[WIP] Script for importing materials

[kurtwheeler]

Issue Number

https://github.com/AlexsLemonade/resources-portal-admin/issues/22#issuecomment-831407834

Include an issue number if applicable.

Adds a script for importing materials provided by the Reynolds Lab.

This is definitely a work in progress as we iterate on the data they provide

Describe the big picture of your changes.

• New feature (non-breaking change which adds functionality)

Functional tests

I've imported the resources with this script! It went okay. See a screenshot below for what one of them looked like.

Checklist

• Lint and unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)
• Any dependent changes have been merged and published in downstream modules

Screenshots

[kurtwheeler]

My first thought for improving this would be to fix their column names to match our readable names. This is the additional_metadata field for one of the materials. The script tried to convert each readable name to the key that is expected for display, but as you can see there's some that didn't get translated:

{'age': '6.3',
 'gender': 'Female',
 'diagnosis': 'Neuroblstoma',
 'ethnicity': None,
 'pubmed_id': '',
 'patient_id': 'Neuroblastoma ALT+ PDX COG-N-700x',
 'tumor_type': 'Primary',
 'Tumor OMICS': '>99% Human',
 'Contact Name': 'Jonas Nance',
 'Contact Email': '[email protected]',
 'model_organism': 'Mouse',
 'virology_status': 'EBV negative',
 'Submitter PDX ID': 'COG-N-700x',
 'consent_to_share': 'yes',
 'engraftment_rate': '',
 'engraftment_time': '',
 'specific_markers': 'qPCR: MCYN -, TERT -, TH +; PCR: C Circle +',
 'tissue_histology': 'Neuroblastoma',
 'tumor_preparation': 'cell suspension',
 'Treatment, passage': 'p2',
 'submitter_tumor_id': 'COG-N-700x',
 'treatment_protocol': 'Cyclo+topo in progress',
 'treatment_response': None,
 'Is Strain Humanized?': 'no',
 'Is not of EBV Origin': 'yes; human vs. mouse 99%, EBV negative',
 'Passage QA Performed': 'passage 1-2; STR match to patient',
 'animal_health_status': 'no impact other than tumor size',
 'type_of_humanization': None,
 'specimen_tumor_tissue': 'Primary tumor',
 'Current Treatment Drug': 'sample obtained at diagnosis',
 'pdx_model_availability': 'Available',
 'injection_type_and_site': 'subcuaneous',
 'model_strain_and_source': 'NOD.Cg-Prkdc<scid>Il2rg<tm1Wj>l/SzJ, The Jackson Laboratory; Hsd:Athymic Nude-Foxn1nu, Envigo',
 'Primary Tissue of Origin': 'adrenal gland',
 'Prior Treatment Protocol': None,
 'prior_treatment_response': 'sample obtained at diagnosis',
 'Current Treatment protocol': ' ANBL1531',
 'Original Tumor sample type': 'tumor',
 'number_of_available_models': 'Available',
 'Tumor Grade; Classification': 'unfavorable, Diploid',
 'response_to_standard_of_care': '',
 'Disease Stage; Classification': '4',
 'Lag Time/ Doubling Time of Tumor': '65 days',
 'Tumor characterization Technology': 'histology',
 'Organism Treatment for Engraftment': 'No',
 'Development of metastases in strain': 'No',
 'Governance Restriction for Distribution': 'N/A',
 'Is the tumor from an untreated patient?': 'yes',
 'Tumor from an existing PDX Model? Why sub-line?': 'no'}