[codex] Add FAIR artifact access gate

README.md

@@ -1,2 +1,6 @@
 # deepevents.ai
 deepevents.ai main codebase
+
+## Bounty modules
+
+- [FAIR Artifact Access Gate](fair-artifact-access-gate/README.md) - validates scientific data and code hosting readiness for SCIBASE issue #14.

fair-artifact-access-gate/README.md

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+# FAIR Artifact Access Gate
+
+This module is a focused implementation slice for SCIBASE issue #14, "Scientific/Engineering Data & Code Hosting." It models the pre-publication gate a hosted scientific project should pass before SCIBASE exposes datasets, notebooks, source code, figures, raw instrument outputs, and model files to collaborators, reviewers, or the public.
+
+The gate answers four practical hosting questions:
+
+- Does the project expose machine-readable metadata through JSON-LD, DataCite, and schema.org?
+- Are scientific artifacts cataloged by family, access policy, preview capability, versioning, and deterministic hashes?
+- Do the hosted materials satisfy FAIR signals for findability, accessibility, interoperability, and reuse?
+- Can SCIBASE produce a reviewer export packet that includes metadata, artifact links, access-policy evidence, and checksums?
+
+## Files
+
+- `src/fair-artifact-access-gate.js` contains the deterministic assessment logic.
+- `data/sample-artifacts.json` provides a realistic mixed scientific artifact set.
+- `test/fair-artifact-access-gate.test.js` covers success and failure paths.
+- `scripts/demo.js` prints a concise readiness report for the sample project.
+- `docs/demo.svg` and `docs/demo.mp4` show the intended product surface.
+
+## Run
+
+```sh
+npm test
+npm run demo
+npm run demo:video
+```
+
+The implementation is intentionally dependency-free so it can be reviewed without installing a framework or service runtime.

fair-artifact-access-gate/data/sample-artifacts.json

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+{
+  "projectId": "lab-astrocyte-calcium-atlas",
+  "title": "Astrocyte Calcium Imaging Atlas",
+  "doi": "10.5555/scibase.astrocyte-calcium.2026.v2",
+  "version": "2.1.0",
+  "license": "CC-BY-4.0",
+  "indexed": true,
+  "publisher": "SCIBASE Demo Repository",
+  "persistentBaseUrl": "https://scibase.ai/artifacts/lab-astrocyte-calcium-atlas",
+  "metadata": {
+    "jsonLd": {
+      "@context": "https://schema.org",
+      "@type": "Dataset",
+      "name": "Astrocyte Calcium Imaging Atlas",
+      "identifier": "10.5555/scibase.astrocyte-calcium.2026.v2"
+    },
+    "dataCite": {
+      "identifier": "10.5555/scibase.astrocyte-calcium.2026.v2",
+      "creators": ["SCIBASE Demo Lab"],
+      "publisher": "SCIBASE Demo Repository",
+      "publicationYear": 2026,
+      "resourceType": "Dataset"
+    },
+    "schemaOrg": {
+      "name": "Astrocyte Calcium Imaging Atlas",
+      "description": "Processed calcium imaging events, notebooks, source code, model weights, and raw instrument outputs.",
+      "license": "https://creativecommons.org/licenses/by/4.0/",
+      "distribution": "https://scibase.ai/artifacts/lab-astrocyte-calcium-atlas"
+    }
+  },
+  "tags": {
+    "keywords": ["calcium imaging", "astrocyte", "time series", "neuroscience"],
+    "instruments": ["two-photon microscope", "scientific CMOS camera"],
+    "organisms": ["Mus musculus"],
+    "variables": ["event amplitude", "event duration", "field of view", "stimulus epoch"]
+  },
+  "artifacts": [
+    {
+      "path": "data/processed/calcium-events.parquet",
+      "family": "dataset",
+      "format": "parquet",
+      "access": "public",
+      "preview": "table",
+      "versioned": true,
+      "diffable": true,
+      "machineReadable": true,
+      "sizeBytes": 9420800
+    },
+    {
+      "path": "code/notebooks/event-detection.ipynb",
+      "family": "notebook",
+      "format": "ipynb",
+      "access": "public",
+      "preview": "notebook",
+      "versioned": true,
+      "diffable": true,
+      "machineReadable": true,
+      "sizeBytes": 184220
+    },
+    {
+      "path": "code/src/extract_events.py",
+      "family": "code",
+      "format": "python",
+      "access": "public",
+      "preview": "syntax-highlight",
+      "versioned": true,
+      "diffable": true,
+      "machineReadable": true,
+      "sizeBytes": 38291
+    },
+    {
+      "path": "supplementary/figures/field-of-view.png",
+      "family": "figure",
+      "format": "png",
+      "access": "public",
+      "preview": "image",
+      "versioned": true,
+      "diffable": false,
+      "machineReadable": false,
+      "sizeBytes": 308204
+    },
+    {
+      "path": "raw/instrument/session-0423.tiff",
+      "family": "raw-instrument-output",
+      "format": "tiff",
+      "access": "restricted",
+      "restrictionReason": "contains pre-release animal cohort metadata",
+      "reviewerAccess": true,
+      "preview": "thumbnail",
+      "versioned": true,
+      "diffable": false,
+      "machineReadable": false,
+      "sizeBytes": 182002284
+    },
+    {
+      "path": "models/event-classifier.onnx",
+      "family": "model",
+      "format": "onnx",
+      "access": "public",
+      "preview": "model-card",
+      "versioned": true,
+      "diffable": false,
+      "machineReadable": true,
+      "sizeBytes": 14082112
+    }
+  ]
+}

