From 2fe830a1d8d01a74c6a925cfe42ed46750c8fdc0 Mon Sep 17 00:00:00 2001 From: Rutuja Rane Date: Mon, 5 Oct 2020 17:58:37 -0700 Subject: [PATCH 1/6] #459 fixed: Karma 2.3+ upload source file fails with NullPointerException on macOS 10.14.6 --- .../commands-alignment-openrdf/.factorypath | 121 ------ .../commands-alignment/.factorypath | 94 ----- karma-commands/commands-bloom/.factorypath | 158 ------- karma-commands/commands-common/.factorypath | 78 ---- .../commands-import/import-avro/.factorypath | 78 ---- .../import-common/.factorypath | 78 ---- .../commands-import/import-csv/.factorypath | 78 ---- .../import-database/.factorypath | 82 ---- .../commands-import/import-excel/.factorypath | 78 ---- .../commands-import/import-file/.factorypath | 78 ---- .../commands-import/import-json/.factorypath | 94 ----- .../import-ontology/.factorypath | 78 ---- .../import-service/.factorypath | 78 ---- .../import-spatial/.factorypath | 102 ----- .../commands-import/import-xml/.factorypath | 78 ---- .../.factorypath | 121 ------ .../commands-publish-jdbc/.factorypath | 82 ---- karma-commands/commands-publish/.factorypath | 79 ---- karma-commands/commands-python/.factorypath | 94 ----- .../commands-update-jdbc/.factorypath | 81 ---- karma-commands/commands-update/.factorypath | 78 ---- .../commands-worksheet/.factorypath | 94 ----- karma-common/.factorypath | 78 ---- .../java/edu/isi/karma/util/FileUtil.java | 19 +- karma-jdbc/.factorypath | 81 ---- karma-mr/.factorypath | 311 -------------- karma-offline/.factorypath | 175 -------- karma-spark/.factorypath | 388 ------------------ karma-typer/.factorypath | 26 -- karma-util/.factorypath | 18 - .../web-services-publish-es/.factorypath | 208 ---------- .../web-services-rdf/.factorypath | 192 --------- karma-web/.factorypath | 152 ------- 33 files changed, 12 insertions(+), 3618 deletions(-) delete mode 100644 karma-commands/commands-alignment-openrdf/.factorypath delete mode 100644 karma-commands/commands-alignment/.factorypath delete mode 100644 karma-commands/commands-bloom/.factorypath delete mode 100644 karma-commands/commands-common/.factorypath delete mode 100644 karma-commands/commands-import/import-avro/.factorypath delete mode 100644 karma-commands/commands-import/import-common/.factorypath delete mode 100644 karma-commands/commands-import/import-csv/.factorypath delete mode 100644 karma-commands/commands-import/import-database/.factorypath delete mode 100644 karma-commands/commands-import/import-excel/.factorypath delete mode 100644 karma-commands/commands-import/import-file/.factorypath delete mode 100644 karma-commands/commands-import/import-json/.factorypath delete mode 100644 karma-commands/commands-import/import-ontology/.factorypath delete mode 100644 karma-commands/commands-import/import-service/.factorypath delete mode 100644 karma-commands/commands-import/import-spatial/.factorypath delete mode 100644 karma-commands/commands-import/import-xml/.factorypath delete mode 100644 karma-commands/commands-publish-alignment-openrdf/.factorypath delete mode 100644 karma-commands/commands-publish-jdbc/.factorypath delete mode 100644 karma-commands/commands-publish/.factorypath delete mode 100644 karma-commands/commands-python/.factorypath delete mode 100644 karma-commands/commands-update-jdbc/.factorypath delete mode 100644 karma-commands/commands-update/.factorypath delete mode 100644 karma-commands/commands-worksheet/.factorypath delete mode 100644 karma-common/.factorypath delete mode 100644 karma-jdbc/.factorypath delete mode 100644 karma-mr/.factorypath delete mode 100644 karma-offline/.factorypath delete mode 100644 karma-spark/.factorypath delete mode 100644 karma-typer/.factorypath delete mode 100644 karma-util/.factorypath delete mode 100644 karma-web-services/web-services-publish-es/.factorypath delete mode 100644 karma-web-services/web-services-rdf/.factorypath delete mode 100644 karma-web/.factorypath diff --git a/karma-commands/commands-alignment-openrdf/.factorypath b/karma-commands/commands-alignment-openrdf/.factorypath deleted file mode 100644 index 262a26f93..000000000 --- a/karma-commands/commands-alignment-openrdf/.factorypath +++ /dev/null @@ -1,121 +0,0 @@ - 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Write file to the ultimate location. uploadedFile = new File(destinationDir, item.getName()); - if (item instanceof DiskFileItem) { - DiskFileItem t = (DiskFileItem)item; - if (!t.getStoreLocation().renameTo(uploadedFile)) - item.write(uploadedFile); + // if (item instanceof DiskFileItem) { + DiskFileItem t = (DiskFileItem)item; + if (t.getStoreLocation()!