diff --git a/.github/workflows/dev-build.yml b/.github/workflows/dev-build.yml
index 583a0f5..336817e 100644
--- a/.github/workflows/dev-build.yml
+++ b/.github/workflows/dev-build.yml
@@ -35,19 +35,19 @@ jobs:
steps:
# Clone repository code to runner
- name: Check out the repo
- uses: actions/checkout@v4
+ uses: actions/checkout@v7
# Enable multi-architecture builds via QEMU emulation
- name: Set up QEMU
- uses: docker/setup-qemu-action@v3
+ uses: docker/setup-qemu-action@v4
# Enable advanced Docker build features (required for caching)
- name: Set up Docker Buildx
- uses: docker/setup-buildx-action@v3
+ uses: docker/setup-buildx-action@v4
# Authenticate with Docker Hub for image push access
- name: Log in to Docker Hub
- uses: docker/login-action@v3
+ uses: docker/login-action@v4
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
@@ -55,7 +55,7 @@ jobs:
# Detect changes in nmr-cli folder to skip unnecessary builds
- name: Check for file changes
id: changes
- uses: dorny/paths-filter@v3
+ uses: dorny/paths-filter@v4
with:
filters: |
nmr-cli:
@@ -63,7 +63,7 @@ jobs:
# Build main nmrKit image with registry caching for faster builds
- name: Build and push nmrKit Docker image
- uses: docker/build-push-action@v6
+ uses: docker/build-push-action@v7
with:
context: .
file: ./Dockerfile
@@ -77,7 +77,7 @@ jobs:
# Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
- name: Build and push nmr-cli Docker image
if: steps.changes.outputs.nmr-cli == 'true'
- uses: docker/build-push-action@v6
+ uses: docker/build-push-action@v7
with:
context: ./app/scripts/nmr-cli/
file: ./app/scripts/nmr-cli/Dockerfile
diff --git a/.github/workflows/doc-deploy.yml b/.github/workflows/doc-deploy.yml
index 8c6678c..319710e 100644
--- a/.github/workflows/doc-deploy.yml
+++ b/.github/workflows/doc-deploy.yml
@@ -29,7 +29,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
- uses: actions/checkout@v4
+ uses: actions/checkout@v7
with:
fetch-depth: 0 # Not needed if lastUpdated is not enabled
# - uses: pnpm/action-setup@v2 # Uncomment this if you're using pnpm
diff --git a/.github/workflows/prod-build.yml b/.github/workflows/prod-build.yml
index 1cfdcc2..628048b 100644
--- a/.github/workflows/prod-build.yml
+++ b/.github/workflows/prod-build.yml
@@ -71,19 +71,19 @@ jobs:
steps:
# Clone repository code to runner
- name: Check out the repo
- uses: actions/checkout@v4
+ uses: actions/checkout@v7
# Enable multi-architecture builds via QEMU emulation
- name: Set up QEMU
- uses: docker/setup-qemu-action@v3
+ uses: docker/setup-qemu-action@v4
# Enable advanced Docker build features (required for caching)
- name: Set up Docker Buildx
- uses: docker/setup-buildx-action@v3
+ uses: docker/setup-buildx-action@v4
# Authenticate with Docker Hub for image push access
- name: Log in to Docker Hub
- uses: docker/login-action@v3
+ uses: docker/login-action@v4
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
@@ -91,7 +91,7 @@ jobs:
# Detect changes in nmr-cli folder to skip unnecessary builds
- name: Check for file changes
id: changes
- uses: dorny/paths-filter@v3
+ uses: dorny/paths-filter@v4
with:
filters: |
nmr-cli:
@@ -107,7 +107,7 @@ jobs:
# Build main nmrKit image with registry caching for faster builds
- name: Build and push nmrKit Docker image
- uses: docker/build-push-action@v6
+ uses: docker/build-push-action@v7
with:
context: .
file: ./Dockerfile
@@ -123,7 +123,7 @@ jobs:
# Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
- name: Build and push nmr-cli Docker image
if: steps.changes.outputs.nmr-cli == 'true'
- uses: docker/build-push-action@v6
+ uses: docker/build-push-action@v7
with:
context: ./app/scripts/nmr-cli/
file: ./app/scripts/nmr-cli/Dockerfile
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1ef0a94..845d3a0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -31,7 +31,7 @@ jobs:
python-version: ["3.10"]
steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v7
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
diff --git a/Dockerfile b/Dockerfile
index e9f73d1..0964b23 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3:24.1.2-0 AS nmrkit-ms
+FROM continuumio/miniconda3:25.3.1-1 AS nmrkit-ms
ARG TARGETARCH=amd64
ENV PYTHON_VERSION=3.10
@@ -24,8 +24,13 @@ RUN apt-get update && \
RUN apt-get update && apt-get -y install docker.io
-RUN conda install -c conda-forge python>=PYTHON_VERSION
-RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
+RUN conda config --remove-key channels && \
+ conda config --add channels conda-forge && \
+ conda config --set channel_priority strict
+
+RUN conda install -y \
+ "python=${PYTHON_VERSION}" \
+ "openbabel>=${OPENBABEL_VERSION}"
RUN pip3 install rdkit
@@ -51,8 +56,11 @@ RUN python3 -m pip install uvicorn[standard]
COPY ./app /code/app
-RUN curl -sL https://deb.nodesource.com/setup_current.x | bash -
-RUN apt-get install -y nodejs
+# Download the setup script first so a failure fails the build instead of being masked by the pipe
+RUN curl -fsSL https://deb.nodesource.com/setup_24.x -o /tmp/nodesource_setup.sh && \
+ bash /tmp/nodesource_setup.sh && \
+ apt-get install -y nodejs && \
+ rm -rf /var/lib/apt/lists/* /tmp/nodesource_setup.sh
RUN npm install -g npm@latest
RUN npm install -g /code/app/scripts/nmr-cli
diff --git a/README.md b/README.md
index 80a5b7a..76a686e 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,9 @@
-
+
[](https://opensource.org/licenses/MIT)
[](https://github.com/NFDI4Chem/nmrkit/graphs/commit-activity)
[](https://github.com/NFDI4Chem/nmrkit/issues)
-[]([https://GitHub.com/Steinbeck-Lab/cheminformatics-python-microservice/graphs/contributors/](https://github.com/NFDI4Chem/nmrkit/graphs/contributors))
+[](<[https://GitHub.com/Steinbeck-Lab/cheminformatics-python-microservice/graphs/contributors/](https://github.com/NFDI4Chem/nmrkit/graphs/contributors)>)
[](https://cdk.github.io)
[](https://www.rdkit.org/)
@@ -12,7 +12,6 @@
[](https://fastapi.tiangolo.com/)
[](https://doi.org/10.5281/zenodo.8211374)
-
# Welcome to NMRKit ๐
NMRKit features a collection of powerful microservices designed to simplify your NMR data processing and analysis. Whether you're a seasoned researcher or a curious chemist, our suite of tools offers NMR Prediction, Validation, and Depiction via the nmrium library, along with seamless Format Conversion using the nmr-load-save package. With our robust API, functionalities, and developer-friendly documentation, exploring and interpreting NMR spectra has never been easier.
