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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| // Functions to auto-detect types and convert a batch of files into an array of Modus JSON's, | ||
| // with suggested output filenames. Just give each input file a filename whose extension | ||
| // reflects its type, and | ||
| import debug from 'debug'; | ||
| import jszip from 'jszip'; | ||
| import { parse as csvParse, supportedFormats, SupportedFormats } from './csv.js'; | ||
| import { parseModusResult as xmlParseModusResult } from './xml.js'; | ||
| import { convertUnits } from '@modusjs/units'; | ||
| import { simpleConvert } from '@modusjs/units/dist/index.js'; | ||
| import { modusTests } from '@modusjs/industry'; | ||
| import type ModusResult from '@oada/types/modus/v1/modus-result.js'; | ||
| // @ts-ignore | ||
| import wicket from 'wicket'; | ||
| import type { NutrientResult } from '@modusjs/units'; | ||
| import type { LabConfig } from './labs/index.js'; | ||
| import type { GeoJSON } from 'geojson'; | ||
|
|
||
| const error = debug('@modusjs/convert#togeojson:error'); | ||
| const warn = debug('@modusjs/convert#togeojson:error'); | ||
| const info = debug('@modusjs/convert#togeojson:info'); | ||
| const trace = debug('@modusjs/convert#togeojson:trace'); | ||
| const DEPTHUNITS = 'cm'; | ||
| const wkt = new wicket.Wkt(); | ||
|
|
||
| export type SupportedFileType = 'xml' | 'csv' | 'xlsx' | 'json' | 'zip'; | ||
| export const supportedFileTypes = ['xml', 'csv', 'xlsx', 'json', 'zip']; | ||
|
|
||
| export type ModusJSONConversionResult = { | ||
| original_filename: string; | ||
| original_type: SupportedFileType; | ||
| output_filename: string; | ||
| modus: ModusResult; | ||
| }; | ||
|
|
||
| export type InputFile = { | ||
| filename: string; // can include the path on the front | ||
| format?: 'generic'; // only for CSV/XLSX files, default generic (same as generic for now) | ||
| str?: string; | ||
| // zip or xlsx can either be ArrayBuffer or base64 string of original file. | ||
| // Do not use for other types, they should all just be strings. | ||
| arrbuf?: ArrayBuffer; | ||
| base64?: string; | ||
| }; | ||
|
|
||
| // This function will attempt to convert all the input files into an array of Modus JSON files | ||
| export async function toGeoJson( | ||
| input: ModusResult | ||
| ): Promise<GeoJSON> { | ||
| let results: GeoJSON = { | ||
| type: 'FeatureCollection', | ||
| features: [] | ||
| }; | ||
| for (const event of input.Events || []) { | ||
| for (const [type, eventSamples] of Object.entries(event.EventSamples!) as [string, any]) { | ||
| const sampleName = `${type}Samples`; | ||
| for (const samples of eventSamples[sampleName]) { | ||
| const nutrientResults = type === 'Soil' ? | ||
| //TODO: Map Element names into something like Depth + Element Name | ||
| samples.Depths.map((d: any) => d.NutrientResults).flat(1) | ||
| : samples.NutrientResults; | ||
| if (!samples.Geometry.wkt) continue; | ||
| const feat = wkt.read(samples.Geometry.wkt).toJson(); | ||
| for (const nr of nutrientResults) { | ||
|
|
||
| } | ||
| } | ||
| } | ||
| } | ||
| return results; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,213 @@ | ||
| // Functions to auto-detect types and convert a batch of files into an array of Modus JSON's, | ||
| // with suggested output filenames. Just give each input file a filename whose extension | ||
| // reflects its type, and | ||
| import debug from 'debug'; | ||
| import jszip from 'jszip'; | ||
| import md5 from 'md5'; | ||
| import { parse as csvParse, supportedFormats, SupportedFormats } from './csv.js'; | ||
| import { parseModusResult as xmlParseModusResult } from './xml.js'; | ||
| import { convertUnits } from '@modusjs/units'; | ||
| import { simpleConvert } from '@modusjs/units/dist/index.js'; | ||
| import { modusTests } from '@modusjs/industry'; | ||
| import type ModusResult from '@oada/types/modus/v1/modus-result.js'; | ||
| import type Slim from '@oada/types/modus/slim/v1/0.js'; | ||
| import jp from 'json-pointer'; | ||
