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merge from master, and before version change
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alx652 committed Oct 22, 2024
2 parents 0b538b5 + 1745aca commit 3c3ddda
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93 changes: 93 additions & 0 deletions .github/workflows/codeql.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,93 @@
# For most projects, this workflow file will not need changing; you simply need
# to commit it to your repository.
#
# You may wish to alter this file to override the set of languages analyzed,
# or to provide custom queries or build logic.
#
# ******** NOTE ********
# We have attempted to detect the languages in your repository. Please check
# the `language` matrix defined below to confirm you have the correct set of
# supported CodeQL languages.
#
name: "CodeQL"

on:
push:
branches: [ "master" ]
pull_request:
branches: [ "master" ]
schedule:
- cron: '38 1 * * 2'

jobs:
analyze:
name: Analyze (${{ matrix.language }})
# Runner size impacts CodeQL analysis time. To learn more, please see:
# - https://gh.io/recommended-hardware-resources-for-running-codeql
# - https://gh.io/supported-runners-and-hardware-resources
# - https://gh.io/using-larger-runners (GitHub.com only)
# Consider using larger runners or machines with greater resources for possible analysis time improvements.
runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
permissions:
# required for all workflows
security-events: write

# required to fetch internal or private CodeQL packs
packages: read

# only required for workflows in private repositories
actions: read
contents: read

strategy:
fail-fast: false
matrix:
include:
- language: java-kotlin
build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
# CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
# Use `c-cpp` to analyze code written in C, C++ or both
# Use 'java-kotlin' to analyze code written in Java, Kotlin or both
# Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
# To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
# see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
steps:
- name: Checkout repository
uses: actions/checkout@v4

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
build-mode: ${{ matrix.build-mode }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.

# For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
# queries: security-extended,security-and-quality

# If the analyze step fails for one of the languages you are analyzing with
# "We were unable to automatically build your code", modify the matrix above
# to set the build mode to "manual" for that language. Then modify this step
# to build your code.
# ℹ️ Command-line programs to run using the OS shell.
# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
- if: matrix.build-mode == 'manual'
shell: bash
run: |
echo 'If you are using a "manual" build mode for one or more of the' \
'languages you are analyzing, replace this with the commands to build' \
'your code, for example:'
echo ' make bootstrap'
echo ' make release'
exit 1
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v3
with:
category: "/language:${{matrix.language}}"
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8 changes: 5 additions & 3 deletions gsrs-fda-substance-extension/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>gsrs-module-substances</artifactId>
<groupId>gov.nih.ncats</groupId>
<version>3.1.1-SNAPSHOT</version>
<version>3.1.1.1</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand Down Expand Up @@ -110,7 +110,7 @@
<dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>applications-api</artifactId>
<version>3.1-SNAPSHOT</version>
<version>3.1.1-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
Expand Down Expand Up @@ -193,7 +193,7 @@
</exclusions>
</dependency>
</dependencies>
<!-- Uncomment this for maven public release deployment
<!-- Uncomment this for maven public release deployment start
<build>
<plugins>
<plugin>
Expand All @@ -216,6 +216,7 @@
<additionalparam>-Xdoclint:none</additionalparam>
<additionalOptions>-Xdoclint:none</additionalOptions>
<additionalJOption>-Xdoclint:none</additionalJOption>
<release>11</release>
</configuration>
<executions>
<execution>
Expand All @@ -228,4 +229,5 @@
</plugin>
</plugins>
</build> -->
<!-- Uncomment this for maven public release deployment end -->
</project>
Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,10 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
if(!allCurrentBdNums.contains(bd)){
if(! ("SUPERSEDED".equalsIgnoreCase(bdnumType) || "SUPERCEDED".equalsIgnoreCase(bdnumType))){
//1. If the BDNUM literal that existed in the old record (e.g. XXXXXX) no longer exists in the current record, throw an error unless that BDNUM was marked as type "superseded".
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE(bdnumType + " BDNUM " + bd + " has been removed, but only SUPERSEDED BDNUM codes may be removed"));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("%s BDNUM %s has been removed, but only SUPERSEDED BDNUM codes may be removed", bdnumType, bd));

}else {
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE(bdnumType + " BDNUM " + bd + " has been removed"));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("%s BDNUM %s has been removed", bdnumType, bd));
}
}
}
Expand All @@ -75,7 +75,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
//or if it has been removed (in which case we alrady added an error above for that)
if(primaries !=null && primaries.size() > 1){
//2. If there are 2 or more BDNUMs where both are type "PRIMARY", throw an error.
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("can not have more than 1 PRIMARY BDNUM but have : " + primaries));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Cannot have more than 1 PRIMARY BDNUM but have : %s", primaries));
}