@@ -27,7 +26,7 @@ Key Features:
API Reference (Scalar) - https://dev.nmrkit.nmrxiv.org/latest/docs
๐ข Found a bug or have a feature request? We'd love to hear from you! Please open an issue: [https://github.com/NFDI4Chem/nmrkit/issues]
-Happy NMR exploring! ๐งช๐"
+Happy NMR exploring..! ๐งช๐"
## Help Desk
@@ -46,9 +45,9 @@ Licensed under the [MIT license](https://opensource.org/licenses/MIT).
Venkata, C., Sharma, N. , Stefan Kuhn, Hamed Musallam nmrKit [Computer software]. https://doi.org/10.5281/zenodo.8211374
## Maintained by
-NMRKit is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany.
-The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
+NMRKit is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany.
+The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
diff --git a/app/routers/spectra.py b/app/routers/spectra.py
index 1e46e3c..1fa8ef9 100644
--- a/app/routers/spectra.py
+++ b/app/routers/spectra.py
@@ -3,7 +3,7 @@
import io
from app.schemas import HealthCheck
from pydantic import BaseModel, HttpUrl, Field
-from typing import Optional
+from typing import Optional, List
import subprocess
import tempfile
import os
@@ -50,6 +50,10 @@ class UrlParseRequest(BaseModel):
)
raw_data: bool = Field(
False, description="Include raw data in the output (default: data source)")
+ include: Optional[List[str]] = Field(
+ None, description="Only include files matching pattern(s) (glob/regex string)")
+ exclude: Optional[List[str]] = Field(
+ None, description="Exclude files matching pattern(s) (glob/regex string)")
model_config = {
"json_schema_extra": {
@@ -95,6 +99,8 @@ def run_command(
auto_processing: bool = False,
auto_detection: bool = False,
raw_data: bool = False,
+ include: Optional[List[str]] = None,
+ exclude: Optional[List[str]] = None,
) -> StreamingResponse:
"""Execute nmr-cli parse-spectra command in Docker container."""
@@ -113,6 +119,12 @@ def run_command(
cmd.append("-d")
if raw_data:
cmd.append("-r")
+ if include:
+ cmd.append("--include")
+ cmd.extend(include)
+ if exclude:
+ cmd.append("--exclude")
+ cmd.extend(exclude)
try:
result = subprocess.run(
@@ -362,7 +374,11 @@ async def parse_spectra_from_file(
description="Enable ranges and zones automatic detection",
),
raw_data: bool = Form(
- False, description="Include raw data in the output (default: data source references)")
+ False, description="Include raw data in the output (default: data source references)"),
+ include: Optional[List[str]] = Form(
+ None, description="Only include files matching pattern(s) (glob/regex string)"),
+ exclude: Optional[List[str]] = Form(
+ None, description="Exclude files matching pattern(s) (glob/regex string)"),
):
"""
## Parse spectra from an uploaded file
@@ -376,6 +392,8 @@ async def parse_spectra_from_file(
| `auto_processing` | Automatically process FID โ FT spectra |
| `auto_detection` | Automatically detect ranges and zones |
| `raw_data` | Include raw data in the output (default: data source) |
+ | `include` | Only include files matching pattern(s) |
+ | `exclude` | Exclude files matching pattern(s) |
### Returns
Parsed spectra data in NMRium-compatible JSON format.
"""
@@ -405,6 +423,8 @@ async def parse_spectra_from_file(
auto_processing=auto_processing,
auto_detection=auto_detection,
raw_data=raw_data,
+ include=include,
+ exclude=exclude,
)
except HTTPException:
@@ -452,6 +472,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
| `auto_processing` | Automatically process FID โ FT spectra |
| `auto_detection` | Automatically detect ranges and zones |
| `raw_data` | Include raw data in the output (default: data source) |
+ | `include` | Only include files matching pattern(s) |
+ | `exclude` | Exclude files matching pattern(s) |
### Returns
Parsed spectra data in NMRium-compatible JSON format.
@@ -463,6 +485,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
auto_processing=request.auto_processing,
auto_detection=request.auto_detection,
raw_data=request.raw_data,
+ include=request.include,
+ exclude=request.exclude,
)
except HTTPException:
diff --git a/app/scripts/nmr-cli/Dockerfile b/app/scripts/nmr-cli/Dockerfile
index 2e38276..f7877d5 100644
--- a/app/scripts/nmr-cli/Dockerfile
+++ b/app/scripts/nmr-cli/Dockerfile
@@ -1,13 +1,21 @@
# build the image ` docker build --tag nmr-cli . `
# run the container ` docker run -it nmr-cli bash `
-FROM mcr.microsoft.com/playwright:v1.58.2-noble
+# NOTE: if `docker run` prints
+# "Error while loading conda entry point: conda-libmamba-solver (module 'libmambapy' has no attribute 'QueryFormat')"
+# this is unrelated to this image/container โ it comes from a version mismatch between
+# conda-libmamba-solver and libmambapy in your HOST shell's conda (base) environment.
