@datagrok/bio 2.1.12 → 2.4.3

package/dockerfiles/Dockerfile

@@ -0,0 +1,86 @@
+# Add ability to easily change python version
+ARG PYTHON_VERSION=3.8
+
+# Use our base image which is optimised and secured by our flow
+FROM datagrok/python:${PYTHON_VERSION}
+
+MAINTAINER Volodymyr Dyma <vdyma@datagrok.ai>
+
+# Use pipefail to avoid errors after piping
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+ARG HOME_DIR=/home/grok
+# It is important to run docker container as user and not as root
+RUN groupadd --gid 2001 grok ; \
+    useradd --system --create-home --home ${HOME_DIR} --gid grok --uid 1001 grok
+
+# Remove unzip after unpacking
+ARG DEBIAN_FRONTEND=noninteractive
+RUN savedAptMark="$(apt-mark showmanual)" ; \
+    apt-get update ; \
+    apt-get install -y --no-install-recommends \
+      unzip \
+      wget \
+    ; \
+    apt-mark auto '.*' > /dev/null ; \
+    [ -z "$savedAptMark" ] || apt-mark manual $savedAptMark ; \
+	wget https://mafft.cbrc.jp/alignment/software/mafft_7.511-1_amd64.deb -O mafft.deb; \
+	apt install -y ./mafft.deb; \
+	rm -rf mafft.deb; \
+    wget https://github.com/Merck/PepSeA/archive/refs/heads/main.zip -O PepSeA.zip; \
+    unzip -q PepSeA.zip -d /opt ; \
+	rm -rf PepSeA.zip; \
+    chown -R grok:grok /opt/PepSeA-main ; \
+    apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false ; \
+    apt-get clean ; \
+    rm -rf /var/lib/apt/lists/* /var/cache/* /var/tmp/* /tmp/* /opt/PepSeA-main/alignment/mafft /opt/PepSeA-main/local.env; \
+    sed -i "s/files = glob.glob(f'\*{timestamp}\*')/files = glob.glob(f'\*{timestamp}\*.txt')/" /opt/PepSeA-main/alignment/AlignSubPeptides.py; \
+    echo $'\n\
+@api.get("/distout", response_class=PlainTextResponse)\n\
+def distout():\n\
+    """Returns the output of --distout parameter as a plain text."""\n\
+    \n\
+    distout_output = None\n\
+\n\
+    for file in os.listdir("./"):\n\
+        if not file.endswith(".hat2"):\n\
+            continue\n\
+\n\
+        path = os.path.join("./", file)\n\
+        with open(path, "r", encoding="utf-8") as f:\n\
+            distout_output = "".join(f.readlines())\n\
+        os.remove(path)\n\
+        break\n\
+\n\
+    if distout_output is None:\n\
+        raise FileNotFoundError("distance matrix is not found")\n\
+\n\
+    return distout_output\n' >> /opt/PepSeA-main/alignment/api.py;
+
+USER grok:grok
+
+# Command source does not work for Docker, cause it will apply only to one layer
+# The PATH works better for Docker
+ARG VIRTUAL_ENV=${HOME_DIR}/venv
+ENV PATH "${VIRTUAL_ENV}/bin:$PATH"
+RUN mkdir -p ${VIRTUAL_ENV} ; \
+    python -m venv ${VIRTUAL_ENV} ; \
+    pip install --no-cache-dir --upgrade pip ; \
+    pip install --no-cache-dir --upgrade wheel setuptools ; \
+    pip install --timeout 3600 --no-cache-dir \
+      --requirement /opt/PepSeA-main/requirements.txt ; \
+    find ${VIRTUAL_ENV} -type d \( -path *tensorflow \) -prune -false -depth \( \
+      \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
+          -o \( -type f -a \( -name '*.pyc' -o -name '*.pyo' \) \) \
+      \) -exec rm -rf '{}' + ; \
+    rm -rf /var/cache/* /var/tmp/* /tmp/*
+
+WORKDIR /opt/PepSeA-main
+
+ENV ADD_HTTPS_MIDDLEWARE=""
+ENV MAFFT_DIR="/usr/bin/"
+
+# CMD can be changed easially, you need ENTRYPOINT in this case
+ENTRYPOINT ["uvicorn", "--host", "0.0.0.0", "alignment.api:api"]
+
+EXPOSE 8000

package/files/icons/composition-analysis.svg

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package/files/icons/sequence-diversity-viewer.svg