}
Expand Down
20 changes: 8 additions & 12 deletions gsrs-module-substance-example/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>gsrs-module-substances</artifactId>
<groupId>gov.nih.ncats</groupId>
<version>3.1.1-SNAPSHOT</version>
<version>3.1.1.1</version>
</parent>
<modelVersion>4.0.0</modelVersion>

Expand All @@ -31,11 +31,11 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>8</source>
<target>8</target>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
<!-- Uncomment this for maven public release deployment
<!-- Uncomment this for maven public release deployment start
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
Expand All @@ -56,6 +56,7 @@
<additionalparam>-Xdoclint:none</additionalparam>
<additionalOptions>-Xdoclint:none</additionalOptions>
<additionalJOption>-Xdoclint:none</additionalJOption>
<release>11</release>
</configuration>
<executions>
<execution>
Expand All @@ -66,6 +67,7 @@
</execution>
</executions>
</plugin> -->
<!-- Uncomment this for maven public release deployment end -->
</plugins>
<!--
<plugins><plugin>
Expand Down Expand Up @@ -252,7 +254,7 @@
<dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch-cdk</artifactId>
<version>1.0.18</version>
<version>1.0.21</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
Expand Down Expand Up @@ -333,12 +335,6 @@
<version>0.4.0</version>
<type>pom</type>
</dependency>
<!--dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>gsrs-core</artifactId>
<version>3.1.1-SNAPSHOT</version>
<scope>test</scope>
</dependency-->