+# It does not affect the container. To fix it on the host, run:
+# conda update -n base -c conda-forge conda conda-libmamba-solver libmambapy
+# or, if that doesn't resolve it:
+# conda install -n base -c conda-forge --force-reinstall conda-libmamba-solver libmambapy
+# or, to bypass libmamba entirely:
+# conda config --set solver classic
+
+FROM mcr.microsoft.com/playwright:v1.62.1-noble
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-# Downgrade to Node 22
-RUN npm install -g n && n 22 && hash -r
-
WORKDIR /app
#ENV BASE_NMRIUM_URL=https://nmrium.nmrxiv.org/
diff --git a/app/scripts/nmr-cli/package-lock.json b/app/scripts/nmr-cli/package-lock.json
index dd4eebf..91f5f24 100644
--- a/app/scripts/nmr-cli/package-lock.json
+++ b/app/scripts/nmr-cli/package-lock.json
@@ -9,27 +9,28 @@
"version": "1.0.0",
"license": "ISC",
"dependencies": {
- "@zakodium/nmr-types": "^0.5.12",
- "@zakodium/nmrium-core": "0.7.30",
- "@zakodium/nmrium-core-plugins": "0.7.39",
- "axios": "^1.13.6",
+ "@zakodium/nmr-types": "^0.5.26",
+ "@zakodium/nmrium-core": "0.7.65",
+ "@zakodium/nmrium-core-plugins": "0.7.87",
+ "axios": "^1.19.0",
"fifo-logger": "^2.0.1",
- "file-collection": "^6.6.1",
- "json-stream-stringify": "^3.1.6",
+ "file-collection": "^6.7.0",
+ "json-stream-stringify": "^3.1.7",
"lodash.merge": "^4.6.2",
- "mf-parser": "^3.7.1",
- "ml-spectra-processing": "^14.22.0",
- "nmr-processing": "^22.5.2",
- "openchemlib": "^9.20.0",
- "playwright": "1.58.2",
- "yargs": "^18.0.0"
+ "mf-parser": "^3.9.2",
+ "ml-spectra-processing": "^14.34.0",
+ "nmr-correlation": "^3.0.2",
+ "nmr-processing": "^22.23.6",
+ "openchemlib": "^9.25.0",
+ "playwright": "1.62.1",
+ "yargs": "^18.1.0"
},
"bin": {
"nmr-cli": "build/index.js"
},
"devDependencies": {
"@types/lodash.merge": "^4.6.9",
- "@types/node": "^25.3.5",
+ "@types/node": "^26.2.0",
"@types/yargs": "^17.0.35",
"ts-node": "^10.9.2",
"typescript": "^5.9.3"
@@ -128,13 +129,14 @@
}
},
"node_modules/@types/node": {
- "version": "25.3.5",
- "resolved": "https://registry.npmjs.org/@types/node/-/node-25.3.5.tgz",
- "integrity": "sha512-oX8xrhvpiyRCQkG1MFchB09f+cXftgIXb3a7UUa4Y3wpmZPw5tyZGTLWhlESOLq1Rq6oDlc8npVU2/9xiCuXMA==",
+ "version": "26.4.0",
+ "resolved": "https://registry.npmjs.org/@types/node/-/node-26.4.0.tgz",
+ "integrity": "sha512-faiGnoIrLH/V8cibOMEAZ8pMw6oXqSukl29ra4mN8GdaB2ZewzeaLj+INpV5N+Z1eKWzY+IzaIZH2EIR6YZRNQ==",
"dev": true,
"license": "MIT",
+ "peer": true,
"dependencies": {
- "undici-types": "~7.18.0"
+ "undici-types": "~8.3.0"
}
},
"node_modules/@types/yargs": {
@@ -155,73 +157,84 @@
"license": "MIT"
},
"node_modules/@zakodium/nmr-types": {
- "version": "0.5.23",
- "resolved": "https://registry.npmjs.org/@zakodium/nmr-types/-/nmr-types-0.5.23.tgz",
- "integrity": "sha512-a8zmplUHOevUeOQ69yFwzCNNiUi867q2RY63GXg4Clhm+3BnXonBeHXicSycOoJzSz2V0pQ4LFPuqJMxKNjLvw==",
+ "version": "0.5.26",
+ "resolved": "https://registry.npmjs.org/@zakodium/nmr-types/-/nmr-types-0.5.26.tgz",
+ "integrity": "sha512-Da7K23q8O3EK8gslzyx5Hgd3k4TXq0w8JW+Qt2pDBZNY1M+uyVE97R9vcQKtcZiGVl/O0f57+qJ3kxvqVEnRgQ==",
"license": "CC-BY-NC-SA-4.0",
"dependencies": {
+ "cheminfo-types": "^1.15.0",
"ml-peak-shape-generator": "^5.5.0",
"ml-signal-processing": "^2.2.2",
- "ml-spectra-processing": "^14.33.0"
- }
- },
- "node_modules/@zakodium/nmr-types/node_modules/ml-peak-shape-generator": {
- "version": "5.5.0",
- "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-5.5.0.tgz",
- "integrity": "sha512-DyBq/u5S+/0F49Hm0OWHwWvPPM1aaCZIs/eI7/fUTWfIm86Yu03YXWMQ3874eq33MLZVgM8KguGkfeGDffCLog==",
- "license": "MIT",
- "dependencies": {
- "cheminfo-types": "^1.15.0"
+ "ml-spectra-processing": "^14.33.0",
+ "zod": "^4.4.3"
}
},
"node_modules/@zakodium/nmrium-core": {
- "version": "0.7.30",
- "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core/-/nmrium-core-0.7.30.tgz",
- "integrity": "sha512-uds3UysKrAgm38Yt2swNnt8nmf5SHqt1LuVnewwDTolztl3Lead0RtgOYsRjnL30k6gpvGrgaoENkIMxSY0/kQ==",
+ "version": "0.7.65",
+ "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core/-/nmrium-core-0.7.65.tgz",
+ "integrity": "sha512-mXXylnGVMbYRdz23kalRziwMK6OCkJkS3HW9izjatH/6/VZgnbiSa5DBm+SazBuNe5QAutrXIFUWa+t2D/5Esw==",
