From ec776be52983337e21046a6616b75908e28b47cf Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Tue, 16 Apr 2024 13:50:24 +0200
Subject: [PATCH 01/10] Implemented unit test for load.lcms.R

---
 R/mbr_test0_copy.mzml           | 26908 ++++++++++++++++++++++++++++++
 tests/testthat/test-load.lcms.R |    23 +
 2 files changed, 26931 insertions(+)
 create mode 100644 R/mbr_test0_copy.mzml
 create mode 100644 tests/testthat/test-load.lcms.R

diff --git a/R/mbr_test0_copy.mzml b/R/mbr_test0_copy.mzml
new file mode 100644
index 00000000..3361d331
--- /dev/null
+++ b/R/mbr_test0_copy.mzml
@@ -0,0 +1,26908 @@
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=69477">1878740</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=69541">1883061</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=69636">1887301</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=69863">1906855</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=70436">1926545</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70478">1930361</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70521">1934546</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70572">1938353</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70615">1942487</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70681">1946210</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70885">1950529</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=70972">1954808</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=71032">1958895</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=71114">1963352</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=71147">1968335</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=71291">1977244</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=71416">1982199</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=71942">1986400</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=73325">1990303</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=73422">1994866</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=73969">1998903</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74248">2003337</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74348">2008086</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74460">2012309</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74558">2016307</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74663">2020392</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=74998">2024392</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75424">2028685</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75510">2032252</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75528">2036184</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75589">2040069</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75597">2043941</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75636">2047740</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75675">2051733</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75767">2056340</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75859">2060785</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=75950">2065002</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=76438">2069099</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=76450">2072604</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=76525">2076388</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=76614">2083825</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=76700">2091537</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=76918">2095163</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77427">2098637</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77517">2102171</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77557">2105863</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77606">2109900</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77693">2113569</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=77775">2117134</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=78240">2120628</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=78455">2124889</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79152">2128351</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79248">2132208</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79445">2136237</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79529">2140160</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79612">2144125</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79692">2148307</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=79880">2159730</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=79961">2163554</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80039">2167512</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80119">2171510</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80197">2175832</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80279">2180235</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80357">2184722</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80440">2189040</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=80523">2193017</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=81290">2196773</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=81391">2200574</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=81999">2204430</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82045">2207960</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82076">2211633</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82157">2215290</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82165">2218822</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82180">2222439</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82256">2226270</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82263">2230066</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82275">2233516</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82346">2237436</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82434">2241453</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82470">2245337</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82547">2249208</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82567">2253084</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82626">2256972</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82701">2260994</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82791">2264906</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=82879">2268582</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=83369">2272167</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=83486">2275885</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=84980">2279721</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=85050">2283502</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=85123">2287379</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=85192">2291167</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=85214">2294905</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=85314">2298947</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=87968">2303116</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88095">2306716</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88165">2310400</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88239">2314259</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88315">2318300</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88317">2322198</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88381">2325902</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88450">2329773</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88473">2333344</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=88525">2336891</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=88971">2344116</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89028">2348072</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89093">2351939</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89158">2355716</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89224">2359645</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89287">2363546</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89855">2367238</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89903">2371086</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=89972">2378558</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=89978">2382136</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90042">2386102</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90049">2390061</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90116">2394391</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90123">2398254</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90191">2402617</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90194">2406608</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90259">2411051</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90261">2414719</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90324">2418981</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90325">2422771</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90389">2426417</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90825">2430097</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90896">2434045</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90952">2438179</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=90967">2441823</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91020">2445963</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91036">2449647</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91084">2453875</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91100">2457676</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91151">2462056</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91167">2465804</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91234">2469798</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91304">2473755</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91379">2477398</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=91464">2481055</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92113">2484679</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92168">2488404</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92183">2492017</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92238">2495975</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92249">2499652</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92303">2503647</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92318">2507303</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=92389">2511184</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94116">2514904</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94183">2518552</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94258">2522503</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94332">2526517</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94729">2530126</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94857">2534084</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94919">2538185</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=94980">2541937</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=95063">2545506</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=96694">2549319</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=96764">2552999</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=96836">2556647</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=96918">2560122</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=96993">2563742</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=97169">2567598</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=99329">2571216</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=99385">2574908</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=99446">2578708</offset>
+    </index>
+    <index name="chromatogram">
+    </index>
+  </indexList>
+  <indexListOffset>2582386</indexListOffset>
+  <fileChecksum>23b8703ddaf744e69e1ba72be2584fd3df6f2dc4</fileChecksum>
+</indexedmzML>
diff --git a/tests/testthat/test-load.lcms.R b/tests/testthat/test-load.lcms.R
new file mode 100644
index 00000000..47acdba7
--- /dev/null
+++ b/tests/testthat/test-load.lcms.R
@@ -0,0 +1,23 @@
+patrick::with_parameters_test_that(
+  "test load.lcms reads mzML file",
+  {
+    # Arrange: Set up test inputs
+    testdata <- file.path("..", "testdata")
+    input_path <- file.path(testdata, filename)
+
+    # Act: Execute the function with the test inputs
+    sut <- load.lcms(input_path)
+
+    # Assert: Verify the function output matches expected results
+    # Check that the function returns an object of the expected type
+    testthat::expect_s3_class(sut, "tbl_df")
+  },
+  patrick::cases(
+    test_case_1 = list(
+      filename = c("mbr_test0_copy.mzml")
+    ),
+    test_case_2 = list(
+      filename = c("mbr_test0_copy.mzxml")
+    )
+  )
+)
\ No newline at end of file

