From 1689ee6b264e3b9775e62ac76e8c5e8e9b5a2e6a Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Fri, 6 Sep 2024 10:26:51 -0400 Subject: [PATCH 01/16] python upgrades --- python-utils/pyproject.toml | 2 +- pythonCopasiOpt/vcell-opt/pyproject.toml | 2 +- pythonVtk/pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/python-utils/pyproject.toml b/python-utils/pyproject.toml index a34105f452..22fb8e95ea 100644 --- a/python-utils/pyproject.toml +++ b/python-utils/pyproject.toml @@ -19,7 +19,7 @@ classifiers = [ ] [tool.poetry.dependencies] -python = "^3.9" +python = "^3.10" requests = "^2.31.0" pydantic = "^2.5.2" python-dotenv = "^1.0.0" diff --git a/pythonCopasiOpt/vcell-opt/pyproject.toml b/pythonCopasiOpt/vcell-opt/pyproject.toml index 8601fc6291..f23b044019 100644 --- a/pythonCopasiOpt/vcell-opt/pyproject.toml +++ b/pythonCopasiOpt/vcell-opt/pyproject.toml @@ -6,7 +6,7 @@ authors = ["Jim Schaff "] readme = "README.md" [tool.poetry.dependencies] -python = "^3.9" +python = "3.10.*" copasi-basico = "0.40" python-copasi = "4.37.264" jupyter = "^1.0.0" diff --git a/pythonVtk/pyproject.toml b/pythonVtk/pyproject.toml index 26ae66167c..b7c6522bec 100644 --- a/pythonVtk/pyproject.toml +++ b/pythonVtk/pyproject.toml @@ -6,7 +6,7 @@ authors = ["Jim Schaff "] readme = "README.md" [tool.poetry.dependencies] -python = "^3.9" +python = "3.10.*" vtk = "^9.2.6" thrift = "^0.16.0" From 2141d0097cf335f9a2f65c985766d48867bb11bc Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 15 Apr 2024 12:15:48 -0400 Subject: [PATCH 02/16] attempt to ensure correct python version is available --- .github/workflows/CI-full.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI-full.yml b/.github/workflows/CI-full.yml index ef37e52e37..46ba90a517 100644 --- a/.github/workflows/CI-full.yml +++ b/.github/workflows/CI-full.yml @@ -43,7 +43,8 @@ jobs: cache: "pip" - name: Install Dependencies - run: pip install -r requirements.txt + # We want to make sure the poetry installation is attached to the correct python version, or it may not find said version. + run: python${{ env.python-version }} -m pip install -r requirements.txt - name: build vcell-cli-utils package run: | From a12dfeacef53733ec486fc67e321439218a3e890 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 15 Apr 2024 12:55:49 -0400 Subject: [PATCH 03/16] Directly invoked poetry through python --- .github/workflows/CI-full.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/CI-full.yml b/.github/workflows/CI-full.yml index 46ba90a517..73796e5f74 100644 --- a/.github/workflows/CI-full.yml +++ b/.github/workflows/CI-full.yml @@ -49,38 +49,38 @@ jobs: - name: build vcell-cli-utils package run: | cd vcell-cli-utils - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build vcell-admin package run: | cd docker/swarm/vcell-admin - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build pythonCopasiOpt package run: | cd pythonCopasiOpt/vcell-opt - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build pythonVtk package run: | cd pythonVtk - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build vcutils package run: | cd python-utils - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build python-restclient package run: | cd python-restclient - poetry install - poetry run python -m pytest + python${{ env.python-version }} -m poetry install + python${{ env.python-version }} -m poetry run python -m pytest - name: build vcelldata package run: | From c5eb48379b8ba3a804e0cec0df908872c17528e8 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 15 Apr 2024 14:18:45 -0400 Subject: [PATCH 04/16] Updating docker files to python 3.10 --- docker/build/Dockerfile-api-dev | 4 ++-- docker/build/Dockerfile-data-dev | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker/build/Dockerfile-api-dev b/docker/build/Dockerfile-api-dev index 17b3f0240b..653cb5e82e 100644 --- a/docker/build/Dockerfile-api-dev +++ b/docker/build/Dockerfile-api-dev @@ -10,12 +10,12 @@ RUN $JAVA_HOME/bin/jlink \ --output /javaruntime # Define base image and copy in jlink created minimal Java 17 environment -FROM python:3.9.7-slim +FROM python:3.10.14-slim ENV JAVA_HOME=/opt/java/openjdk ENV PATH "${JAVA_HOME}/bin:${PATH}" COPY --from=jre-build /javaruntime $JAVA_HOME -# now we have Java 17 and Python 3.9 +# now we have Java 17 and Python 3.10 RUN apt-get -y update && \ apt-get install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu && \ diff --git a/docker/build/Dockerfile-data-dev b/docker/build/Dockerfile-data-dev index db5e6e64dd..a7b2b7d626 100644 --- a/docker/build/Dockerfile-data-dev +++ b/docker/build/Dockerfile-data-dev @@ -10,12 +10,12 @@ RUN $JAVA_HOME/bin/jlink \ --output /javaruntime # Define base image and copy in jlink created minimal Java 17 environment -FROM python:3.9.7-slim +FROM python:3.10.14-slim ENV JAVA_HOME=/opt/java/openjdk ENV PATH "${JAVA_HOME}/bin:${PATH}" COPY --from=jre-build /javaruntime $JAVA_HOME -# now we have Java 17 and Python 3.9 +# now we have Java 17 and Python 3.10 RUN apt-get -y update && \ apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \ From dc90384df40fa72d3be8a32f27c9a327cd497eb4 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 15 Apr 2024 15:07:56 -0400 Subject: [PATCH 05/16] more docker conversion --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index f91a45c016..28b4b08a16 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,7 @@ RUN $JAVA_HOME/bin/jlink \ # Define base image and copy in jlink created minimal Java 17 environment FROM ubuntu:jammy +FROM python:3.10.14-slim ENV JAVA_HOME=/opt/java/openjdk ENV PATH "${JAVA_HOME}/bin:${PATH}" COPY --from=jre-build /javaruntime $JAVA_HOME From 6cbb1c774638d69dde3f5e02084eac3968914dea Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Fri, 6 Sep 2024 10:29:55 -0400 Subject: [PATCH 06/16] Forgot copasi docker file --- pythonCopasiOpt/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pythonCopasiOpt/Dockerfile b/pythonCopasiOpt/Dockerfile index f88764e4f8..a33445540a 100644 --- a/pythonCopasiOpt/Dockerfile +++ b/pythonCopasiOpt/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.10-slim-buster +FROM python:3.10.9-slim-buster RUN apt -y update && apt -y upgrade && \ apt-get install -y curl From 067bb6e9a9f518eac4bebd8494aeac2f9417856f Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Tue, 16 Apr 2024 09:54:51 -0400 Subject: [PATCH 07/16] removed deadsnakes --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 28b4b08a16..f91a45c016 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,6 @@ RUN $JAVA_HOME/bin/jlink \ # Define base image and copy in jlink created minimal Java 17 environment FROM ubuntu:jammy -FROM python:3.10.14-slim ENV JAVA_HOME=/opt/java/openjdk ENV PATH "${JAVA_HOME}/bin:${PATH}" COPY --from=jre-build /javaruntime $JAVA_HOME From a1ce3ddc833d4d47a21b0a2db00367fbdb9a68ee Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Fri, 6 Sep 2024 10:57:21 -0400 Subject: [PATCH 08/16] keeping python3.10 consistent, and updating lockfiles --- docker/swarm/vcell-admin/poetry.lock | 570 +++-- python-restclient/poetry.lock | 1516 +++++------ python-restclient/pyproject.toml | 2 +- python-utils/poetry.lock | 489 ++-- python-utils/pyproject.toml | 2 +- pythonCopasiOpt/vcell-opt/poetry.lock | 2897 +++++++++++++--------- pythonCopasiOpt/vcell-opt/pyproject.toml | 2 +- pythonData/poetry.lock | 1921 +++++++------- pythonData/pyproject.toml | 2 +- pythonVtk/poetry.lock | 865 ++++--- pythonVtk/pyproject.toml | 2 +- vcell-cli-utils/poetry.lock | 2364 ++++++++++-------- 12 files changed, 5882 insertions(+), 4750 deletions(-) diff --git a/docker/swarm/vcell-admin/poetry.lock b/docker/swarm/vcell-admin/poetry.lock index 0d8627c8bd..f840c604d5 100644 --- a/docker/swarm/vcell-admin/poetry.lock +++ b/docker/swarm/vcell-admin/poetry.lock @@ -1,33 +1,39 