"license": "CC-BY-NC-SA-4.0",
"dependencies": {
+ "@zakodium/utils": "^0.5.1",
"cheminfo-types": "^1.15.0",
"fifo-logger": "^2.0.1",
- "file-collection": "^6.6.1",
+ "file-collection": "^6.7.0",
"is-any-array": "^3.0.0",
"lodash.merge": "^4.6.2",
- "ml-spectra-processing": "^14.28.1",
- "nmr-correlation": "^2.3.5"
+ "ml-spectra-processing": "^14.33.0"
},
"peerDependencies": {
"zod": "^4.4.3"
}
},
"node_modules/@zakodium/nmrium-core-plugins": {
- "version": "0.7.39",
- "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core-plugins/-/nmrium-core-plugins-0.7.39.tgz",
- "integrity": "sha512-WFO8UmUB4ZGwO+eCTjC1RfUBeCtv+raQmsuVx6L7zf1/BuD0N3Lq0q+JpKkdn85sfFGckyejJr1yo2qd91EVMQ==",
+ "version": "0.7.87",
+ "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core-plugins/-/nmrium-core-plugins-0.7.87.tgz",
+ "integrity": "sha512-g/JwP7tgfndzQAy8xmVBWb0PASoQc/IabMHONC7uZ+juXpYizX/XM31WwNSnmAWlbGVmKHM53xU7F+mCJX2Imw==",
"license": "CC-BY-NC-SA-4.0",
"dependencies": {
"@date-fns/utc": "^2.1.1",
- "@zakodium/nmrium-core": "^0.7.30",
+ "@zakodium/nmrium-core": "^0.7.65",
"cheminfo-types": "^1.15.0",
- "convert-to-jcamp": "^7.0.0",
- "date-fns": "^4.1.0",
- "file-collection": "^6.6.1",
+ "convert-to-jcamp": "^7.0.1",
+ "date-fns": "^4.4.0",
+ "file-collection": "^6.7.0",
"gyromagnetic-ratio": "^2.0.0",
"is-any-array": "^3.0.0",
- "jcampconverter": "^12.3.3",
+ "jcampconverter": "^12.5.5",
"linear-sum-assignment": "^1.0.9",
"lodash.merge": "^4.6.2",
- "ml-spectra-processing": "^14.28.1",
- "nmr-processing": "^22.13.0",
- "openchemlib": "^9.22.0",
- "openchemlib-utils": "^8.15.0",
- "sdf-parser": "^8.0.0",
+ "ml-spectra-processing": "^14.33.0",
+ "nmr-processing": "^22.23.6",
+ "openchemlib": "^9.24.0",
+ "openchemlib-utils": "^8.17.1",
+ "sdf-parser": "^9.0.0",
"ts-pattern": "^5.9.0",
"zod": "^4.4.3"
+ },
+ "peerDependencies": {
+ "react": "*",
+ "react-dom": "*"
+ },
+ "peerDependenciesMeta": {
+ "react": {
+ "optional": true
+ },
+ "react-dom": {
+ "optional": true
+ }
}
},
+ "node_modules/@zakodium/utils": {
+ "version": "0.5.1",
+ "resolved": "https://registry.npmjs.org/@zakodium/utils/-/utils-0.5.1.tgz",
+ "integrity": "sha512-aRtHXol0w/nL4ZYiVNicw/7batBasftRDmYSCXj54AWf1MvLrKZNk9hthzp8I+wm7jL938HAIv8eg/45J+XyOg==",
+ "license": "MIT"
+ },
"node_modules/@zip.js/zip.js": {
- "version": "2.8.23",
- "resolved": "https://registry.npmjs.org/@zip.js/zip.js/-/zip.js-2.8.23.tgz",
- "integrity": "sha512-RB+RLnxPJFPrGvQ9rgO+4JOcsob6lD32OcF0QE0yg24oeW9q8KnTTNlugcDaIveEcCbclobJcZP+fLQ++sH0bw==",
+ "version": "2.8.61",
+ "resolved": "https://registry.npmjs.org/@zip.js/zip.js/-/zip.js-2.8.61.tgz",
+ "integrity": "sha512-F9RnQJXgvCSdAJfMtSrH5Uh/LcLg8fZlg5ARC4u5N4w9v/DG27cN3C/ngUrY1JdJGX2LRv5DDViXeZJgbcppWA==",
"license": "BSD-3-Clause",
"engines": {
"bun": ">=0.7.0",
@@ -255,6 +268,18 @@
"node": ">=0.4.0"
}
},
+ "node_modules/agent-base": {
+ "version": "6.0.2",
+ "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
+ "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
+ "license": "MIT",
+ "dependencies": {
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- }
- },
- "node_modules/nmr-processing/node_modules/ml-peak-shape-generator": {
- "version": "5.5.0",
- "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-5.5.0.tgz",
- "integrity": "sha512-DyBq/u5S+/0F49Hm0OWHwWvPPM1aaCZIs/eI7/fUTWfIm86Yu03YXWMQ3874eq33MLZVgM8KguGkfeGDffCLog==",
- "license": "MIT",
- "dependencies": {
- "cheminfo-types": "^1.15.0"
- }
- },
- "node_modules/nmr-processing/node_modules/nmr-correlation": {
- "version": "3.0.1",
- "resolved": "https://registry.npmjs.org/nmr-correlation/-/nmr-correlation-3.0.1.tgz",
- "integrity": "sha512-0iuce3dLBpdcHn0Q/SX3gHvshRCUyN8X6iL6Y97VcK7JS3g8yZSQCIKjft8jsAOUzWP1rX8c1aCxw3BnCjrBEQ==",
- "license": "MIT",
- "dependencies": {
- "cheminfo-types": "^1.8.1",
- "ml-matrix-peaks-finder": "^2.0.0",
- "ml-peak-shape-generator": "^4.2.0"
- }
- },
- "node_modules/nmr-processing/node_modules/nmr-correlation/node_modules/ml-peak-shape-generator": {
- "version": "4.2.0",
- "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-4.2.0.tgz",
- "integrity": "sha512-BDtR0rhUor5/4J9pJOEMRnD+QQ5v6ohx+o6MfRRg2e2IOTeZfp/uJcy5Y852v5CsNec1GmYMkd5PYrY0245qlQ==",