From 232a03b3359718bceb4a1fdd2da4adbf1e62a5bb Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Tue, 16 Apr 2024 13:57:09 +0200
Subject: [PATCH 02/10] added mzxml file for testing

---
 .../Galaxy2-[mbr_test0_copy.mzXML].mzxml      | 12279 ++++++++++++++++
 1 file changed, 12279 insertions(+)
 create mode 100644 tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml

diff --git a/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml b/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml
new file mode 100644
index 00000000..0be57236
--- /dev/null
+++ b/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml
@@ -0,0 +1,12279 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">
+  <msRun scanCount="583" startTime="PT2125.86S" endTime="PT8081.98S">
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.raw"
+                fileType="RAWData"
+                fileSha1="6f65a1287b2d7522c5fb90a8a5304212b3568b67"/>
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.mzXML"
+                fileType="processedData"
+                fileSha1="d9c6278c1c6a8f8ca6c69133bacd00efc5f2e706"/>
+    <msInstrument msInstrumentID="1">
+      <msManufacturer category="msManufacturer" value="Thermo Finnigan"/>
+      <msModel category="msModel" value="unknown"/>
+      <msIonisation category="msIonisation" value="NSI"/>
+      <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>
+      <msDetector category="msDetector" value="unknown"/>
+      <software type="acquisition" name="Xcalibur" version="2.6-264001/2.6.0.2640"/>
+    </msInstrument>
+    <dataProcessing centroided="1">
+      <processingOperation name="peak picking"/>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="processing" name="ReAdW" version="2015.1.0(build Jun 29 2015 14:09:50)"/>
+      <comment>type: conversion</comment>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>
+      <processingOperation name="Conversion to mzML"/>
+    </dataProcessing>
+    <scan num="10613"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="26"
+          polarity="+"
+          retentionTime="PT2125.86S"
+          lowMz="91.7452"
+          highMz="1020.45"
+          basePeakMz="624.329"
+          basePeakIntensity="39941"
+          totIonCurrent="290992"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="10611" precursorIntensity="123964" precursorCharge="2" activationMethod="HCD">624.29266819296</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="275"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">eJxzCHu/kQEIHNaWxTiA6PijE8D0ZrU+MJ2g7HIARB+6VdUAohMZfyWA6POfRMDySclzwPwtNxeC6WTGi2DzNl9bvwBEpwbNAvNX9ywAy6c9ngemdzssBstnsuSD6XM3KsF0lmAQmL682BWsLkvIWwFEP1LPPwDh3wDL7/ta+wDMd/4JpvdayoLdk6NoB9a3jsUK7N7cxQ5g/WvDksD8giQrsLpdfBFgupbZEKz+oJ082JzaYBEwf2NQLJjf1MQN5m97qwz2R7OVH5jeu+IChG/nDTZn7zxOMN3cBAmHxw3zwe5tbqsDq9sp8QVsf/ulR2D3b595Amx+921PsL4tkSxg9f2PZ4Dde6mgASQPAOoAb+o=</peaks>
+    </scan>
+    <scan num="11140"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="30"
+          polarity="+"
+          retentionTime="PT2169.75S"
+          lowMz="95.7689"
+          highMz="1163.47"
+          basePeakMz="208"
+          basePeakIntensity="78214.4"
+          totIonCurrent="393771"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="11139" precursorIntensity="161835" precursorCharge="2" activationMethod="HCD">673.80972467574</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="316"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">eJxzCP9omsDAwOCwTiWmAURHRS1WAPMdYx6A6GiVVQdA9Jp/6WA62swZLL7eVBzMj2FWB9MbAsIWgOjkJY5g/s0MHjA/Nc3UAURvfJkONjf18XEwf0PYVLC9aYk9YHufVKeD1aerSILN36GpBTYnk9kbov/be7B85v+/YPWfJdLA6rKPT4C4Z3UoWH2ey2Wwus2iv8DqChs7wPZecJ/KAKJLJouBxZ8nZIDVlTbuBotvkC4G09WH68Hqt7beA5vbcPIr2P6tX3LB7m3lWgRWd7CpDsIX2gA256CNBZhue9QApvf5JIH1tXPXgM3bWJsGpntWQ8LtMAsrmN/XLQixr/Y42F39l/PB5m4L6QDb33+7GszfGv0IzJ/o+hzi3mc6YPMnaf4Hi19rzgbbO0n3GVj93tLHIHUAs1mG8g==</peaks>
+    </scan>
+    <scan num="12331"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="70"
+          polarity="+"
+          retentionTime="PT2257.94S"
+          lowMz="84.0448"
+          highMz="974.46"
+          basePeakMz="86.0969"
+          basePeakIntensity="67235.6"
+          totIonCurrent="870037"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="12329" precursorIntensity="306036" precursorCharge="2" activationMethod="HCD">560.28000000000</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="676"
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From d15210cd1fa3efc1bd6da4502beef0095589a621 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Tue, 16 Apr 2024 13:57:44 +0200
Subject: [PATCH 03/10] renamed mzxml file