| // @ts-expect-error no types | ||
| import wicket from 'wicket'; | ||
|
|
||
| const error = debug('@modusjs/convert#slim:error'); | ||
| const warn = debug('@modusjs/convert#slim:error'); | ||
| const info = debug('@modusjs/convert#slim:info'); | ||
| const trace = debug('@modusjs/convert#slim:trace'); | ||
|
|
||
| export type SupportedFileType = 'xml' | 'csv' | 'xlsx' | 'json' | 'zip'; | ||
| export const supportedFileTypes = ['xml', 'csv', 'xlsx', 'json', 'zip']; | ||
|
|
||
| export type ModusJSONConversionResult = { | ||
| original_filename: string; | ||
| original_type: SupportedFileType; | ||
| output_filename: string; | ||
| modus: ModusResult; | ||
| }; | ||
|
|
||
| export type InputFile = { | ||
| filename: string; // can include the path on the front | ||
| format?: 'generic'; // only for CSV/XLSX files, default generic (same as generic for now) | ||
| str?: string; | ||
| // zip or xlsx can either be ArrayBuffer or base64 string of original file. | ||
| // Do not use for other types, they should all just be strings. | ||
| arrbuf?: ArrayBuffer; | ||
| base64?: string; | ||
| }; | ||
|
|
||
| // This function will attempt to convert all the input files into an array of Modus JSON files | ||
| export function toSlim( | ||
| input: ModusResult | ||
| ): Slim { | ||
| let result : any = { | ||
| _type: 'application/vnd.modus.slim.v1.0+json', | ||
| }; | ||
| for (const event of input.Events || []) { | ||
| setPath(event, `/EventMetaData/EventCode`, result, `/id`); | ||
| setPath(event, `/EventMetaData/EventDate`, result, `/date`); | ||
|
|
||
| setPath(event, `/EventMetaData/EventType`, result, `/type`, (v) => Object.keys(v)[0]!.toLowerCase()) | ||
| if (result.type === 'plant') result.type === 'plant-tissue'; | ||
|
|
||
| //Lab | ||
| setPath(event, `/LabMetaData/LabEventID`, result, `/lab/id/value`); | ||
| setPath(event, `/LabMetaData/LabEventID`, result, `/lab/id/source`, () => 'local'); | ||
| setPath(event, `/LabMetaData/LabName`, result, `/lab/name`); | ||
|
|
||
| setPath(event, `/LabMetaData/Contact/Name`, result, `/lab/contact/name`); | ||
| setPath(event, `/LabMetaData/Contact/Phone`, result, `/lab/contact/phone`); | ||
| setPath(event, `/LabMetaData/Contact/Address`, result, `/lab/contact/address`); | ||
| setPath(event, `/LabMetaData/Contact/Email`, result, `/lab/contact/email`); | ||
| setPath(event, `/LabMetaData/Contact/City`, result, `/lab/contact/city`); | ||
| setPath(event, `/LabMetaData/Contact/State`, result, `/lab/contact/state`); | ||
| //TODO: the spec uses 'address', not city + state | ||
|
|
||
| setPath(event, `/LabMetaData/ReceivedDate`, result, `/lab/dateReceived`); | ||
| setPath(event, `/LabMetaData/ProcessedDate`, result, `/lab/dateProcessed`); | ||
|
|
||
| setPath(event, `/LabMetaData/ClientAccount/Name`, result, `/lab/clientAccount/name`); | ||
| setPath(event, `/LabMetaData/ClientAccount/AccountNumber`, result, `/lab/clientAccount/accountNumber`); | ||
| setPath(event, `/LabMetaData/ClientAccount/Company`, result, `/lab/clientAccount/company`); | ||
|
|
||
|
|
||
| setPath(event, `/FMISMetaData/FMISEventID`, result, `/source/report/id`); | ||
| setPath(event, `/FMISMetaData/FMISProfile/Farm`, result, `/source/farm/name`); | ||
| setPath(event, `/FMISMetaData/FMISProfile/Field`, result, `/source/field/name`); | ||
| setPath(event, `/FMISMetaData/FMISProfile/Grower`, result, `/source/grower/name`); | ||
| setPath(event, `/FMISMetaData/FMISProfile/Sub-Field`, result, `/source/subfield/name`); | ||
|
|
||
| // Lab report | ||
| setPath(event, `/LabMetaData/ProcessedDate`, result, `/lab/report/date`); | ||
| setPath(event, `/LabMetaData/Reports/0/LabReportID`, result, `/lab/report/id`); | ||
| setPath(event, `/LabMetaData/Reports`, result, `/lab/files`, (reports) => | ||
| reports.map((r: any) => { | ||
| const file: any = {}; | ||
| setPath(r, `/File/ReportID`, file, `/id`); | ||
| setPath(r, `/File/FileData`, file, `/base64`); | ||
| setPath(r, `/File/URL/Path`, file, `/uri`); | ||
| setPath(r, `/File/URL/FileName`, file, `/name`); | ||