=null) { + logger.info("File is on disk"); + if (!t.getStoreLocation().renameTo(uploadedFile)){ + item.write(uploadedFile); + } + } + else{ + logger.info("File is in memory"); + item.write(uploadedFile); } - else - item.write(uploadedFile); } } } catch (FileUploadException ex) { diff --git a/karma-jdbc/.factorypath b/karma-jdbc/.factorypath deleted file mode 100644 index 312088b69..000000000 --- a/karma-jdbc/.factorypath +++ /dev/null @@ -1,81 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/karma-mr/.factorypath b/karma-mr/.factorypath deleted file mode 100644 index 467e68086..000000000 --- a/karma-mr/.factorypath +++ /dev/null @@ -1,311 +0,0 @@ - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From dcf57ab74336acd422016d7e937aa878f699ddc1 Mon Sep 17 00:00:00 2001 From: Rutuja Rane Date: Mon, 5 Oct 2020 18:03:53 -0700 Subject: [PATCH 2/6] Edit to logger debug --- .../src/main/java/edu/isi/karma/util/FileUtil.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/karma-common/src/main/java/edu/isi/karma/util/FileUtil.java b/karma-common/src/main/java/edu/isi/karma/util/FileUtil.java index d2fac2772..da3205052 100644 --- a/karma-common/src/main/java/edu/isi/karma/util/FileUtil.java +++ b/karma-common/src/main/java/edu/isi/karma/util/FileUtil.java @@ -60,6 +60,7 @@ static public File downloadFileFromHTTPRequest(HttpServletRequest request, Strin // Download the file to the upload file folder File destinationDir = new File(destinationDirString); + logger.debug("File upload destination directory: " + destinationDir.getAbsolutePath()); DiskFileItemFactory fileItemFactory = new DiskFileItemFactory(); @@ -84,20 +85,20 @@ static public File downloadFileFromHTTPRequest(HttpServletRequest request, Strin // Ignore Form Fields. if (item.isFormField()) { // Do nothing - logger.info("Form Field"); + logger.debug("Form Field"); } else { //Handle Uploaded files. Write file to the ultimate location. uploadedFile = new File(destinationDir, item.getName()); // if (item instanceof DiskFileItem) { DiskFileItem t = (DiskFileItem)item; if (t.getStoreLocation()!=null) { - logger.info("File is on disk"); + logger.debug("File is on disk"); if (!t.getStoreLocation().renameTo(uploadedFile)){ item.write(uploadedFile); } } else{ - logger.info("File is in memory"); + logger.debug("File is in memory"); item.write(uploadedFile); } } From 75ff1e026fdd0f40db54ac4759b9e4bff2a526ef Mon Sep 17 00:00:00 2001 From: Rutuja Rane Date: Thu, 8 Oct 2020 13:23:02 -0700 Subject: [PATCH 3/6] Security alerts fixed: #463 Bump electron from 9.2.1 to 10.1.3 in /karma-app/desktop --- karma-app/desktop/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/karma-app/desktop/package.json b/karma-app/desktop/package.json index 7df734db9..60429e590 100644 --- a/karma-app/desktop/package.json +++ b/karma-app/desktop/package.json @@ -30,7 +30,7 @@ }, "devDependencies": { "chai": "^3.5.0", - "electron": "9.2.1", + "electron": "10.1.3", "electron-builder": "^5.12.1", "electron-mocha": "^3.0.0", "fs-jetpack": "^0.9.0", From 7c8a192cb7cf70c21dc0835e2a0b344fdba344b9 Mon Sep 17 00:00:00 2001 From: Rutuja Rane Date: Mon, 19 Oct 2020 11:26:24 -0700 Subject: [PATCH 4/6] #465 #466 #464 Bump junit from 4.12 to 4.13.1 fixed in development branch --- karma-jsonld/pom.xml | 2 +- karma-spark/pom.xml | 2 +- pom.xml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/karma-jsonld/pom.xml b/karma-jsonld/pom.xml index 248b8ed7a..fbf0dd532 100644 --- a/karma-jsonld/pom.xml +++ b/karma-jsonld/pom.xml @@ -12,7 +12,7 @@ UTF-8 2.10.3 - 4.12 + 4.13.1 1.7.9 diff --git