From e048df7e23a5afd1e0941b7e20af6482c7efdb18 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Tue, 4 Aug 2020 13:21:05 -0700
Subject: [PATCH 1/2] switching to use new USI identifiers

---
 metabolomics-snets-v2/Makefile                     |  2 +-
 .../metabolomics-snets-v2/result.xml               | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/metabolomics-snets-v2/Makefile b/metabolomics-snets-v2/Makefile
index 9f563af4..1b2f7055 100644
--- a/metabolomics-snets-v2/Makefile
+++ b/metabolomics-snets-v2/Makefile
@@ -3,6 +3,6 @@ include ../Makefile.deploytemplate
 
 WORKFLOW_NAME=metabolomics-snets-v2
 TOOL_FOLDER_NAME=metabolomicsnetsv2
-WORKFLOW_VERSION=release_23
+WORKFLOW_VERSION=release_25
 WORKFLOW_DESCRIPTION="Molecular networks are visual displays of the chemical space present in tandem mass spectrometry (MS/MS) experiments. This visualization approach can detect sets of spectra from related molecules (molecular networks), even when the spectra themselves are not matched to any known compounds. Classical molecular networking is well suited for discovery and can be analyzed directly from raw mass spectrometry files. Feature-based Molecular Networking (FBMN) is better when quantification analysis is necessary, but requires preprocessing with feature finding tools."
 
diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/result.xml b/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
index 152d9132..0c34eb0e 100644
--- a/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
+++ b/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
@@ -103,18 +103,18 @@
         <row expander="USI Links" expandericontype="text">
             <column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/mirror/"/>\
-                <parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[#Scan#]"/>
-                <parameter name="REQUESTPARAMETER=usi2" value="mzspec:GNPSLIBRARY:[SpectrumID]"/>
+                <parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[#Scan#]"/>
+                <parameter name="REQUESTPARAMETER=usi2" value="mzspec:GNPS:GNPS-LIBRARY:accession:[SpectrumID]"/>
                 <parameter name="LABEL" value="Mirror Match USI"/>
             </column>
             <column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
-                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[#Scan#]"/>
+                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[#Scan#]"/>
                 <parameter name="LABEL" value="Query Spectrum USI"/>
             </column>
             <column label="USI-Library" type="genericurlgenerator" width="3"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
-                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSLIBRARY:[SpectrumID]"/>
+                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:GNPS-LIBRARY:accession:[SpectrumID]"/>
                 <parameter name="LABEL" value="Library Spectrum USI"/>
             </column>
         </row>
@@ -255,7 +255,7 @@
         <row expander="USI Links" expandericontype="text">
             <column label="USI-Spectrum" type="genericurlgenerator" width="3" field="cluster index"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
-                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[cluster index]"/>
+                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[cluster index]"/>
                 <parameter name="LABEL" value="Spectrum USI"/>
             </column>
         </row>
@@ -1125,8 +1125,8 @@
         <row expander="USI Links" expandericontype="text">
             <column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
-                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:[Original_Path]:scan:[ScanNumber]"/>
-                <parameter name="LABEL" value="Spectrum USI"/>
+                <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-[Original_Path]:scan:[ScanNumber]"/>
+                <parameter name="LABEL" value="[usi]"/>
             </column>
         </row>
     </block>

From 5042d285721642833bebeb9022af014f0aebcb02 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Tue, 4 Aug 2020 14:01:42 -0700
Subject: [PATCH 2/2] slight bug fix for usi link

---
 metabolomics-snets-v2/metabolomics-snets-v2/result.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/result.xml b/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
index 0c34eb0e..85c0296f 100644
--- a/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
+++ b/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
@@ -1126,7 +1126,7 @@
             <column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
                 <parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
                 <parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-[Original_Path]:scan:[ScanNumber]"/>
-                <parameter name="LABEL" value="[usi]"/>
+                <parameter name="LABEL" value="Spectrum USI"/>
             </column>
         </row>
     </block>