fair-artifact-access-gate/docs/requirement-map.md

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+# Requirement Map
+
+Issue #14 asks for a platform to host scientific and engineering data plus code. This implementation focuses on the acceptance gate that decides whether a hosted project is ready to expose those artifacts.
+
+| Issue need | Implementation surface |
+| --- | --- |
+| Store datasets, code, figures, notebooks, raw outputs, and model files | `buildArtifactCatalog` normalizes each artifact family with persistent links, access policy, preview state, versioning, and hashes. |
+| Support scientific discovery and citation | `buildMetadataStandardsIndex` checks JSON-LD, DataCite, and schema.org metadata. |
+| Keep restricted materials reviewable | `evaluateFairSignals` blocks restricted artifacts without reviewer access and a restriction reason. |
+| Produce evidence for maintainers, reviewers, and collaborators | `planReviewerExportPacket` creates a deterministic export manifest with metadata, policy, FAIR report, artifact hashes, and audit digest. |
+| Make regressions obvious | `test/fair-artifact-access-gate.test.js` covers the ready path plus metadata, access, and reuse failures. |
+
+The slice is intentionally narrow: it does not build object storage, upload UI, billing, or auth. It defines the deterministic hosting contract those surfaces can call before publication.

fair-artifact-access-gate/package.json

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+{
+  "name": "fair-artifact-access-gate",
+  "version": "0.1.0",
+  "private": true,
+  "description": "FAIR scientific artifact hosting readiness gate for SCIBASE issue #14.",
+  "type": "module",
+  "scripts": {
+    "test": "node test/fair-artifact-access-gate.test.js",
+    "demo": "node scripts/demo.js",
+    "demo:video": "clang -fobjc-arc -framework Foundation -framework AppKit -framework AVFoundation -framework CoreMedia -framework CoreVideo scripts/render-demo-video.m -o /tmp/scibase-fair-artifact-access-demo && /tmp/scibase-fair-artifact-access-demo docs/demo.mp4"
+  },
+  "engines": {
+    "node": ">=18"
+  }
+}

fair-artifact-access-gate/scripts/demo.js

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+import { readFile } from "node:fs/promises";
+import { fileURLToPath } from "node:url";
+import { dirname, join } from "node:path";
+import { assessFairArtifactAccessGate } from "../src/fair-artifact-access-gate.js";
+
+const here = dirname(fileURLToPath(import.meta.url));
+const samplePath = join(here, "..", "data", "sample-artifacts.json");
+const sample = JSON.parse(await readFile(samplePath, "utf8"));
+const report = assessFairArtifactAccessGate(sample);
+
+console.log(`Project: ${sample.title}`);
+console.log(`Ready: ${report.ready ? "yes" : "no"}`);
+console.log(`Artifact families: ${report.catalog.families.join(", ")}`);
+console.log(
+  `FAIR: ${report.fairSignals.signals
+    .map((signal) => `${signal.key}=${signal.ready ? "pass" : "fail"}`)
+    .join(", ")}`
+);
+console.log(`Reviewer packet entries: ${report.reviewerPacket.entryCount}`);
+console.log(`Reviewer packet hash: ${report.reviewerPacket.packetHash}`);
+console.log(
+  `Audit digest: standards=${report.reviewerPacket.auditDigest.standardsReady}, fair=${report.reviewerPacket.auditDigest.fairReady}, restricted=${report.reviewerPacket.auditDigest.restrictedArtifactCount}`
+);
+console.log(`Blockers: ${report.blockers.length === 0 ? "none" : report.blockers.join("; ")}`);