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [[package]] name = "uritools" version = "4.0.3" @@ -2245,4 +2281,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "5c3cf867a3d98b1df9726c5f7a9797ce8c3eb2904f17e2edbc74e105bc0929d2" +content-hash = "7d4e4316e23b4bc0fb0a26b17babe88f9fbfc6f61f22f3b00ac33f043f277134" diff --git a/vcell-cli-utils/pyproject.toml b/vcell-cli-utils/pyproject.toml index e42cfaa006..a19e53226b 100644 --- a/vcell-cli-utils/pyproject.toml +++ b/vcell-cli-utils/pyproject.toml @@ -25,7 +25,7 @@ biosimulators_utils = "^0.1.180" python-libcombine = "0.2.19" fire = "^0.5.0" PyYAML = "^6.0" -pandas = "^1.5.3" +pandas = "^2.2.2" matplotlib = "^3.5.2" seaborn = "^0.12.2" python-libsbml-experimental = "^5.20.1" From 89fef4393c09eabd49ccb2a44d6aa2774cc8c128 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 9 Sep 2024 12:09:56 -0400 Subject: [PATCH 10/16] Cleanup of some logging / error messages --- .../org/vcell/cli/biosimulation/BiosimulationsCommand.java | 4 ++-- vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java b/vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java index 4a2095b35c..239c37ab09 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java +++ b/vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java @@ -106,14 +106,14 @@ public Integer call() { try { CLIPythonManager.getInstance().closePythonProcess(); // WARNING: Python will need reinstantiation after this is called } catch (Exception e) { - logger.error(e.getMessage(), e); + logger.error("Error closing python process:", e); } logger.debug("Finished all execution."); } } catch (Exception e) { if (!bQuiet) { Tracer.reportErrors(bDebug); - logger.error(e.getMessage(), e); + logger.error("Unexpected Error in BioSimulations execution:", e); } return 1; } diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java index 24d739be3a..ee3598b8c0 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java @@ -91,13 +91,13 @@ public void preprocessArchive() throws PythonStreamException, IOException { this.omexHandler.extractOmex(); this.sedmlLocations = omexHandler.getSedmlLocationsAbsolute(); } catch (IOException e){ - String error = e.getMessage() + ", error for OmexHandler with " + inputFilePath; + String error = "Error for OmexHandler with " + inputFilePath; this.cliRecorder.writeErrorList(bioModelBaseName); this.cliRecorder.writeDetailedResultList(bioModelBaseName + ", " + "IO error with OmexHandler"); logger.error(error); throw new RuntimeException(error, e); } catch (Exception e) { - String error = e.getMessage() + ", error for archive " + inputFilePath; + String error = "Error for archive " + inputFilePath; logger.error(error); if (omexHandler!=null) omexHandler.deleteExtractedOmex(); this.cliRecorder.writeErrorList(bioModelBaseName); From f6247006d12bbdcf893ea6ec19ea9251153255ab Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 9 Sep 2024 12:11:05 -0400 Subject: [PATCH 11/16] Fixed bug where we'd attempt to edit RDF of omexes we execute, not build --- .../java/org/vcell/cli/run/ExecutionJob.java | 2 +- .../main/java/org/vcell/cli/run/OmexHandler.java | 16 +++++++++++----- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java index ee3598b8c0..d07b319597 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java @@ -87,7 +87,7 @@ public void preprocessArchive() throws PythonStreamException, IOException { // Unpack the Omex Archive try { // It's unlikely, but if we get errors here they're fatal. this.sedmlPath2d3d = Paths.get(outputDir, "temp"); - this.omexHandler = new OmexHandler(inputFilePath, outputDir); + this.omexHandler = new OmexHandler(inputFilePath, outputDir, true); this.omexHandler.extractOmex(); this.sedmlLocations = omexHandler.getSedmlLocationsAbsolute(); } catch (IOException e){ diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java index 7b0857cc4d..19b636faf3 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java @@ -23,10 +23,10 @@ public class OmexHandler { CombineArchive archive; private final static Logger logger = LogManager.getLogger(OmexHandler.class); - + // Assuming omexPath will always be absolute path // NB: Need to convert class to use Log4j2 - public OmexHandler(String omexPath, String outDir) throws IOException { + public OmexHandler(String omexPath, String outDir, boolean readOnlyMode) throws IOException { this.omexPath = omexPath; this.outDirPath = outDir; @@ -41,7 +41,7 @@ public OmexHandler(String omexPath, String outDir) throws IOException { this.omexName = omexPath.substring(indexOfLastSlash + 1); this.tempPath = RunUtils.getTempDir(); try { - replaceMetadataRdfFiles(Paths.get(omexPath)); + if (!readOnlyMode) replaceMetadataRdfFiles(Paths.get(omexPath)); this.archive = new CombineArchive(new File(omexPath)); if (this.archive.hasErrors()){ String message = "Unable to initialise OMEX archive "+this.omexName+": "+this.archive.getErrors(); @@ -55,8 +55,12 @@ public OmexHandler(String omexPath, String outDir) throws IOException { } } - private void replaceMetadataRdfFiles(Path zipFilePath) throws IOException { - try( FileSystem fs = FileSystems.newFileSystem(zipFilePath) ) { + public OmexHandler(String omexPath, String outDir) throws IOException { + this(omexPath, outDir, false); + } + + private void replaceMetadataRdfFiles(Path zipFilePath) { + try (FileSystem fs = FileSystems.newFileSystem(zipFilePath)) { for (Path root : fs.getRootDirectories()) { Files.walk(root) .filter(Files::isRegularFile) @@ -82,6 +86,8 @@ private void replaceMetadataRdfFiles(Path zipFilePath) throws IOException { }); } + } catch (IOException | ReadOnlyFileSystemException e) { + throw new RuntimeException("Unable to delete metadata.rdf file from OMEX archive: ", e); } } From 6968b5da461e7e6c1b7de83ed69dab5ed24d2a75 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 9 Sep 2024 12:51:09 -0400 Subject: [PATCH 12/16] Attempting to delay RDF fixes unless needed --- .../java/org/vcell/cli/run/ExecutionJob.java | 2 +- .../java/org/vcell/cli/run/OmexHandler.java | 22 +++++++++++++------ 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java index d07b319597..ee3598b8c0 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java @@ -87,7 +87,7 @@ public void preprocessArchive() throws PythonStreamException, IOException { // Unpack the Omex Archive try { // It's unlikely, but if we get errors here they're fatal. this.sedmlPath2d3d = Paths.get(outputDir, "temp"); - this.omexHandler = new OmexHandler(inputFilePath, outputDir, true); + this.omexHandler = new OmexHandler(inputFilePath, outputDir); this.omexHandler.extractOmex(); this.sedmlLocations = omexHandler.getSedmlLocationsAbsolute(); } catch (IOException e){ diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java index 19b636faf3..577a9c1242 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java @@ -26,11 +26,12 @@ public class OmexHandler { // Assuming omexPath will always be absolute path // NB: Need to convert class to use Log4j2 - public OmexHandler(String omexPath, String outDir, boolean readOnlyMode) throws IOException { + public OmexHandler(String omexPath, String outDir) throws IOException { this.omexPath = omexPath; this.outDirPath = outDir; - if (!new File(omexPath).exists()) { + File omexFile = new File(omexPath); + if (!omexFile.exists()) { String[] omexNameArray = omexPath.split("/", -2); String omexName = omexNameArray[omexNameArray.length - 1]; IOException e = new IOException("Provided OMEX `" + omexName + "` is not present at path: " + omexPath); @@ -40,9 +41,16 @@ public OmexHandler(String omexPath, String outDir, boolean readOnlyMode) throws int indexOfLastSlash = omexPath.lastIndexOf("/"); this.omexName = omexPath.substring(indexOfLastSlash + 1); this.tempPath = RunUtils.getTempDir(); + try { - if (!readOnlyMode) replaceMetadataRdfFiles(Paths.get(omexPath)); - this.archive = new CombineArchive(new File(omexPath)); + try (CombineArchive initialArchive = new CombineArchive(omexFile)){ + // Archive may have RDF errors; we can try and clear them here. + if (!omexFile.canWrite() || !initialArchive.hasErrors() + || !initialArchive.getErrors().contains(".rdf")) return; + + this.replaceMetadataRdfFiles(Paths.get(omexPath)); + } + this.archive = new CombineArchive(omexFile); if (this.archive.hasErrors()){ String message = "Unable to initialise OMEX archive "+this.omexName+": "+this.archive.getErrors(); logger.error(message); @@ -55,9 +63,9 @@ public OmexHandler(String omexPath, String outDir, boolean readOnlyMode) throws } } - public OmexHandler(String omexPath, String outDir) throws IOException { - this(omexPath, outDir, false); - } +// public OmexHandler(String omexPath, String outDir) throws IOException { +// this(omexPath, outDir); +// } private void replaceMetadataRdfFiles(Path zipFilePath) { try (FileSystem fs = FileSystems.newFileSystem(zipFilePath)) { From ea388b4007aac85ae437b0796ea6fdd2d522e31f Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Mon, 9 Sep 2024 13:19:33 -0400 Subject: [PATCH 13/16] Added code to insert RDF is none exsits --- .../java/org/vcell/cli/run/OmexHandler.java | 46 ++++++++++++------- 1 file changed, 29 insertions(+), 17 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java index 577a9c1242..8109a3223f 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java @@ -14,6 +14,7 @@ import java.nio.file.*; import java.text.ParseException; import java.util.*; +import java.util.stream.Stream; public class OmexHandler { String tempPath; @@ -70,30 +71,41 @@ public OmexHandler(String omexPath, String outDir) throws IOException { private void replaceMetadataRdfFiles(Path zipFilePath) { try (FileSystem fs = FileSystems.newFileSystem(zipFilePath)) { for (Path root : fs.getRootDirectories()) { - Files.walk(root) + try (Stream rdfFiles = Files.walk(root) .filter(Files::isRegularFile) - .filter(path -> path.toString().endsWith(".rdf")) - .forEach(path -> { - try { - // write empty RDF file to temp file and replace the file inside the zip - Path tempFile = Files.createTempFile("temp", ".rdf"); - String new_rdf_content = + .filter(path -> path.toString().endsWith(".rdf"))){ + + if (rdfFiles.findAny().isEmpty()){ + Path targetPath = Paths.get(root.toString(), "metadata.rdf"); + Files.write(targetPath, "fileToBeReplaced".getBytes()); + } + } + + try (Stream rdfFiles = Files.walk(root) + .filter(Files::isRegularFile) + .filter(path -> path.toString().endsWith(".rdf"))){ + + rdfFiles.forEach(path -> { + try { + // write empty RDF file to temp file and replace the file inside the zip + Path tempFile = Files.createTempFile("temp", ".rdf"); + String new_rdf_content = """ """; - Files.write(tempFile, new_rdf_content.getBytes()); - // replace fileInsideZipPath with temp file - Files.delete(path); - Files.copy(tempFile, path); - Files.delete(tempFile); - } catch (IOException e) { - logger.error("Unable to delete metadata.rdf file from OMEX archive: " + e.getMessage(), e); - } - }); + Files.write(tempFile, new_rdf_content.getBytes()); + // replace fileInsideZipPath with temp file + Files.delete(path); + Files.copy(tempFile, path); + Files.delete(tempFile); + } catch (IOException e) { + logger.error("Unable to delete metadata.rdf file from OMEX archive: " + e.getMessage(), e); + } + }); + } } - } catch (IOException | ReadOnlyFileSystemException e) { throw new RuntimeException("Unable to delete metadata.rdf file from OMEX archive: ", e); } From 0a3102384064d9f6c059b4d38baad4e41407aa7e Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Tue, 10 Sep 2024 13:17:20 -0400 Subject: [PATCH 14/16] Fixed issue with RDF handling --- .../java/org/vcell/cli/run/OmexHandler.java | 41 +++++++++++-------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java index 8109a3223f..801f17db24 