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package/files/icons/sequence-similarity-viewer.svg

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package/files/tests/testUrl.csv

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+https://datagrok.ai/help/domains/chem/functions/si.md
+https://datagrok.ai/help/domains/chem/functions/ga-pt.md
+https://datagrok.ai/help/domains/chem/functions/m12.md
+https://datagrok.ai/help/domains/chem/functions/mu1-15.html
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package/files/tests/toAtomicLevelTest.csv

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package/package.json

@@ -5,8 +5,8 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.1.12",
-  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
+  "version": "2.4.3",
+  "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
     "url": "https://github.com/datagrok-ai/public.git",
@@ -14,38 +14,34 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.16.0",
+    "@datagrok-libraries/bio": "^5.27.0",
     "@datagrok-libraries/chem-meta": "^1.0.1",
-    "@datagrok-libraries/ml": "^6.3.3",
-    "@datagrok-libraries/utils": "^1.19.4",
+    "@datagrok-libraries/ml": "^6.3.13",
+    "@datagrok-libraries/utils": "^2.1.3",
     "cash-dom": "^8.0.0",
-    "datagrok-api": "^1.11.1",
+    "css-loader": "^6.7.3",
+    "datagrok-api": "^1.13.3",
     "dayjs": "^1.11.4",
     "openchemlib": "6.0.1",
     "rxjs": "^6.5.5",
+    "source-map-loader": "^4.0.1",
+    "style-loader": "^3.3.1",
     "wu": "latest"
   },
   "devDependencies": {
-    "@types/js-yaml": "^4.0.5",
     "@types/node": "^17.0.24",
-    "@types/node-fetch": "^2.6.2",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "^4.20.0",
     "@typescript-eslint/parser": "^4.20.0",
     "eslint": "^7.23.0",
     "eslint-config-google": "latest",
-    "js-yaml": "^4.1.0",
-    "node-fetch": "^2.6.7",
-    "puppeteer": "^13.7.0",
     "ts-loader": "^9.2.5",
     "typescript": "^4.2.3",
-    "webpack": "^5.64.1",
+    "webpack": "^5.76.0",
     "webpack-bundle-analyzer": "latest",
-    "webpack-cli": "^4.6.0"
-  },
-  "grokDependencies": {
-    "@datagrok/chem": "latest",
-    "@datagrok/helm": "latest"
+    "webpack-cli": "^4.6.0",
+    "@datagrok/chem": "1.4.21",
+    "@datagrok/helm": "2.1.7"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",
@@ -53,16 +49,16 @@
     "link-ml": "npm link @datagrok-libraries/ml",
     "link-utils": "npm link @datagrok-libraries/utils",
     "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio @datagrok-libraries/ml",
-    "debug-sequences1": "grok publish",
-    "release-sequences1": "grok publish --release",
+    "debug-sequences1": "webpack && grok publish",
+    "release-sequences1": "webpack && grok publish --release",
     "build-sequences1": "webpack",
-    "debug-local": "grok publish local",
-    "release-local": "grok publish local --release",
     "build": "webpack",
-    "debug-sequences1-public": "grok publish public",
-    "release-sequences1-public": "grok publish public --release",
-    "debug-sequences1-local": "grok publish local",
-    "release-sequences1-local": "grok publish local --release",
+    "debug-sequences1-local": "webpack && grok publish local",
+    "release-sequences1-local": "webpack && grok publish local --release",
+    "debug-sequences1-dev": "webpack && grok publish dev",
+    "release-sequences1-dev": "webpack && grok publish dev --release",
+    "debug-sequences1-public": "webpack && grok publish public",
+    "release-sequences1-public": "webpack && grok publish public --release",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix",
     "test": "grok test",
@@ -73,6 +69,9 @@
   "canEdit": [
     "Developers"
   ],
+  "canView": [
+    "All users"
+  ],
   "sources": [
     "css/helm.css"
   ],

package/src/analysis/sequence-activity-cliffs.ts

@@ -4,26 +4,28 @@ import * as DG from 'datagrok-api/dg';
 