fair-artifact-access-gate/scripts/render-demo-video.m

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+#import <Foundation/Foundation.h>
+#import <AppKit/AppKit.h>
+#import <AVFoundation/AVFoundation.h>
+#import <CoreVideo/CoreVideo.h>
+
+static void FillRounded(NSRect rect, CGFloat radius, NSColor *color) {
+  NSBezierPath *path = [NSBezierPath bezierPathWithRoundedRect:rect xRadius:radius yRadius:radius];
+  [color setFill];
+  [path fill];
+}
+
+static void StrokeRounded(NSRect rect, CGFloat radius, NSColor *color) {
+  NSBezierPath *path = [NSBezierPath bezierPathWithRoundedRect:rect xRadius:radius yRadius:radius];
+  [color setStroke];
+  [path setLineWidth:2.0];
+  [path stroke];
+}
+
+static void DrawText(NSString *text, NSRect rect, CGFloat size, NSColor *color, NSFontWeight weight) {
+  NSMutableParagraphStyle *style = [[NSMutableParagraphStyle alloc] init];
+  style.lineBreakMode = NSLineBreakByWordWrapping;
+  NSDictionary *attrs = @{
+    NSFontAttributeName: [NSFont systemFontOfSize:size weight:weight],
+    NSForegroundColorAttributeName: color,
+    NSParagraphStyleAttributeName: style
+  };
+  [text drawInRect:rect withAttributes:attrs];
+}
+
+static NSColor *RGB(CGFloat r, CGFloat g, CGFloat b) {
+  return [NSColor colorWithCalibratedRed:r / 255.0 green:g / 255.0 blue:b / 255.0 alpha:1.0];
+}
+
+static void DrawCard(NSString *title, NSArray<NSString *> *lines, NSRect rect, NSColor *fill, NSColor *stroke, NSColor *titleColor, NSColor *bodyColor) {
+  FillRounded(rect, 14.0, fill);
+  StrokeRounded(rect, 14.0, stroke);
+  DrawText(title, NSMakeRect(rect.origin.x + 22, rect.origin.y + rect.size.height - 56, rect.size.width - 44, 30), 22, titleColor, NSFontWeightBold);
+  for (NSUInteger i = 0; i < lines.count; i++) {
+    DrawText(lines[i], NSMakeRect(rect.origin.x + 22, rect.origin.y + rect.size.height - 96 - (CGFloat)i * 31, rect.size.width - 44, 28), 18, bodyColor, NSFontWeightRegular);
+  }
+}
+
+static void DrawFrame(CGContextRef cg, int width, int height, int frame) {
+  [NSGraphicsContext saveGraphicsState];
+  NSGraphicsContext *context = [NSGraphicsContext graphicsContextWithCGContext:cg flipped:NO];
+  [NSGraphicsContext setCurrentContext:context];
+
+  [[NSColor colorWithCalibratedRed:245.0 / 255.0 green:247.0 / 255.0 blue:249.0 / 255.0 alpha:1.0] setFill];
+  NSRectFill(NSMakeRect(0, 0, width, height));
+
+  FillRounded(NSMakeRect(64, 54, 1152, 612), 18, [NSColor whiteColor]);
+  StrokeRounded(NSMakeRect(64, 54, 1152, 612), 18, RGB(207, 216, 223));
+
+  CGFloat progress = MIN(1.0, MAX(0.0, ((CGFloat)frame - 8.0) / 64.0));
+  DrawText(@"FAIR Artifact Access Gate", NSMakeRect(104, 595, 760, 48), 36, RGB(23, 33, 43), NSFontWeightBold);
+  DrawText(@"Scientific data and code hosting readiness for SCIBASE issue #14", NSMakeRect(104, 563, 820, 28), 18, RGB(82, 99, 113), NSFontWeightRegular);
+
+  DrawCard(@"Metadata Standards", @[@"JSON-LD", @"DataCite", @"schema.org"], NSMakeRect(104, 362, 252, 152), RGB(233, 246, 240), RGB(159, 208, 186), RGB(23, 72, 49), RGB(39, 99, 74));
+  DrawCard(@"FAIR Signals", @[@"Findable", @"Accessible", @"Reusable"], NSMakeRect(386, 362, 252, 152), RGB(237, 242, 251), RGB(171, 192, 231), RGB(32, 60, 105), RGB(49, 85, 143));
+  DrawCard(@"Access Policy", @[@"Public links", @"Reviewer URLs", @"Restriction reasons"], NSMakeRect(668, 362, 252, 152), RGB(255, 246, 223), RGB(228, 195, 109), RGB(106, 77, 7), RGB(122, 92, 17));
+  DrawCard(@"Export Packet", @[@"Metadata", @"Manifest", @"Checksums"], NSMakeRect(950, 362, 226, 152), RGB(248, 237, 247), RGB(213, 171, 208), RGB(90, 40, 84), RGB(115, 56, 107));
+
+  FillRounded(NSMakeRect(104, 136, 1072, 174), 14, RGB(23, 33, 43));
+  DrawText(@"Astrocyte Calcium Imaging Atlas", NSMakeRect(132, 250, 700, 34), 24, [NSColor whiteColor], NSFontWeightBold);