| setPath(r, `/File/FileData/FileName`, file, `/name`); | ||
| return file; | ||
| }) | ||
| ); | ||
| if (result.lab.files.length === 0) delete result.lab.files | ||
|
|
||
| for (const [type, eventSamples] of Object.entries(event.EventSamples!) as [string, any]) { | ||
| // Handle depths | ||
| //TODO: Or nematode?? | ||
| const depths = type === 'Soil' ? eventSamples.DepthRefs.map((dr: any) => ({ | ||
| name: dr.Name, | ||
| top: dr.StartingDepth, | ||
| bottom: dr.EndingDepth, | ||
| units: dr.DepthUnit | ||
| })) : undefined; | ||
| if (depths.length === 1) result.depth = depths[0]; | ||
|
|
||
| const sampleName = `${type}Samples`; | ||
|
|
||
| // Samples | ||
| for (const eventSample of eventSamples[sampleName]) { | ||
| const sample: any = {}; | ||
| setPath(eventSample, `/SampleMetaData/SampleNumber`, sample, `/lab/sampleid`); | ||
| setPath(eventSample, `/SampleMetaData/SampleContainerID`, sample, `/source/sampleid`); | ||
|
|
||
| // Nutrient results | ||
| const nutrientResults = type === 'Soil' ? | ||
| eventSample.Depths.map((d: any) => d.NutrientResults).flat(1) | ||
| : eventSample.NutrientResults; | ||
| sample.nutrientResult = Object.fromEntries(nutrientResults.map((d: any) => { | ||
| const nr = {}; | ||
| setPath(d, `/ModusTestID`, nr, `/analyte`, (v) => v.split('_')[3]) | ||
| setPath(d, `/Element`, nr, `/analyte`); | ||
| setPath(d, `/Value`, nr, `/value`); | ||
| setPath(d, `/ValueUnit`, nr, `/units`); | ||
| setPath(d, `/ModusTestID`, nr, `/modusTestID`); | ||
| // d.ValueDesc??? | ||
| // d.ValueType??? | ||
| // TODO: Some other | ||
| const nrid = md5(JSON.stringify(nr)); | ||
| return [nrid, nr]; | ||
| })) | ||
|
|
||
| //Geolocation | ||
| setPath(eventSample, `/SampleMetaData/Geometry`, sample, `/geolocation`, (wkt) => { | ||
| if (wkt.toLowerCase().startsWith('point')) { | ||
| const ll = wkt.split('(')[1].replace(/\)$/, '').split(' ') | ||
| return { | ||
| lat: ll[1], | ||
| lon: ll[0], | ||
| } | ||
| } | ||
| return { | ||
| geojson: new wicket.Wkt().read(wkt).toJson(), | ||
| } | ||
| }) | ||
|
|
||
| const sampleid = md5(JSON.stringify(sample)); | ||
| result.samples = result.samples || {}; | ||
| result.samples[sampleid] = sample; | ||
| } | ||
| } | ||
| } | ||
| return result as unknown as Slim; | ||
| } | ||
|
|
||
| // Handles a few little things: | ||
| // - don't set things when it doesn't exist on the ModusResult | ||
| // - creates parents down to the given path | ||
| // - falls back to previous attempts to set the new path value | ||
| // - won't set values that are undefined or empty arrays; will set values === 0 | ||
| function setPath(obj: any, objPath: string, newObj: any, newPath: string, func?: (v:any) => any) { | ||
| if (jp.has(obj, objPath)) { | ||
| const newVal = func ? | ||
| func(jp.get(obj, objPath)) ?? jp.get(newObj, newPath) | ||
| : jp.get(obj, objPath) ?? jp.get(newObj, newPath); | ||
| if (Array.isArray(newVal) && newVal.length > 0) { | ||
| jp.set(newObj, newPath, newVal); | ||
| } else if (newVal || newVal === 0) { | ||
| jp.set(newObj, newPath, newVal); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| // TODO: What else to flatten? | ||
| // Should it return only samples part of input? | ||
| // Should it return an object or array? | ||
| export function flatten(input: Slim) { | ||
| const samples = Object.fromEntries( | ||
| Object.entries(input.samples || {}).map(([sampleid, sample]) => { | ||
| const newSample: any = { | ||
| ...sample, | ||
| lab: { | ||
| ...input.lab, | ||
| ...sample.lab, | ||
| }, | ||
| source: { | ||
| ...input.source, | ||
| ...sample.lab, | ||
| } | ||
| } | ||
| if (input.depth) | ||
| sample = { | ||
| depth: input.depth, | ||
| ...sample | ||
| } | ||
| if (input.geolocation) | ||
| sample = { | ||
| geolocation: input.geolocation, | ||
| ...sample | ||
| }; | ||
| return [sampleid, newSample]; | ||
| }) | ||
| ); | ||
|
|
||
| return { | ||
| ...input, | ||
| samples, | ||
| } | ||
| } |
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