<dependency>
<groupId>commons-io</groupId>
Expand All @@ -348,7 +344,7 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.21</version>
<version>1.26.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
Expand Down
84 changes: 84 additions & 0 deletions gsrs-module-substance-example/salt_data_public.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
InChI Key SMILES Occurrences
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FKNQFGJONOIPTF-UHFFFAOYSA-N [Na+] 3488
XLYOFNOQVPJJNP-UHFFFAOYSA-N O 1608
NPYPAHLBTDXSSS-UHFFFAOYSA-N [K+] 811
XLYOFNOQVPJJNP-UHFFFAOYSA-M [OH-] 791
CPELXLSAUQHCOX-UHFFFAOYSA-N Br 645
BHPQYMZQTOCNFJ-UHFFFAOYSA-N [Ca+2] 526
QAOWNCQODCNURD-UHFFFAOYSA-N OS(=O)(=O)O 510
AFVFQIVMOAPDHO-UHFFFAOYSA-N CS(=O)(=O)O 350
XMBWDFGMSWQBCA-UHFFFAOYSA-N I 326
JLVVSXFLKOJNIY-UHFFFAOYSA-N [Mg+2] 316
QGZKDVFQNNGYKY-UHFFFAOYSA-N N 300
QTBSBXVTEAMEQO-UHFFFAOYSA-N CC(=O)O 280
GPRLSGONYQIRFK-UHFFFAOYSA-N [H+] 277
REDXJYDRNCIFBQ-UHFFFAOYSA-N [Al+3] 270
VZCYOOQTPOCHFL-UPHRSURJSA-N OC(=O)/C=C\C(O)=O 259
PTFCDOFLOPIGGS-UHFFFAOYSA-N [Zn+2] 241
VEXZGXHMUGYJMC-UHFFFAOYSA-M [Cl-] 240
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KRKNYBCHXYNGOX-UHFFFAOYSA-N C(C(=O)O)C(CC(=O)O)(C(=O)O)O 162
VTLYFUHAOXGGBS-UHFFFAOYSA-N [Fe+3] 139
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JZMJDSHXVKJFKW-UHFFFAOYSA-M COS(=O)(=O)[O-] 126
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RVPVRDXYQKGNMQ-UHFFFAOYSA-N [Pb+2] 59
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WPYMKLBDIGXBTP-UHFFFAOYSA-N c1ccc(cc1)C(=O)O 45
WLZRMCYVCSSEQC-UHFFFAOYSA-N [Cd+2] 43
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NBIIXXVUZAFLBC-UHFFFAOYSA-K O=P([O-])([O-])[O-] 39
MUBZPKHOEPUJKR-UHFFFAOYSA-L C(=O)(C(=O)[O-])[O-] 39
GLUUGHFHXGJENI-UHFFFAOYSA-N C1CNCCN1 39
VEQPNABPJHWNSG-UHFFFAOYSA-N [Ni+2] 38
RJOJUSXNYCILHH-UHFFFAOYSA-N [Gd+3] 38
RWSOTUBLDIXVET-UHFFFAOYSA-M [SH-] 37
DTQVDTLACAAQTR-UHFFFAOYSA-N C(=O)(C(F)(F)F)O 37
JOXIMZWYDAKGHI-UHFFFAOYSA-M Cc1ccc(cc1)S(=O)(=O)[O-] 35
XQTIWNLDFPPCIU-UHFFFAOYSA-N [Ce+3] 34
CRBHXDCYXIISFC-UHFFFAOYSA-N C[N+](C)(C)CC[O-] 33
KIWBPDUYBMNFTB-UHFFFAOYSA-M CCOS(=O)(=O)[O-] 33
JAWGVVJVYSANRY-UHFFFAOYSA-N [Co+3] 32
ZMZDMBWJUHKJPS-UHFFFAOYSA-N C(#N)S 32
RGHNJXZEOKUKBD-SQOUGZDYSA-N C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O 31
CKLJMWTZIZZHCS-REOHCLBHSA-L C([C@@H](C(=O)[O-])N)C(=O)[O-] 31
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
InChI Key SMILES Occurrences
VEXZGXHMUGYJMC-UHFFFAOYSA-N Cl 7206
FKNQFGJONOIPTF-UHFFFAOYSA-N [Na+] 3488
XLYOFNOQVPJJNP-UHFFFAOYSA-N O 1608
NPYPAHLBTDXSSS-UHFFFAOYSA-N [K+] 811
XLYOFNOQVPJJNP-UHFFFAOYSA-M [OH-] 791
CPELXLSAUQHCOX-UHFFFAOYSA-N Br 645
BHPQYMZQTOCNFJ-UHFFFAOYSA-N [Ca+2] 526
QAOWNCQODCNURD-UHFFFAOYSA-N OS(=O)(=O)O 510
AFVFQIVMOAPDHO-UHFFFAOYSA-N CS(=O)(=O)O 350
XMBWDFGMSWQBCA-UHFFFAOYSA-N I 326
JLVVSXFLKOJNIY-UHFFFAOYSA-N [Mg+2] 316
QGZKDVFQNNGYKY-UHFFFAOYSA-N N 300
QTBSBXVTEAMEQO-UHFFFAOYSA-N CC(=O)O 280
GPRLSGONYQIRFK-UHFFFAOYSA-N [H+] 277
REDXJYDRNCIFBQ-UHFFFAOYSA-N [Al+3] 270
VZCYOOQTPOCHFL-UPHRSURJSA-N OC(=O)/C=C\C(O)=O 259
PTFCDOFLOPIGGS-UHFFFAOYSA-N [Zn+2] 241
VEXZGXHMUGYJMC-UHFFFAOYSA-M [Cl-] 240
FEWJPZIEWOKRBE-JCYAYHJZSA-N [C@@H]([C@H](C(=O)O)O)(C(=O)O)O 214
NBIIXXVUZAFLBC-UHFFFAOYSA-N OP(=O)(O)O 212
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VZCYOOQTPOCHFL-OWOJBTEDSA-N OC(=O)/C=C/C(O)=O 164
KRKNYBCHXYNGOX-UHFFFAOYSA-N C(C(=O)O)C(CC(=O)O)(C(=O)O)O 162
VTLYFUHAOXGGBS-UHFFFAOYSA-N [Fe+3] 139
HBBGRARXTFLTSG-UHFFFAOYSA-N [Li+] 139
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GSEJCLTVZPLZKY-UHFFFAOYSA-N C(CO)N(CCO)CCO 80
GRYLNZFGIOXLOG-UHFFFAOYSA-N [N+](=O)(O)[O-] 77
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LELOWRISYMNNSU-UHFFFAOYSA-N C#N 70
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QGZKDVFQNNGYKY-UHFFFAOYSA-O [NH4+] 65
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FOIXSVOLVBLSDH-UHFFFAOYSA-N [Ag+] 63
CPELXLSAUQHCOX-UHFFFAOYSA-M [Br-] 63
KRKNYBCHXYNGOX-UHFFFAOYSA-K C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O 62
JDIBGQFKXXXXPN-UHFFFAOYSA-N [Bi+3] 61
KDXKERNSBIXSRK-YFKPBYRVSA-N C(CCN)C[C@@H](C(=O)O)N 59
BFGKITSFLPAWGI-UHFFFAOYSA-N [Cr+3] 59
RVPVRDXYQKGNMQ-UHFFFAOYSA-N [Pb+2] 59
HRGDZIGMBDGFTC-UHFFFAOYSA-N [Pt+2] 59
PWYYWQHXAPXYMF-UHFFFAOYSA-N [Sr+2] 58
HZAXFHJVJLSVMW-UHFFFAOYSA-N C(CO)N 57
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BQPIGGFYSBELGY-UHFFFAOYSA-N [Hg+2] 39
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GLUUGHFHXGJENI-UHFFFAOYSA-N C1CNCCN1 39
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RJOJUSXNYCILHH-UHFFFAOYSA-N [Gd+3] 38
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