+  DrawText(@"6 artifact families: dataset, notebook, code, figure, raw instrument output, model", NSMakeRect(132, 209, 920, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+  DrawText(@"Ready: standards pass, FAIR pass, restricted reviewer export pass", NSMakeRect(132, 172, 820, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+  DrawText(@"Deterministic packet hash supports reviewer and collaborator handoff", NSMakeRect(132, 135, 820, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+
+  CGFloat barWidth = 980.0 * progress;
+  FillRounded(NSMakeRect(132, 93, barWidth, 10), 5, RGB(64, 175, 120));
+  DrawText(@"reviewer packet ready", NSMakeRect(132 + barWidth + 14, 84, 220, 28), 14, RGB(82, 99, 113), NSFontWeightMedium);
+
+  [NSGraphicsContext restoreGraphicsState];
+}
+
+int main(int argc, const char *argv[]) {
+  @autoreleasepool {
+    if (argc < 2) {
+      fprintf(stderr, "usage: render-demo-video output.mp4\n");
+      return 2;
+    }
+
+    NSString *outputPath = [NSString stringWithUTF8String:argv[1]];
+    NSURL *outputURL = [NSURL fileURLWithPath:outputPath];
+    [[NSFileManager defaultManager] removeItemAtURL:outputURL error:nil];
+
+    const int width = 1280;
+    const int height = 720;
+    NSError *error = nil;
+    AVAssetWriter *writer = [[AVAssetWriter alloc] initWithURL:outputURL fileType:AVFileTypeMPEG4 error:&error];
+    if (!writer) {
+      NSLog(@"writer error: %@", error);
+      return 1;
+    }
+
+    NSDictionary *videoSettings = @{
+      AVVideoCodecKey: AVVideoCodecTypeH264,
+      AVVideoWidthKey: @(width),
+      AVVideoHeightKey: @(height)
+    };
+    AVAssetWriterInput *input = [AVAssetWriterInput assetWriterInputWithMediaType:AVMediaTypeVideo outputSettings:videoSettings];
+    input.expectsMediaDataInRealTime = NO;
+
+    NSDictionary *pixelBufferAttributes = @{
+      (NSString *)kCVPixelBufferPixelFormatTypeKey: @(kCVPixelFormatType_32ARGB),
+      (NSString *)kCVPixelBufferWidthKey: @(width),
+      (NSString *)kCVPixelBufferHeightKey: @(height)
+    };
+    AVAssetWriterInputPixelBufferAdaptor *adaptor = [AVAssetWriterInputPixelBufferAdaptor assetWriterInputPixelBufferAdaptorWithAssetWriterInput:input sourcePixelBufferAttributes:pixelBufferAttributes];
+
+    if (![writer canAddInput:input]) {
+      NSLog(@"cannot add writer input");
+      return 1;
+    }
+    [writer addInput:input];
+    [writer startWriting];
+    [writer startSessionAtSourceTime:kCMTimeZero];
+
+    CGColorSpaceRef colorSpace = CGColorSpaceCreateDeviceRGB();
+    for (int frame = 0; frame < 96; frame++) {
+      while (!input.readyForMoreMediaData) {
+        [NSThread sleepForTimeInterval:0.01];
+      }
+
+      CVPixelBufferRef buffer = NULL;
+      CVPixelBufferPoolCreatePixelBuffer(NULL, adaptor.pixelBufferPool, &buffer);
+      CVPixelBufferLockBaseAddress(buffer, 0);
+      void *baseAddress = CVPixelBufferGetBaseAddress(buffer);
+      size_t bytesPerRow = CVPixelBufferGetBytesPerRow(buffer);
+      CGContextRef cg = CGBitmapContextCreate(baseAddress, width, height, 8, bytesPerRow, colorSpace, kCGImageAlphaNoneSkipFirst);
+      DrawFrame(cg, width, height, frame);
+      CGContextRelease(cg);
+      CVPixelBufferUnlockBaseAddress(buffer, 0);
+
+      CMTime presentationTime = CMTimeMake(frame, 24);
+      [adaptor appendPixelBuffer:buffer withPresentationTime:presentationTime];
+      CVPixelBufferRelease(buffer);
+    }
+
+    CGColorSpaceRelease(colorSpace);
+    [input markAsFinished];
+
+    dispatch_semaphore_t sema = dispatch_semaphore_create(0);
+    [writer finishWritingWithCompletionHandler:^{
+      dispatch_semaphore_signal(sema);
+    }];
+    dispatch_semaphore_wait(sema, DISPATCH_TIME_FOREVER);
+
+    if (writer.status != AVAssetWriterStatusCompleted) {
+      NSLog(@"writer failed: %@", writer.error);
+      return 1;
+    }
+  }
+
+  return 0;
+}