- "license": "MIT",
- "dependencies": {
- "cheminfo-types": "^1.1.0"
- }
- },
"node_modules/num-sort": {
"version": "2.1.0",
"resolved": "https://registry.npmjs.org/num-sort/-/num-sort-2.1.0.tgz",
@@ -1341,7 +1336,8 @@
"version": "9.25.0",
"resolved": "https://registry.npmjs.org/openchemlib/-/openchemlib-9.25.0.tgz",
"integrity": "sha512-FGTaZLJRTGXNC7khx8QvX/EiQBHpH1ncUbT7YXDJhw/Y/aDUKe5WrUIqTguMEtSs3GUHcRUjNUhfkpxulx2UXw==",
- "license": "BSD-3-Clause"
+ "license": "BSD-3-Clause",
+ "peer": true
},
"node_modules/openchemlib-utils": {
"version": "8.18.0",
@@ -1361,62 +1357,55 @@
"openchemlib": ">=9.25.0"
}
},
- "node_modules/openchemlib-utils/node_modules/sdf-parser": {
- "version": "9.0.0",
- "resolved": "https://registry.npmjs.org/sdf-parser/-/sdf-parser-9.0.0.tgz",
- "integrity": "sha512-yi69gjBudryiKrLsT35OkyoGmskvXbVpUjkcd9tX4M4sLVmqeptsZtcx6Etf/bvdk9Ts1Wy6PuyXVIPktn6ZNQ==",
- "license": "MIT",
- "dependencies": {
- "dynamic-typing": "^2.0.0",
- "ensure-string": "^2.0.0"
- }
- },
"node_modules/papaparse": {
- "version": "5.6.0",
- "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.6.0.tgz",
- "integrity": "sha512-N2vuNQAYGK1/4vs6HJX86+VYU6OkiSTgdJz3JQfTk1y51cFCO/U8gnaeTF4iNE4r57Tt0sV47dUua1/19pxO6Q==",
+ "version": "5.7.0",
+ "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.7.0.tgz",
+ "integrity": "sha512-qBGxg/7Q3Kl9Wfhrz2Z74UnvnHTXLNG6jmKJFeBvP2+y4lV7So+7SR62+Zd47JvdrCkX+nDcnr0ObPzek/+6RA==",
"license": "MIT"
},
"node_modules/playwright": {
- "version": "1.58.2",
- "resolved": "https://registry.npmjs.org/playwright/-/playwright-1.58.2.tgz",
- "integrity": "sha512-vA30H8Nvkq/cPBnNw4Q8TWz1EJyqgpuinBcHET0YVJVFldr8JDNiU9LaWAE1KqSkRYazuaBhTpB5ZzShOezQ6A==",
+ "version": "1.62.1",
+ "resolved": "https://registry.npmjs.org/playwright/-/playwright-1.62.1.tgz",
+ "integrity": "sha512-0M+L3LAD8/nm554LOla9Ayx0j0tmFZ0FBcoQ7F1VuVHpM/XpiC8RcDzBQB8W5+hA8L22THxELzeF+2WcUzvcLg==",
"license": "Apache-2.0",
"dependencies": {
- "playwright-core": "1.58.2"
+ "playwright-core": "1.62.1"
},
"bin": {
"playwright": "cli.js"
},
"engines": {
- "node": ">=18"
+ "node": ">=20"
},
"optionalDependencies": {
"fsevents": "2.3.2"
}
},
"node_modules/playwright-core": {
- "version": "1.58.2",
- "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.58.2.tgz",
- "integrity": "sha512-yZkEtftgwS8CsfYo7nm0KE8jsvm6i/PTgVtB8DL726wNf6H2IMsDuxCpJj59KDaxCtSnrWan2AeDqM7JBaultg==",
+ "version": "1.62.1",
+ "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.62.1.tgz",
+ "integrity": "sha512-wPYSwEBJY9GHraISXqyqtx0na0LpO3XEX7jNDhntbex7tzUS7kLnZsOlFruFJB4Hi/rhDMjXGqHewDZ68nYZVw==",
"license": "Apache-2.0",
"bin": {
"playwright-core": "cli.js"
},
"engines": {
- "node": ">=18"
+ "node": ">=20"
}
},
"node_modules/proxy-from-env": {
- "version": "1.1.0",
- "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-1.1.0.tgz",
- "integrity": "sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg==",
- "license": "MIT"
+ "version": "2.1.0",
+ "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-2.1.0.tgz",
+ "integrity": "sha512-cJ+oHTW1VAEa8cJslgmUZrc+sjRKgAKl3Zyse6+PV38hZe/V6Z14TbCuXcan9F9ghlz4QrFr2c92TNF82UkYHA==",
+ "license": "MIT",
+ "engines": {
+ "node": ">=10"
+ }
},
"node_modules/sdf-parser": {
- "version": "8.0.0",
- "resolved": "https://registry.npmjs.org/sdf-parser/-/sdf-parser-8.0.0.tgz",
- "integrity": "sha512-Mh+FbnUGfu+I7/xN0JOiuQ9GP3H36USFXg3ZpeuUMXpGmYHmzmv763poF1u152Xz76nmqRLTL2ibA4dfU0yzjw==",
+ "version": "9.0.0",
+ "resolved": "https://registry.npmjs.org/sdf-parser/-/sdf-parser-9.0.0.tgz",
+ "integrity": "sha512-yi69gjBudryiKrLsT35OkyoGmskvXbVpUjkcd9tX4M4sLVmqeptsZtcx6Etf/bvdk9Ts1Wy6PuyXVIPktn6ZNQ==",
"license": "MIT",
"dependencies": {
"dynamic-typing": "^2.0.0",
@@ -1433,15 +1422,6 @@
"ml-spectra-processing": "^14.28.1"
}
},
- "node_modules/spectrum-generator/node_modules/ml-peak-shape-generator": {
- "version": "5.5.0",
- "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-5.5.0.tgz",
- "integrity": "sha512-DyBq/u5S+/0F49Hm0OWHwWvPPM1aaCZIs/eI7/fUTWfIm86Yu03YXWMQ3874eq33MLZVgM8KguGkfeGDffCLog==",
- "license": "MIT",
- "dependencies": {
- "cheminfo-types": "^1.15.0"
- }
- },