---
 .../Galaxy2-[mbr_test0_copy.mzXML].mzxml      | 12279 ----------------
 1 file changed, 12279 deletions(-)
 delete mode 100644 tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml

diff --git a/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml b/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml
deleted file mode 100644
index 0be57236..00000000
--- a/tests/testdata/Galaxy2-[mbr_test0_copy.mzXML].mzxml
+++ /dev/null
@@ -1,12279 +0,0 @@
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-      <msModel category="msModel" value="unknown"/>
-      <msIonisation category="msIonisation" value="NSI"/>
-      <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>
-      <msDetector category="msDetector" value="unknown"/>
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-    <dataProcessing>
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-  </index>
-  <indexOffset>1203724</indexOffset>
-  <sha1>184f263cfeb065c2c78d1bcb900bf9ebc18ecb8f</sha1>
-</mzXML>

From 073e966d5b64c80abeaf6153689720ab0770b454 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Tue, 16 Apr 2024 14:27:09 +0200
Subject: [PATCH 04/10] update

---
 tests/testdata/test0_copy.mzxml | 12279 ++++++++++++++++++++++++++++++
 tests/testthat/test-load.lcms.R |     2 +-
 2 files changed, 12280 insertions(+), 1 deletion(-)
 create mode 100644 tests/testdata/test0_copy.mzxml

diff --git a/tests/testdata/test0_copy.mzxml b/tests/testdata/test0_copy.mzxml
new file mode 100644
index 00000000..0be57236
--- /dev/null
+++ b/tests/testdata/test0_copy.mzxml
@@ -0,0 +1,12279 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">
+  <msRun scanCount="583" startTime="PT2125.86S" endTime="PT8081.98S">
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.raw"
+                fileType="RAWData"
+                fileSha1="6f65a1287b2d7522c5fb90a8a5304212b3568b67"/>
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.mzXML"
+                fileType="processedData"
+                fileSha1="d9c6278c1c6a8f8ca6c69133bacd00efc5f2e706"/>
+    <msInstrument msInstrumentID="1">
+      <msManufacturer category="msManufacturer" value="Thermo Finnigan"/>
+      <msModel category="msModel" value="unknown"/>
+      <msIonisation category="msIonisation" value="NSI"/>
+      <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>
+      <msDetector category="msDetector" value="unknown"/>
+      <software type="acquisition" name="Xcalibur" version="2.6-264001/2.6.0.2640"/>
+    </msInstrument>
+    <dataProcessing centroided="1">
+      <processingOperation name="peak picking"/>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="processing" name="ReAdW" version="2015.1.0(build Jun 29 2015 14:09:50)"/>
+      <comment>type: conversion</comment>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>
+      <processingOperation name="Conversion to mzML"/>
+    </dataProcessing>
+    <scan num="10613"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="26"
+          polarity="+"
+          retentionTime="PT2125.86S"
+          lowMz="91.7452"
+          highMz="1020.45"
+          basePeakMz="624.329"
+          basePeakIntensity="39941"
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+  </index>
+  <indexOffset>1203724</indexOffset>
+  <sha1>184f263cfeb065c2c78d1bcb900bf9ebc18ecb8f</sha1>
+</mzXML>
diff --git a/tests/testthat/test-load.lcms.R b/tests/testthat/test-load.lcms.R
index 47acdba7..8bfae4a3 100644
--- a/tests/testthat/test-load.lcms.R
+++ b/tests/testthat/test-load.lcms.R
@@ -17,7 +17,7 @@ patrick::with_parameters_test_that(
       filename = c("mbr_test0_copy.mzml")
     ),
     test_case_2 = list(
-      filename = c("mbr_test0_copy.mzxml")
+      filename = c("test0_copy.mzxml")
     )
   )
 )
\ No newline at end of file