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java @@ -8,6 +8,7 @@ import org.jdom2.JDOMException; import org.vcell.cli.CLIUtils; +import javax.xml.transform.TransformerException; import java.io.File; import java.io.IOException; import java.net.URI; @@ -42,32 +43,38 @@ public OmexHandler(String omexPath, String outDir) throws IOException { int indexOfLastSlash = omexPath.lastIndexOf("/"); this.omexName = omexPath.substring(indexOfLastSlash + 1); this.tempPath = RunUtils.getTempDir(); - - try { - try (CombineArchive initialArchive = new CombineArchive(omexFile)){ - // Archive may have RDF errors; we can try and clear them here. - if (!omexFile.canWrite() || !initialArchive.hasErrors() - || !initialArchive.getErrors().contains(".rdf")) return; - + boolean initiallyEncounteredErrors = false; + try (CombineArchive initialArchive = new CombineArchive(omexFile, true)){ + // With the `continueOnError` flag set, an exception won't be thrown. + initiallyEncounteredErrors = initialArchive.hasErrors(); + // We want to try and repair any RDF issue the archive has, because we don't care that much about RDF validity. + // so, if (1) We have RDF errors; OR (2) have no rdf file, then we add / find & replace + if ((initiallyEncounteredErrors && omexFile.canWrite() && initialArchive.getErrors().contains(".rdf")) + || initialArchive.getEntries().stream().map(ArchiveEntry::getFileName).noneMatch(name->name.endsWith(".rdf"))) + this.replaceMetadataRdfFiles(Paths.get(omexPath)); // Replace the offending files + } catch (CombineArchiveException | JDOMException | ParseException e) { + // Alright, we got errors, AND an exception. Let's try a hail mary. + if (omexFile.canWrite() && e.getMessage().contains(".rdf")) this.replaceMetadataRdfFiles(Paths.get(omexPath)); - } + } + + try { // If we still have problems here, we're bombing out. this.archive = new CombineArchive(omexFile); - if (this.archive.hasErrors()){ - String message = "Unable to initialise OMEX archive "+this.omexName+": "+this.archive.getErrors(); - logger.error(message); - throw new IOException(message); + if (!this.archive.hasErrors()){ + if (initiallyEncounteredErrors) logger.info("Successfully Repaired `" + this.omexName + "`"); + return; } - }catch (CombineArchiveException | JDOMException | ParseException e) { + // We're unable to solve the remaining errors, so we're officially rejecting this archive. + String message = "Unable to initialise OMEX archive " + this.omexName + ": " + this.archive.getErrors(); + logger.error(message); + throw new IOException(message); + } catch (CombineArchiveException | JDOMException | ParseException e) { String message = String.format("Unable to initialise OMEX archive \"%s\", archive maybe corrupted", this.omexName); logger.error(message+": "+e.getMessage(), e); throw new IOException(e); } } -// public OmexHandler(String omexPath, String outDir) throws IOException { -// this(omexPath, outDir); -// } - private void replaceMetadataRdfFiles(Path zipFilePath) { try (FileSystem fs = FileSystems.newFileSystem(zipFilePath)) { for (Path root : fs.getRootDirectories()) { From 32b379ac1999498e8b426041bd26b788ed94d664 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Wed, 11 Sep 2024 08:05:46 -0400 Subject: [PATCH 15/16] "Fixed" uncaught exception issue (by just replacing the problematic file --- .../java/org/vcell/cli/run/OmexHandler.java | 5 +++-- vcell-cli/src/test/resources/BioModel1.omex | Bin 5874 -> 43388 bytes 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java index 801f17db24..34ed8a17ed 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java @@ -5,6 +5,7 @@ import de.unirostock.sems.cbarchive.CombineArchiveException; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; +import org.jdom2.IllegalNameException; import org.jdom2.JDOMException; import org.vcell.cli.CLIUtils; @@ -52,9 +53,9 @@ public OmexHandler(String omexPath, String outDir) throws IOException { if ((initiallyEncounteredErrors && omexFile.canWrite() && initialArchive.getErrors().contains(".rdf")) || initialArchive.getEntries().stream().map(ArchiveEntry::getFileName).noneMatch(name->name.endsWith(".rdf"))) this.replaceMetadataRdfFiles(Paths.get(omexPath)); // Replace the offending files - } catch (CombineArchiveException | JDOMException | ParseException e) { + } catch (CombineArchiveException | JDOMException | IllegalNameException | ParseException e) { // Alright, we got errors, AND an exception. Let's try a hail mary. - if (omexFile.canWrite() && e.getMessage().contains(".rdf")) + if (omexFile.canWrite()) this.replaceMetadataRdfFiles(Paths.get(omexPath)); } diff --git a/vcell-cli/src/test/resources/BioModel1.omex b/vcell-cli/src/test/resources/BioModel1.omex index 338d5a6375758795496464dd5e62e322a0acdc75..4debe9da46e5e133c3497440f47e5972ac924654 100755 GIT binary patch literal 43388 zcmZ^}18*)2)UH|E+_i1nwr$(C?LIYk-R|19ZQHhe-kHovPQIC0$@&X-t{aLnpkQb~ zP*6}nL;^HgK>x>~03idZnz^_NTRF%%n3~zryO^2U*{Z3+13|`z?VJDa@77dOIb=uj z@6G%~{P&r7IYlNdd)06)9Ui=Z+Nbfzo6p;NGRcyf!&~Jpc5lDeiwp4<1g!G<0f!Q$gLN)0Dmh!0a;R#rB%m^6Qpn}d63^JeLvN4i6U#Z~8|=zGx%7f3Ng{lsaQ$)=B*kiyQ%FHP zpCisn6b)hd5$x~C9;O@qWl|IMk?Vh2zG$!GHdEY@8K;%u3_BRPFM`c9ro?GP#1|4P z6|KqWng-h~DVZ;dZx}5pIhjBAfEtq#FQ|jXt)~Z1tmgD@B%0J(?1K!Zs>&i%30vOE znWYmQZb2>7c27)LNvkWEum)YFnO6SpF$Ba|L83<*TEe8Ch~UgYFdm|ut(3^dAe_m9 zU*$}=sPs(Vk?@}%tYjwQ`1hq*R^1*+N0AE@tB}DyykDE)Y@#(hP8@n%fR&prE`!qn 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z!v4N;Q2-TzLi=9CS1wk^EmlQ$CWIezV^p!u;q6~+d98U0BPU|DxyfF5uo3ur!Hf1G z=S1@_ZT;j@E)x$O-N@$5aj>^Q;sTiZzy&qism?!_+t&;t;f=KzkJgVTKfr=R?K4-2 z4n}{V^oMnVtlr8f4DzG~;9;rEN`!P~JfD&|Tk8TsuR6va|L9>GEm-{yf7{0Cw}t*= zA5#ZgD@#|mzbEzLL{a;1Tm%yDk=V}m)ya@zT|CZuFn6)5T9GULcd{v_W@LwpxlNb^ z%!9=HEL+h1Xj0gt-vIKAP}>*lS#WHBSa3+wiv1nnsNQY^nuz_ zd#-qDi2HduzNBnt6N;Dor=uEe&6&4KVY3t1`&9ix)M#3%EuJlmfl<~}0+V^*i=cjC z6RA<7$@T{9CZZE9x>3THxdgovGuNfb%MiUE7qn={UoL}Pc69vwX9Y43l2>#fceO+` zF Date: Wed, 11 Sep 2024 11:43:53 -0400 Subject: [PATCH 16/16] Attempting to use temp files to allow for write-ability --- .../java/org/vcell/cli/run/ExecuteImpl.java | 22 +++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java index f1556bee3e..05eaa87d8c 100644 --- a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java +++ b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java @@ -14,8 +14,7 @@ import java.io.File; import java.io.FilenameFilter; import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Paths; +import java.nio.file.*; import java.util.HashMap; import java.util.LinkedList; import java.util.List; @@ -137,9 +136,24 @@ public static void singleMode(File inputFile, File rootOutputDir, CLIRecordable if (!inputFile.getParentFile().getCanonicalPath().contains(adjustedOutputDir.getCanonicalPath())) RunUtils.removeAndMakeDirs(adjustedOutputDir); - PythonCalls.generateStatusYaml(inputFile.getAbsolutePath(), targetOutputDir); // generate Status YAML + File targetInputFile; - ExecuteImpl.singleExecOmex(inputFile, rootOutputDir, cliLogger, bKeepTempFiles, bExactMatchOnly, + if(inputFile.canWrite()){ + targetInputFile = inputFile; + } else { + String namePrefix = inputFile.getName().substring(0, inputFile.getName().lastIndexOf('.')); + Path tempFile = Files.createTempFile(namePrefix, ".omex"); + File writableCopy = Files.copy(inputFile.toPath(), tempFile, StandardCopyOption.REPLACE_EXISTING).toFile(); + if (!writableCopy.canWrite() + && !writableCopy.setWritable(true) // Main Attempt + && !writableCopy.setWritable(true, true)) // Backup Attempt + throw new RuntimeException("Unable to create writable file"); + targetInputFile = writableCopy; + } + + PythonCalls.generateStatusYaml(targetInputFile.getAbsolutePath(), targetOutputDir); // generate Status YAML + + ExecuteImpl.singleExecOmex(targetInputFile, rootOutputDir, cliLogger, bKeepTempFiles, bExactMatchOnly, bEncapsulateOutput, bSmallMeshOverride, bBioSimMode); }