"node_modules/string-width": {
"version": "7.2.0",
"resolved": "https://registry.npmjs.org/string-width/-/string-width-7.2.0.tgz",
@@ -1530,6 +1510,7 @@
"integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==",
"dev": true,
"license": "Apache-2.0",
+ "peer": true,
"bin": {
"tsc": "bin/tsc",
"tsserver": "bin/tsserver"
@@ -1545,9 +1526,9 @@
"license": "MIT"
},
"node_modules/undici-types": {
- "version": "7.18.2",
- "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.18.2.tgz",
- "integrity": "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w==",
+ "version": "8.3.0",
+ "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-8.3.0.tgz",
+ "integrity": "sha512-j375ScV60dom+YkPFIfTLcOiPxkN/buHz5GobjLhixFuANaNs3C9l4GmrWqejgXWJ7BbJcFYpTEUkS1Ge8bpZQ==",
"dev": true,
"license": "MIT"
},
@@ -1585,15 +1566,15 @@
}
},
"node_modules/yargs": {
- "version": "18.0.0",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz",
- "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==",
+ "version": "18.1.0",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.1.0.tgz",
+ "integrity": "sha512-2rAgRKu54VsHkqI0/tYkmluGXHD4KW7yZoycuqDQ15QOTnc2VVfy0nN/1eMhnQLO00A+dwtK20xuCnc1YGeUyg==",
"license": "MIT",
"dependencies": {
"cliui": "^9.0.1",
"escalade": "^3.1.1",
"get-caller-file": "^2.0.5",
- "string-width": "^7.2.0",
+ "string-width": "^8.2.1",
"y18n": "^5.0.5",
"yargs-parser": "^22.0.0"
},
@@ -1610,6 +1591,22 @@
"node": "^20.19.0 || ^22.12.0 || >=23"
}
},
+ "node_modules/yargs/node_modules/string-width": {
+ "version": "8.2.2",
+ "resolved": "https://registry.npmjs.org/string-width/-/string-width-8.2.2.tgz",
+ "integrity": "sha512-GaPUh5gfdrYzqeVNZvUfT23vYYxXzKYidUcnMtJg/3rxRV63EFZy3k6xfKlmfeJD0176lnUV/Usr3XcwSvFzpg==",
+ "license": "MIT",
+ "dependencies": {
+ "get-east-asian-width": "^1.5.0",
+ "strip-ansi": "^7.1.2"
+ },
+ "engines": {
+ "node": ">=20"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
"node_modules/yn": {
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz",
@@ -1625,6 +1622,7 @@
"resolved": "https://registry.npmjs.org/zod/-/zod-4.4.3.tgz",
"integrity": "sha512-ytENFjIJFl2UwYglde2jchW2Hwm4GJFLDiSXWdTrJQBIN9Fcyp7n4DhxJEiWNAJMV1/BqWfW/kkg71UDcHJyTQ==",
"license": "MIT",
+ "peer": true,
"funding": {
"url": "https://github.com/sponsors/colinhacks"
}
diff --git a/app/scripts/nmr-cli/package.json b/app/scripts/nmr-cli/package.json
index 0d3bd4d..9180a20 100644
--- a/app/scripts/nmr-cli/package.json
+++ b/app/scripts/nmr-cli/package.json
@@ -15,24 +15,25 @@
"nmr-cli": "./build/index.js"
},
"dependencies": {
- "@zakodium/nmr-types": "^0.5.12",
- "@zakodium/nmrium-core": "0.7.30",
- "@zakodium/nmrium-core-plugins": "0.7.39",
- "axios": "^1.13.6",
+ "@zakodium/nmr-types": "^0.5.26",
+ "@zakodium/nmrium-core": "0.7.65",
+ "@zakodium/nmrium-core-plugins": "0.7.87",
+ "axios": "^1.19.0",
"fifo-logger": "^2.0.1",
- "file-collection": "^6.6.1",
- "json-stream-stringify": "^3.1.6",
+ "file-collection": "^6.7.0",
+ "json-stream-stringify": "^3.1.7",
"lodash.merge": "^4.6.2",
- "mf-parser": "^3.7.1",
- "ml-spectra-processing": "^14.22.0",
- "nmr-processing": "^22.5.2",
- "openchemlib": "^9.20.0",
- "playwright": "1.58.2",
- "yargs": "^18.0.0"
+ "mf-parser": "^3.9.2",
+ "ml-spectra-processing": "^14.34.0",
+ "nmr-correlation": "^3.0.2",
+ "nmr-processing": "^22.23.6",
+ "openchemlib": "^9.25.0",
+ "playwright": "1.62.1",
+ "yargs": "^18.1.0"
},
"devDependencies": {
"@types/lodash.merge": "^4.6.9",
- "@types/node": "^25.3.5",
+ "@types/node": "^26.2.0",
"@types/yargs": "^17.0.35",
"ts-node": "^10.9.2",
"typescript": "^5.9.3"
diff --git a/app/scripts/nmr-cli/src/correlation.ts b/app/scripts/nmr-cli/src/correlation.ts
new file mode 100644
index 0000000..0c8382b
--- /dev/null
+++ b/app/scripts/nmr-cli/src/correlation.ts
@@ -0,0 +1,115 @@
+import { buildCorrelationData } from 'nmr-correlation'
+import type { Options as CorrelationOptions, Spectra } from 'nmr-correlation'
+import { FifoLogger } from 'fifo-logger'
+import type { NmriumState, Spectrum } from '@zakodium/nmrium-core'
+import {
+ buildWebSource,
+ core,
+ loadFileCollection,
+ parsingOptions,
+ processSpectra,
+} from './parse/prase-spectra'