From 9c06255cda7a1cf7ed3c12be415c18d2a25886ef Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Tue, 16 Apr 2024 14:29:26 +0200
Subject: [PATCH 05/10] updated

---
 R/mbr_test0_copy.mzml | 26908 ----------------------------------------
 1 file changed, 26908 deletions(-)
 delete mode 100644 R/mbr_test0_copy.mzml

diff --git a/R/mbr_test0_copy.mzml b/R/mbr_test0_copy.mzml
deleted file mode 100644
index 3361d331..00000000
--- a/R/mbr_test0_copy.mzml
+++ /dev/null
@@ -1,26908 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
-  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="2016_Jan_12_QE2_47" version="1.1.0">
-    <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.74.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
-      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
-    </cvList>
-    <fileDescription>
-      <fileContent>
-        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
-        <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
-        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
-      </fileContent>
-      <sourceFileList count="3">
-        <sourceFile id="_x0032_016_Jan_12_QE2_47.raw" name="2016_Jan_12_QE2_47.raw" location="">
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-      <offset idRef="controllerType=0 controllerNumber=1 scan=91379">2477398</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=91464">2481055</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92113">2484679</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92168">2488404</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92183">2492017</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92238">2495975</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92249">2499652</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92303">2503647</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92318">2507303</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=92389">2511184</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94116">2514904</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94183">2518552</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94258">2522503</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94332">2526517</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94729">2530126</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94857">2534084</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94919">2538185</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=94980">2541937</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=95063">2545506</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=96694">2549319</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=96764">2552999</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=96836">2556647</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=96918">2560122</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=96993">2563742</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=97169">2567598</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=99329">2571216</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=99385">2574908</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=99446">2578708</offset>
-    </index>
-    <index name="chromatogram">
-    </index>
-  </indexList>
-  <indexListOffset>2582386</indexListOffset>
-  <fileChecksum>23b8703ddaf744e69e1ba72be2584fd3df6f2dc4</fileChecksum>
-</indexedmzML>

From e5aea3062cbc4c688e8f71284af9bdd018c0d649 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Wed, 17 Apr 2024 16:39:20 +0200
Subject: [PATCH 06/10] expanded test to mzdata and cover more parameters

---
 tests/testthat/test-load.lcms.R | 36 ++++++++++++++++++++++++---------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/tests/testthat/test-load.lcms.R b/tests/testthat/test-load.lcms.R
index 8bfae4a3..0b026f90 100644
--- a/tests/testthat/test-load.lcms.R
+++ b/tests/testthat/test-load.lcms.R
@@ -1,23 +1,39 @@
+create_test_case <- function(filename, mz_length, rt_length, intensities_length) {
+  list(
+    filename = filename,
+    expected_type = "list",
+    expected_lengths = c(mz = mz_length, rt = rt_length, intensities = intensities_length),
+    expected_num_na = c(mz = 0, rt = 0, intensities = 0)
+  )
+}
+
 patrick::with_parameters_test_that(
-  "test load.lcms reads mzML file",
+  "test load.lcms reads different file types",
   {
     # Arrange: Set up test inputs
     testdata <- file.path("..", "testdata")
-    input_path <- file.path(testdata, filename)
+    input_path <- file.path(testdata, "input", filename)
 
     # Act: Execute the function with the test inputs
-    sut <- load.lcms(input_path)
+    data <- recetox.aplcms::load.lcms(input_path)
 