 import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {getSimilarityFromDistance} from '@datagrok-libraries/ml/src/distance-metrics-methods';
-import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import {TAGS} from '../utils/constants';
+import {AvailableMetrics, AvailableMetricsTypes, StringMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
 import * as C from '../utils/constants';
 import {GridColumn} from 'datagrok-api/dg';
 import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
-import {getSplitter} from '@datagrok-libraries/bio';
+import {getSplitter, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
   const distances = new Array(stringArray.length).fill(0);
+  const distanceMethod: (x: string, y: string) => number =
+    AvailableMetrics[AvailableMetricsTypes.String][StringMetricsNames.Levenshtein];
   for (let i = 0; i < stringArray.length; ++i) {
-    const distance = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
+    const distance = stringArray[i] ? distanceMethod(stringArray[i], seq) : null;
     distances[i] = distance ? distance / Math.max((stringArray[i] as string).length, seq.length) : null;
   }
   return distances;
 }
 
-export async function getSimilaritiesMarix(dim: number, seqCol: DG.Column, df: DG.DataFrame, colName: string, simArr: DG.Column[])
-  : Promise<DG.Column[]> {
+export async function getSimilaritiesMatrix(
+  dim: number, seqCol: DG.Column, df: DG.DataFrame, colName: string, simArr: DG.Column[]
+): Promise<DG.Column[]> {
   const distances = new Array(simArr.length).fill(null);
   for (let i = 0; i != dim - 1; ++i) {
     const seq: string = seqCol.get(i);
@@ -40,7 +42,7 @@ export async function getSimilaritiesMarix(dim: number, seqCol: DG.Column, df: D
   return simArr;
 }
 
-export async function getChemSimilaritiesMarix(dim: number, seqCol: DG.Column,
+export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column,
   df: DG.DataFrame, colName: string, simArr: DG.Column[])
   : Promise<DG.Column[]> {
   if (seqCol.version !== seqCol.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
@@ -104,7 +106,7 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
 
   const molDifferences: { [key: number]: HTMLCanvasElement } = {};
   const units = params.seqCol.getTag(DG.TAGS.UNITS);
-  const separator = params.seqCol.getTag(TAGS.SEPARATOR);
+  const separator = params.seqCol.getTag(bioTAGS.separator);
   const splitter = getSplitter(units, separator);
   const subParts1 = splitter(sequencesArray[0]);
   const subParts2 = splitter(sequencesArray[1]);
@@ -164,7 +166,7 @@ export function createLinesGrid(df: DG.DataFrame, colNames: string[]): DG.Grid {
     .init((i) => `${df.get(colNames[0], i)}#${df.get(colNames[1], i)}`);
   seqDiffCol.semType = 'MacromoleculeDifference';
   seqDiffCol.setTag(DG.TAGS.UNITS, df.col(colNames[0])!.getTag(DG.TAGS.UNITS));
-  seqDiffCol.setTag(C.TAGS.SEPARATOR, df.col(colNames[0])!.getTag(C.TAGS.SEPARATOR));
+  seqDiffCol.setTag(bioTAGS.separator, df.col(colNames[0])!.getTag(bioTAGS.separator));
   df.columns.add(seqDiffCol);
   const grid = df.plot.grid();
   grid.col(colNames[0])!.visible = false;

package/src/analysis/sequence-search-base-viewer.ts

@@ -3,6 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {CHEM_SIMILARITY_METRICS} from '@datagrok-libraries/ml/src/distance-metrics-methods';
+import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import * as C from '../utils/constants';
 
 export class SequenceSearchBaseViewer extends DG.JsViewer {
@@ -15,7 +16,7 @@ export class SequenceSearchBaseViewer extends DG.JsViewer {
   moleculeColumn?: DG.Column|null;
   moleculeColumnName: string;
   initialized: boolean = false;
-  tags = [DG.TAGS.UNITS, C.TAGS.ALIGNED, C.TAGS.SEPARATOR, C.TAGS.ALPHABET];
+  tags = [DG.TAGS.UNITS, bioTAGS.aligned, bioTAGS.separator, bioTAGS.alphabet];
 
   constructor(name: string) {
     super();