+import { isSpectrum2D } from './parse/data/data2d/isSpectrum2D'
+
+// Default tolerances confirmed by vcnainala on issue #66
+const DEFAULT_TOLERANCE_H = 0.02
+const DEFAULT_TOLERANCE_C = 0.25
+
+export interface CorrelationInput {
+ url?: string
+ dir?: string
+ mf: string
+ toleranceH?: number
+ toleranceC?: number
+}
+
+interface ReadSpectraOptions {
+ url?: string
+ dir?: string
+}
+
+async function readSpectra(
+ options: ReadSpectraOptions,
+ logger: FifoLogger
+): Promise> {
+ const { url, dir } = options
+
+ if (url) {
+ const { state } = await core.readFromWebSource(buildWebSource(url), {
+ ...parsingOptions,
+ logger,
+ })
+ return state
+ }
+
+ if (dir) {
+ const { state } = await core.read(await loadFileCollection(dir), {
+ ...parsingOptions,
+ logger,
+ })
+ return state
+ }
+
+ throw new Error('Either a spectra URL or a local directory path is required')
+}
+
+// buildCorrelationData needs detected ranges (1D) or zones (2D) to find
+// correlations, so require isFt plus at least one detected range/zone.
+// This also excludes spectra that failed to initiate or failed detection,
+// since those never get ranges/zones populated either.
+// Note: a pre-existing bug (see https://github.com/NFDI4Chem/nmrkit/issues/139)
+// currently makes every spectrum fail initiation, so real cross-spectrum correlation links are untested here.
+function filterSpectra(spectra: Spectrum[]): Spectrum[] {
+ return spectra.filter(spectrum => {
+ const { info } = spectrum
+ if (info.isFt !== true) return false
+
+ if (isSpectrum2D(spectrum)) {
+ const { zones } = spectrum
+ return zones.values.length > 0
+ }
+
+ const { ranges } = spectrum
+ return ranges.values.length > 0
+ })
+}
+
+function resolveTolerance(value: number | undefined, fallback: number): number {
+ return value === undefined || Number.isNaN(value) ? fallback : value
+}
+
+export async function generateCorrelationData(input: CorrelationInput) {
+ const { url, dir, mf, toleranceH, toleranceC } = input
+ const logger = new FifoLogger()
+
+ const state = await readSpectra({ url, dir }, logger)
+
+ if (state.data) {
+ processSpectra(
+ state.data,
+ { autoProcessing: true, autoDetection: true },
+ logger
+ )
+ }
+
+ const spectra = filterSpectra(state.data?.spectra ?? [])
+
+ const options: CorrelationOptions = {
+ mf,
+ tolerance: {
+ H: resolveTolerance(toleranceH, DEFAULT_TOLERANCE_H),
+ C: resolveTolerance(toleranceC, DEFAULT_TOLERANCE_C),
+ },
+ }
+
+ let correlationData
+ try {
+ correlationData = buildCorrelationData(spectra as Spectra, options)
+ } catch (error) {
+ throw new Error(
+ `Failed to build correlation data: ${error instanceof Error ? error.message : String(error)}`
+ )
+ }
+
+ return { ...correlationData, logs: logger.getLogs() }
+}
diff --git a/app/scripts/nmr-cli/src/index.ts b/app/scripts/nmr-cli/src/index.ts
index 74c7000..7ca4b70 100755
--- a/app/scripts/nmr-cli/src/index.ts
+++ b/app/scripts/nmr-cli/src/index.ts
@@ -4,6 +4,7 @@ import { parseSpectra } from './parse/prase-spectra'
import { generateSpectrumFromPublicationString } from './publication-string'
import { generateNMRiumFromPeaks } from './peaks-to-nmrium'
import type { PeaksToNMRiumInput } from './peaks-to-nmrium'
+import { generateCorrelationData } from './correlation'
import { hideBin } from 'yargs/helpers'
import { parsePredictionCommand } from './prediction'
import { readFileSync } from 'fs'
@@ -15,8 +16,16 @@ Usage: nmr-cli [options]
Commands:
parse-spectra Parse a spectra file to NMRium file
parse-publication-string resurrect spectrum from the publication string
- predict Predict spectrum from Mol
+ predict Predict spectrum from Mol
peaks-to-nmrium Convert a peak list to NMRium object
+ correlation Build correlation data from NMR spectra fetched from a URL
+
+Options for 'correlation' command:
+ -u, --url Spectra ZIP file URL
+ -dir, --dir-path Local directory path
+ --mf Molecular formula
+ --tolerance-h, --th H tolerance override (default: 0.02)
+ --tolerance-c, --tc C tolerance override (default: 0.25)
Options for 'parse-spectra' command:
-u, --url File URL
@@ -26,6 +35,8 @@ Options for 'parse-spectra' command:
-d, --auto-detection Enable ranges and zones automatic detection.