     # Assert: Verify the function output matches expected results
     # Check that the function returns an object of the expected type
-    testthat::expect_s3_class(sut, "tbl_df")
+    actual_type <- data
+    testthat::expect_type(actual_type, expected_type)
+    
+    # Check the lengths of the vectors in the list
+    actual_lengths <- lengths(data)
+    testthat::expect_equal(actual_lengths, expected_lengths)
+
+    # Check the number of NA values in each vector
+    actual_num_na <- sapply(data, function(x) sum(is.na(x)))
+    testthat::expect_equal(actual_num_na, expected_num_na)
   },
+  
   patrick::cases(
-    test_case_1 = list(
-      filename = c("mbr_test0_copy.mzml")
-    ),
-    test_case_2 = list(
-      filename = c("test0_copy.mzxml")
-    )
+    test_case_1 = create_test_case("RCX_06_shortened.mzML", 879476, 879476, 879476),
+    test_case_2 = create_test_case("test_file.mzXML", 9647575, 9647575, 9647575),
+    test_case_3 = create_test_case("alg3.mzdata", 543894, 543894, 543894)
   )
 )
\ No newline at end of file

From eff14342814c75ea3c98ee86acbec850cbdafd51 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Wed, 17 Apr 2024 18:36:47 +0200
Subject: [PATCH 07/10] added remote links of mzdata and mzxml files

---
 tests/remote-files/input.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/remote-files/input.txt b/tests/remote-files/input.txt
index f955ef46..4afb4bf2 100644
--- a/tests/remote-files/input.txt
+++ b/tests/remote-files/input.txt
@@ -4,4 +4,6 @@ https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_06_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_07_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_08_shortened.mzML
-https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
\ No newline at end of file
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/alg3.mzdata
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/test_file.mzXML
\ No newline at end of file

From 1092dcfc3868b2eb5dea20234a95d238138e37e4 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Thu, 18 Apr 2024 12:55:59 +0200
Subject: [PATCH 08/10] updated ci to node20

---
 .github/workflows/r-conda.yml   | 4 ++--
 tests/testthat/test-load.lcms.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/r-conda.yml b/.github/workflows/r-conda.yml
index df449de7..83e314e3 100644
--- a/.github/workflows/r-conda.yml
+++ b/.github/workflows/r-conda.yml
@@ -28,10 +28,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: recetox-aplcms-dev
           auto-update-conda: true
diff --git a/tests/testthat/test-load.lcms.R b/tests/testthat/test-load.lcms.R
index 0b026f90..dd55f6ef 100644
--- a/tests/testthat/test-load.lcms.R
+++ b/tests/testthat/test-load.lcms.R
@@ -15,7 +15,7 @@ patrick::with_parameters_test_that(
     input_path <- file.path(testdata, "input", filename)
 
     # Act: Execute the function with the test inputs
-    data <- recetox.aplcms::load.lcms(input_path)
+    data <- load.lcms(input_path)
 
     # Assert: Verify the function output matches expected results
     # Check that the function returns an object of the expected type

From ec2da0f3eb659f563d8b57d69cee5e7c1bef7dbc Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Wed, 24 Apr 2024 14:54:03 +0200
Subject: [PATCH 09/10] updated environment

---
 conda/environment-build.yaml | 2 +-
 conda/environment-dev.yaml   | 4 ++--
 conda/environment.yaml       | 4 ++--
 conda/meta.yaml              | 8 ++++----
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/conda/environment-build.yaml b/conda/environment-build.yaml
index 7aa8c457..79fe67b9 100644
--- a/conda/environment-build.yaml
+++ b/conda/environment-build.yaml
@@ -7,4 +7,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - r-base =4.2
+  - r-base
diff --git a/conda/environment-dev.yaml b/conda/environment-dev.yaml
index b43ea0e1..ba6f3754 100644
--- a/conda/environment-dev.yaml
+++ b/conda/environment-dev.yaml
@@ -4,11 +4,11 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - icu <=70.1
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach
diff --git a/conda/environment.yaml b/conda/environment.yaml
index 9c6626cc..3ab1060c 100644
--- a/conda/environment.yaml
+++ b/conda/environment.yaml
@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach
diff --git a/conda/meta.yaml b/conda/meta.yaml
index b64d4f5c..db4da355 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -21,10 +21,10 @@ build:
   
 requirements:
   host:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach
@@ -37,10 +37,10 @@ requirements:
     - r-tibble
 
   run:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach

From ae8b45108ca97c6def370e79287c7294c76039f2 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Wed, 24 Apr 2024 15:54:55 +0200
Subject: [PATCH 10/10] updated changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5eaeb04d..86437e55 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [dev] - unreleased
 ### Added
+- added tests for mzdata and mzxml formats [#216](https://github.com/RECETOX/recetox-aplcms/pull/216)
 ### Changed
 ### Removed