Skip to content

[WIP] Networking Enrichment Query with MassQL #185

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mwang87 wants to merge 1 commit into
base: master
Choose a base branch
from
Open

[WIP] Networking Enrichment Query with MassQL #185

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions proteosafe/msql-network-query-nf/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
-include ../Makefile.credentials
include ../Makefile.deploytemplate

WORKFLOW_NAME=msql-nf
TOOL_FOLDER_NAME=msql-nf
WORKFLOW_VERSION=release_30
WORKFLOW_DESCRIPTION="MassQL Query Workflow - <a href='https://mwang87.github.io/MassQueryLanguage_Documentation/'>Documentation Link</a>. Currently Supports v1.0 of MassQL"
40 changes: 40 additions & 0 deletions proteosafe/msql-network-query-nf/msql-nf/binding.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
<?xml version="1.0" encoding="ISO-8859-1" ?>
<binding>
<bind action="begin" type="download">
<url value="{livesearch.download}"/>
<query name="task" valueRef="@task" />
<query name="user" valueRef="@user"/>
<compression type="zip" />
<download port="flowParams" type="file">
<query name="resource" value="params"/>
</download>
<downloadParams>
<query name="resource" value="params"/>
</downloadParams>
<download port="inputspectra" type="folder">
<query name="resource" value="inputspectra"/>
</download>
</bind>

<bind action="demangle_spectra" tool="demangle_spectra">
<inputAsRequirement port="inputspectra" requirement="inputspectra"/>
<inputAsRequirement port="workflowParameters" requirement="workflowParameters"/>
<productionToOutput port="demangled_spectra" production="demangled_spectra"/>
</bind>

<bind action="msql_nf_process" tool="msql_nf_process">
<inputAsRequirement port="demangled_spectra" requirement="demangled_spectra"/>
<inputAsRequirement port="workflowParameters" requirement="workflowParameters"/>
<productionToOutput port="query_results" production="query_results"/>
</bind>

<bind action="end" type="upload">
<url value="{livesearch.upload}"/>
<query name="task" valueRef="@task"/>
<contentQuery name="content"/>
<compression type="zip"/>
<upload port="query_results" type="folder">
<query name="resource" value="query_results"/>
</upload>
</bind>
</binding>
28 changes: 28 additions & 0 deletions proteosafe/msql-network-query-nf/msql-nf/flow.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
<?xml version="1.0" encoding="ISO-8859-1" ?>
<flow name="msql">
<object name="workflowParameters"/>
<collection name="inputspectra"/>

<action name="begin">
<output port="flowParams" object="workflowParameters"/>
<output port="inputspectra" collection="inputspectra"/>
</action>

<collection name="demangled_spectra"/>
<action name="demangle_spectra">
<input port="inputspectra" collection="inputspectra"/>
<input port="workflowParameters" object="workflowParameters"/>
<output port="demangled_spectra" collection="demangled_spectra"/>
</action>

<collection name="query_results"/>
<action name="msql_nf_process">
<input port="demangled_spectra" collection="demangled_spectra"/>
<input port="workflowParameters" object="workflowParameters"/>
<output port="query_results" collection="query_results"/>
</action>

<action name="end">
<input port="query_results" collection="query_results"/>
</action>
</flow>
138 changes: 138 additions & 0 deletions proteosafe/msql-network-query-nf/msql-nf/input.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@
<?xml version="1.0" encoding="ISO-8859-1" ?>
<interface id="msql" version="1.2.8">
<workflow-id>MSQL-NF</workflow-id>
<workflow-label>MSQL-NF</workflow-label>

<!-- Parameter declarations -->
<parameters>
<!-- Universal parameters -->
<parameter name="desc" label="Description">
<validator type="length" maximum="1000"/>
</parameter>
<parameter name="email" label="Email">
<validator type="email"/>
</parameter>

<parameter name="spec_on_server" label="Spectrum Files (Required)">
<validator type="required"/>
<fileGenerator type="upload" purpose="spectrum" target="inputspectra"/>
</parameter>

<parameter name="QUERY" label="Enter QUERY (Required)">
<default value="QUERY scaninfo(MS2DATA)"/>
</parameter>

<parameter name="PARALLELFILES" label="Parallelize Across All Files">
<options>
<option value="YES" label="YES"/>
<option value="NO" label="NO"/>
</options>
<validator type="set"/>
<default value="YES"/>
</parameter>

<parameter name="PARALLELPERFILE" label="Parallelize within a single File">
<options>
<option value="NO" label="NO"/>
</options>
<validator type="set"/>
<default value="NO"/>
</parameter>

<parameter name="EXTRACT" label="Extract Found MS Spectra">
<options>
<option value="YES" label="YES"/>
<option value="NO" label="NO"/>
</options>
<validator type="set"/>
<default value="NO"/>
</parameter>

<parameter name="CLUSTERPARALLEL" label="Parallelize Run Across the Cluster (this is an admin thing)">
<options>
<option value="NO" label="NO"/>
<option value="YES" label="YES"/>
</options>
<validator type="set"/>
<default value="NO"/>
</parameter>
</parameters>

<block label="Setting">
<row>
<cell>
<label>
<content parameter="QUERY"/>
</label>
</cell>
<cell>
<input parameter="QUERY" type="textarea">
<attribute name="rows" value="8"/>
<attribute name="cols" value="80"/>
</input>
</cell>
</row>
<row>
<cell>
<label>
<content parameter="spec_on_server"/>
</label>
</cell>
<cell colspan="3">
<module id="spec_on_server" type="fileSelector">
<property name="label">Spectrum Files</property>
</module>
</cell>
</row>
<row>
<cell>
<label>
<content parameter="PARALLELPERFILE"/>
</label>
</cell>

<cell>
<input type="select" parameter="PARALLELPERFILE">
</input>
</cell>
</row>
<row>
<cell>
<label>
<content parameter="PARALLELFILES"/>
</label>
</cell>

<cell>
<input type="select" parameter="PARALLELFILES">
</input>
</cell>
</row>
<row>
<cell>
<label>
<content parameter="EXTRACT"/>
</label>
</cell>

<cell>
<input type="select" parameter="EXTRACT">
</input>
</cell>
</row>
<row>
<cell>
<label>
<content parameter="CLUSTERPARALLEL"/>
</label>
</cell>

<cell>
<input type="select" parameter="CLUSTERPARALLEL">
</input>
</cell>
</row>
</block>


</interface>
Loading