a/karma-spark/pom.xml b/karma-spark/pom.xml index fce0bc8f2..ccd556814 100644 --- a/karma-spark/pom.xml +++ b/karma-spark/pom.xml @@ -10,7 +10,7 @@ UTF-8 UTF-8 - 4.12 + 4.13.1 1.7.9 true diff --git a/pom.xml b/pom.xml index b18a6e4a4..ca2a47ae3 100644 --- a/pom.xml +++ b/pom.xml @@ -63,7 +63,7 @@ 2.13.3 1.6.0 - 4.11 + 4.13.1 3.4 1.1.2 From 40fdb029a079c420105245b7642d49269ef3d3ea Mon Sep 17 00:00:00 2001 From: saggu Date: Fri, 12 Feb 2021 12:44:18 -0800 Subject: [PATCH 5/6] add docker file --- Dockerfile | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..97e001dbf --- /dev/null +++ b/Dockerfile @@ -0,0 +1,16 @@ +FROM openjdk:8-jdk-alpine +RUN apk add --no-cache curl tar git + +WORKDIR /karma + +RUN wget https://mirrors.sonic.net/apache/maven/maven-3/3.6.3/binaries/apache-maven-3.6.3-bin.tar.gz + +RUN tar xzvf apache-maven-3.6.3-bin.tar.gz + +RUN mkdir /karma/Web-Karma + +RUN git clone https://github.com/usc-isi-i2/Web-Karma /karma/Web-Karma + +RUN cd /karma/Web-Karma && /karma/apache-maven-3.6.3/bin/mvn clean install + +CMD cd /karma/Web-Karma/karma-web && /karma/apache-maven-3.6.3/bin/mvn jetty:run \ No newline at end of file From 8062a5c45449a1affb08e4f92bebe9de5d859745 Mon Sep 17 00:00:00 2001 From: Bidisha010496 Date: Mon, 13 Sep 2021 00:17:54 -0700 Subject: [PATCH 6/6] security updates and build fixes --- karma-app/desktop/package.json | 2 +- karma-commands/commands-common/pom.xml | 2 +- karma-commands/commands-worksheet/pom.xml | 10 +++++----- karma-common/pom.xml | 2 +- karma-jsonld/pom.xml | 6 +++--- karma-web-services/web-services-publish-es/pom.xml | 4 ++-- pom.xml | 12 ++++++------ 7 files changed, 19 insertions(+), 19 deletions(-) diff --git a/karma-app/desktop/package.json b/karma-app/desktop/package.json index 60429e590..d421d535c 100644 --- a/karma-app/desktop/package.json +++ b/karma-app/desktop/package.json @@ -30,7 +30,7 @@ }, "devDependencies": { "chai": "^3.5.0", - "electron": "10.1.3", + "electron": "10.2.0", "electron-builder": "^5.12.1", "electron-mocha": "^3.0.0", "fs-jetpack": "^0.9.0", diff --git a/karma-commands/commands-common/pom.xml b/karma-commands/commands-common/pom.xml index 8b402da9a..fc1570364 100644 --- a/karma-commands/commands-common/pom.xml +++ b/karma-commands/commands-common/pom.xml @@ -22,7 +22,7 @@ org.apache.httpcomponents httpclient - 4.5.2 + 4.5.13 diff --git a/karma-commands/commands-worksheet/pom.xml b/karma-commands/commands-worksheet/pom.xml index 1389f943b..460dee052 100644 --- a/karma-commands/commands-worksheet/pom.xml +++ b/karma-commands/commands-worksheet/pom.xml @@ -37,10 +37,10 @@ karma-common ${project.version} - - edu.isi.karma.services - entityExtraction - 0.0.1 - + + + + + \ No newline at end of file diff --git a/karma-common/pom.xml b/karma-common/pom.xml index 06fa4aeee..b197073cf 100644 --- a/karma-common/pom.xml +++ b/karma-common/pom.xml @@ -131,7 +131,7 @@ org.apache.httpcomponents httpclient - 4.5.2 + 4.5.13 diff --git a/karma-jsonld/pom.xml b/karma-jsonld/pom.xml index fbf0dd532..cd11c69da 100644 --- a/karma-jsonld/pom.xml +++ b/karma-jsonld/pom.xml @@ -11,7 +11,7 @@ UTF-8 UTF-8 - 2.10.3 + 2.12.1 4.13.1 1.7.9 @@ -29,7 +29,7 @@ commons-io commons-io - 2.4 + 2.7 org.apache.spark @@ -109,7 +109,7 @@ commons-io commons-io - 2.4 + 2.7 diff --git a/karma-web-services/web-services-publish-es/pom.xml b/karma-web-services/web-services-publish-es/pom.xml index 9d74ec644..47e106436 100644 --- a/karma-web-services/web-services-publish-es/pom.xml +++ b/karma-web-services/web-services-publish-es/pom.xml @@ -14,7 +14,7 @@ UTF-8 - 1.3.2 + 6.8.17 @@ -74,7 +74,7 @@ org.apache.httpcomponents httpclient - 4.5.2 + 4.5.13 diff --git a/pom.xml b/pom.xml index ca2a47ae3..8029866ae 100644 --- a/pom.xml +++ b/pom.xml @@ -15,17 +15,17 @@ karma-jdbc karma-util karma-commands - karma-mr + karma-web-services karma-typer karma-jsonld - karma-spark + true - 9.4.27.v20200227 + 9.4.41.v20210516 UTF-8 @@ -50,7 +50,7 @@ 2.4 - 2.4 + 2.7 1.5 1.8 @@ -69,7 +69,7 @@ 1.1.2 2.2.2 - 4.5.2 + 4.5.13 29.0-jre 5.2.4.RELEASE @@ -295,7 +295,7 @@ org.apache.poi poi - 3.8-beta5 + 3.17 org.apache.poi