injection_duration": null, + "injection_duration_unit": "minute", + "instrument_id": null, + "procedure_type": "Retro-orbital injection", + "injection_volume": null, + "injection_volume_unit": "microliter", + "injection_eye": null, + "injection_materials": [ + { + "material_type": "Virus", + "name": "AAV-PHP-eB_Syn-Flex TRE-2tTA", + "tars_identifiers": null, + "addgene_id": null, + "titer": 30000000000, + "titer_unit": "gc/mL" + } + ] + } + ], + "notes": null, + "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1" + }, + { + "procedure_type": "Surgery", + "start_date": "2022-01-06", + "experimenter_full_name": "13040", + "iacuc_protocol": "2107", + "animal_weight_prior": null, + "animal_weight_post": null, + "weight_unit": "gram", + "anaesthesia": null, + "workstation_id": null, + "procedures": [ + { + "procedure_type": "Perfusion", + "output_specimen_ids": [ + "609105" + ], + "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66" + } + ], + "notes": null, + "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1" + } + ], + "specimen_procedures": [], + "notes": null +} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/original_plus_materials/609107_procedures.json b/scripts/Exaspim_ingest/original_plus_materials/609107_procedures.json new file mode 100644 index 00000000..8f2cb0ed --- /dev/null +++ b/scripts/Exaspim_ingest/original_plus_materials/609107_procedures.json @@ -0,0 +1,67 @@ +{ + "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py", + "schema_version": "0.13.3", + "subject_id": 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b/scripts/Exaspim_ingest/tars_info/VT3212g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-3x-eGFP", "tars_identifiers": {"virus_tars_id": "AiV300022", "plasmid_tars_alias": null, "prep_lot_number": "VT3212g", "prep_date": "2022-02-04", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT3213g.json b/scripts/Exaspim_ingest/tars_info/VT3213g.json new file mode 100644 index 00000000..01a69d4c --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT3213g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-3x-eGFP", "tars_identifiers": {"virus_tars_id": "AiV300021", "plasmid_tars_alias": null, "prep_lot_number": "VT3213g", "prep_date": "2022-02-04", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT3214g.json b/scripts/Exaspim_ingest/tars_info/VT3214g.json new file mode 100644 index 00000000..8ab7ade6 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT3214g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-Syn-Flex-TREx2-tTA", "tars_identifiers": {"virus_tars_id": "AiV300024", "plasmid_tars_alias": null, "prep_lot_number": "VT3214g", "prep_date": "2023-02-04", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT3215g.json b/scripts/Exaspim_ingest/tars_info/VT3215g.json new file mode 100644 index 00000000..2d2675dc --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT3215g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-tDTomato", "tars_identifiers": {"virus_tars_id": "AiV300023", "plasmid_tars_alias": null, "prep_lot_number": "VT3215g", "prep_date": "2023-02-04", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT3216g.json b/scripts/Exaspim_ingest/tars_info/VT3216g.json new file mode 100644 index 00000000..345be5eb --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT3216g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-tDTomato", "tars_identifiers": {"virus_tars_id": "AiV300007", "plasmid_tars_alias": null, "prep_lot_number": "VT3216g", "prep_date": "2022-02-04", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT4299g.json b/scripts/Exaspim_ingest/tars_info/VT4299g.json new file mode 100644 index 00000000..7d473bb8 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT4299g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-3x-eGFP", "tars_identifiers": {"virus_tars_id": "AiV300001", "plasmid_tars_alias": null, "prep_lot_number": "VT4299g", "prep_date": "2022-09-15", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT4358g.json b/scripts/Exaspim_ingest/tars_info/VT4358g.json new file mode 100644 index 00000000..8dcdd7e6 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT4358g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-Syn-Flex-TREx2-tTA", "tars_identifiers": {"virus_tars_id": "AiV300000", "plasmid_tars_alias": null, "prep_lot_number": "VT4358g", "prep_date": "2022-09-23", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT4359g.json b/scripts/Exaspim_ingest/tars_info/VT4359g.json new file mode 100644 index 00000000..282bf6b5 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT4359g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-3x-eGFP", "tars_identifiers": {"virus_tars_id": "AiV300002", "plasmid_tars_alias": null, "prep_lot_number": "VT4359g", "prep_date": "2022-09-21", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT4360g.json b/scripts/Exaspim_ingest/tars_info/VT4360g.json new file mode 100644 index 00000000..4f13799d --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT4360g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-tDTomato", "tars_identifiers": {"virus_tars_id": "AiV300005", "plasmid_tars_alias": null, "prep_lot_number": "VT4360g", "prep_date": "2022-09-23", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT5048g.json b/scripts/Exaspim_ingest/tars_info/VT5048g.json new file mode 100644 index 00000000..3a255df6 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT5048g.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "pAAV-7x-TRE-tDTomato", "tars_identifiers": {"virus_tars_id": "AiV300008", "plasmid_tars_alias": null, "prep_lot_number": "VT5048g", "prep_date": "2023-02-07", "prep_type": "Purified", "prep_protocol": "SOP#VC003"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT5311C.json b/scripts/Exaspim_ingest/tars_info/VT5311C.json new file mode 100644 index 00000000..5bdb8dfc --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT5311C.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "NA", "tars_identifiers": {"virus_tars_id": "AiV1791_PHPeB", "plasmid_tars_alias": null, "prep_lot_number": "VT5311C", "prep_date": "2023-03-08", "prep_type": "Crude", "prep_protocol": "PHPeB-SOP#VC004"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/scripts/Exaspim_ingest/tars_info/VT5316C.json b/scripts/Exaspim_ingest/tars_info/VT5316C.json new file mode 100644 index 00000000..26930951 --- /dev/null +++ b/scripts/Exaspim_ingest/tars_info/VT5316C.json @@ -0,0 +1 @@ +{"material_type": "Virus", "name": "NA", "tars_identifiers": {"virus_tars_id": "AiV1837_PHPeB", "plasmid_tars_alias": null, "prep_lot_number": "VT5316C", "prep_date": "2023-03-08", "prep_type": "Crude", "prep_protocol": "PHPeB-SOP#VC004"}, "addgene_id": null, "titer": null, "titer_unit": "gc/mL"} \ No newline at end of file diff --git a/tests/test_basic_job.py b/tests/test_basic_job.py index 42fe2b4d..a95afdc9 100644 --- a/tests/test_basic_job.py +++ b/tests/test_basic_job.py @@ -300,7 +300,7 @@ def test_add_processing_to_metadata( mock_datetime: MagicMock, mock_copyfile: MagicMock, mock_json_write: MagicMock, - mock_write_standard_file: MagicMock, + mock_dard_file: MagicMock, ): """Tests that the processing metadata files are compiled correctly.""" mock_datetime.now.return_value = datetime(2023, 4, 9)