-o, --output Output file path (optional)
-r, --raw-data Include raw data in the output instead of data source
+ --include Include only files matching pattern(s) (glob/regex string, repeatable)
+ --exclude Exclude files matching pattern(s) (glob/regex string, repeatable)
Arguments for 'parse-publication-string' command:
publicationString Publication string
@@ -133,6 +144,18 @@ export interface FileOptionsArgs {
*/
r?: boolean;
+ /**
+ * --include
+ * Only include files matching these pattern(s) when reading a directory (file-collection's filter.include).
+ */
+ include?: string[];
+
+ /**
+ * --exclude
+ * Exclude files matching these pattern(s) when reading a directory (file-collection's filter.exclude).
+ */
+ exclude?: string[];
+
}
// Define options for parsing a spectra file
@@ -175,6 +198,16 @@ const fileOptions: { [key in keyof FileOptionsArgs]: Options } = {
default: false,
description: 'Include raw data in the output (default: dataSource)',
},
+ include: {
+ type: 'array',
+ string: true,
+ description: 'Only include files matching pattern(s) when reading a directory (glob/regex string)',
+ },
+ exclude: {
+ type: 'array',
+ string: true,
+ description: 'Exclude files matching pattern(s) when reading a directory (glob/regex string)',
+ },
} as const
const parseFileCommand: CommandModule<{}, FileOptionsArgs> = {
@@ -226,12 +259,73 @@ const peaksToNMRiumCommand: CommandModule = {
},
}
+// Define the correlation command
+const correlationCommand: CommandModule = {
+ command: ['correlation', 'corr'],
+ describe: 'Build correlation data from NMR spectra fetched from a URL or a local directory',
+ builder: yargs => {
+ return yargs
+ .options({
+ u: {
+ alias: 'url',
+ describe: 'Spectra ZIP file URL',
+ type: 'string',
+ nargs: 1,
+ },
+ dir: {
+ alias: 'dir-path',
+ describe: 'Local directory path',
+ type: 'string',
+ nargs: 1,
+ },
+ mf: {
+ describe: 'Molecular formula',
+ type: 'string',
+ demandOption: true,
+ nargs: 1,
+ },
+ 'tolerance-h': {
+ alias: 'th',
+ describe: 'H tolerance override',
+ type: 'number',
+ default: 0.02,
+ },
+ 'tolerance-c': {
+ alias: 'tc',
+ describe: 'C tolerance override',
+ type: 'number',
+ default: 0.25,
+ },
+ })
+ .conflicts('u', 'dir')
+ },
+ handler: async argv => {
+ try {
+ const result = await generateCorrelationData({
+ url: argv.u as string | undefined,
+ dir: argv.dir as string | undefined,
+ mf: argv.mf as string,
+ toleranceH: argv['tolerance-h'] as number | undefined,
+ toleranceC: argv['tolerance-c'] as number | undefined,
+ })
+ console.log(JSON.stringify(result))
+ } catch (error) {
+ console.error(
+ 'Error:',
+ error instanceof Error ? error.message : String(error),
+ )
+ process.exit(1)
+ }
+ },
+}
+
yargs(hideBin(process.argv))
.usage(usageMessage)
.command(parseFileCommand)
.command(parsePublicationCommand)
.command(parsePredictionCommand)
.command(peaksToNMRiumCommand)
+ .command(correlationCommand)
.showHelpOnFail(true)
.help()
.parse()
diff --git a/app/scripts/nmr-cli/src/parse/prase-spectra.ts b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
index 06b521d..e496b12 100644
--- a/app/scripts/nmr-cli/src/parse/prase-spectra.ts
+++ b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
@@ -196,11 +196,9 @@ async function processAndSerialize(
outputResult({ nmriumState: { data, version }, images, logs }, o);
}
-async function loadSpectrumFromURL(options: RequiredKey, logger: FifoLogger) {
- const { u: url } = options;
-
+function buildWebSource(url: string) {
const { pathname: relativePath, origin: baseURL } = new URL(url)
- const source = {
+ return {
entries: [
{
relativePath,
@@ -208,22 +206,32 @@ async function loadSpectrumFromURL(options: RequiredKey, l
],
baseURL,
}
+}
+async function loadSpectrumFromURL(options: RequiredKey, logger: FifoLogger) {
+ const { u: url, include, exclude } = options;
+
+ const source = buildWebSource(url)
- const { state } = await core.readFromWebSource(source, { ...parsingOptions, logger });
+ const { state } = await core.readFromWebSource(source, { ...parsingOptions, fileFilter: { include, exclude }, logger });
processAndSerialize(state, options, logger)
}
-async function loadSpectrumFromFilePath(options: RequiredKey, logger: FifoLogger) {
- const { dir: path } = options;
-
+function loadFileCollection(path: string, include?: string[], exclude?: string[]) {
const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
- const fileCollection = await FileCollection.fromPath(dirPath, {
+ return FileCollection.fromPath(dirPath, {
unzip: { zipExtensions: ['zip', 'nmredata'] },
+ filter: { include, exclude },
})
+}
+
+async function loadSpectrumFromFilePath(options: RequiredKey, logger: FifoLogger) {
+ const { dir: path, include, exclude } = options;
+
+ const fileCollection = await loadFileCollection(path, include, exclude)
const {
state
@@ -256,4 +264,4 @@ function parseSpectra(argv: yargs.ArgumentsCamelCase
-export { loadSpectrumFromFilePath, loadSpectrumFromURL, parseSpectra }
+export { loadSpectrumFromFilePath, loadSpectrumFromURL, parseSpectra, processSpectra, parsingOptions, core, buildWebSource, loadFileCollection }