package/src/analysis/sequence-similarity-viewer.ts

@@ -8,7 +8,7 @@ import * as C from '../utils/constants';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
-import {getSplitter} from '@datagrok-libraries/bio';
+import {TAGS as bioTAGS, getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   hotSearch: boolean;
@@ -83,7 +83,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const propPanel = ui.div();
     const molDifferences: { [key: number]: HTMLCanvasElement } = {};
     const units = resDf.col('sequence')!.getTag(DG.TAGS.UNITS);
-    const separator = resDf.col('sequence')!.getTag(C.TAGS.SEPARATOR);
+    const separator = resDf.col('sequence')!.getTag(bioTAGS.separator);
     const splitter = getSplitter(units, separator);
     const subParts1 = splitter(this.moleculeColumn!.get(this.targetMoleculeIdx));
     const subParts2 = splitter(resDf.get('sequence', resDf.currentRowIdx));
@@ -101,7 +101,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const accIcon = ui.element('i');
     accIcon.className = 'grok-icon svg-icon svg-view-layout';
     acc.addTitle(ui.span([accIcon, ui.label(`Similarity search`)]));
-    acc.addPane('Differeces', () => propPanel, true);
+    acc.addPane('Differences', () => propPanel, true);
     grok.shell.o = acc.root;
   }
 }

package/src/analysis/sequence-space.ts

@@ -47,7 +47,8 @@ export async function sequenceSpaceByFingerprints(spaceParams: ISequenceSpacePar
     methodName: spaceParams.methodName,
     similarityMetric: spaceParams.similarityMetric,
     xAxis: spaceParams.embedAxesNames[0],
-    yAxis: spaceParams.embedAxesNames[1]
+    yAxis: spaceParams.embedAxesNames[1],
+    options: spaceParams.options
   });
   return result;
 }

package/src/calculations/monomerLevelMols.ts

@@ -4,13 +4,13 @@ import * as DG from 'datagrok-api/dg';
 
 import * as C from '../utils/constants';
 import {getHelmMonomers} from '../package';
-import {getSplitter, getStats} from '@datagrok-libraries/bio';
+import {TAGS as bioTAGS, getSplitter, getStats} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 const V2000_ATOM_NAME_POS = 31;
 
-export async function getMonomericMols(mcol: DG.Column,
+export async function getMonomericMols(mcol: DG.Column<string>,
   pattern: boolean = false, monomersDict?: Map<string, string>): Promise<DG.Column> {
-  const separator: string = mcol.tags[C.TAGS.SEPARATOR];
+  const separator: string = mcol.tags[bioTAGS.separator];
   const units: string = mcol.tags[DG.TAGS.UNITS];
   const splitter = getSplitter(units, separator);
   let molV3000Array;
@@ -29,7 +29,7 @@ export async function getMonomericMols(mcol: DG.Column,
   } else {
     molV3000Array = new Array<string>(mcol.length);
     for (let i = 0; i < mcol.length; i++) {
-      const sequenceMonomers = splitter(mcol.get(i)).filter((it) => it !== '');
+      const sequenceMonomers = splitter(mcol.get(i)!).filter((it) => it !== '');
       const molV3000 = molV3000FromNonHelmSequence(sequenceMonomers, monomersDict, pattern);
       molV3000Array[i] = molV3000;
     }

package/src/package-test.ts

@@ -2,13 +2,14 @@ import * as DG from 'datagrok-api/dg';
 
 import {runTests, TestContext, tests} from '@datagrok-libraries/utils/src/test';
 
+import './tests/_first-tests';
 import './tests/Palettes-test';
 import './tests/detectors-tests';
+import './tests/detectors-weak-and-likely-tests';
 import './tests/detectors-benchmark-tests';
 import './tests/msa-tests';
-import './tests/sequence-space-test';
-import './tests/activity-cliffs-tests';
 import './tests/splitters-test';
+import './tests/monomer-libraries-tests';
 import './tests/renderers-test';
 import './tests/converters-test';
 import './tests/fasta-handler-test';
@@ -18,6 +19,13 @@ import './tests/WebLogo-positions-test';
 import './tests/checkInputColumn-tests';
 import './tests/similarity-diversity-tests';
 import './tests/substructure-filters-tests';
+import './tests/pepsea-tests';
+import './tests/viewers';
+
+// Tests hanging github CI
+import './tests/activity-cliffs-tests';
+import './tests/sequence-space-test';
+
 
 export const _package = new DG.Package();
 export {tests};