Merge branch 'main' into usi_example

.github/workflows/linkcheck.yml

@@ -7,15 +7,13 @@ jobs:
     runs-on: ubuntu-latest
     name: Check for broken links
     steps:
-    - name: Check for broken links
-      id: link-report
-      uses: celinekurpershoek/[email protected]
+    - name: Setup Python
+      uses: actions/setup-python@v5
       with:
-        # Required:
-        url: 'https://hupo-psi.github.io/mzQC/'
-        # optional:
-        honorRobotExclusions: false
-        ignorePatterns: 'github,google,slack'
-        recursiveLinks: false # Check all URLs on all reachable pages (could take a while)
+        python-version: '3.10'
+    - run: pip3 install linkchecker
+    - name: Link Checker
+      id: link-report
+      run: linkchecker -ofailures --check-extern --ignore-url="\s*\.md" https://hupo-psi.github.io/mzQC/
     - name: Get the result
-      run: echo "${{steps.link-report.outputs.result}}"
+      run: echo linkchecker/failures

docs/pages/use-case-stories/mzQC_for_analytical_chemists.md

@@ -17,7 +17,7 @@ While many of the papers describing QC metrics for mass spectrometry have been b
 4. What fraction of MS/MS scans came from +2 precursor ions?
     _63.67%_
 
-Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software[1] in “IDFree” mode.
+Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software [1](#bumbershoot) in “IDFree” mode.
 
 
 ## Format metrics in JSON
@@ -124,5 +124,5 @@ Choosing JSON rather than XML is intended to reduce the effort required to write
 
 
 ---
-[1]: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
+<a id="bumbershoot">[1]</a>: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
 Original draft: https://docs.google.com/document/d/16b1n_LXYWsxLK2PQfXWj_WvtiwJOXu2EZx1Q8WzZNlc/edit#

docs/pages/use-cases.md

@@ -6,13 +6,13 @@ permalink: /use-cases/
 This page should give you a (non-exclusive) overview over the use cases covered by mzQC:
 
 ## Handover Format
-It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/individual-runs/).
+It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/).
 
 ## Quality Reports
 With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/USI-example/).
 
 ## Archival
-The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/qc-sample-run/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzML-mzQC/).
+The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/QC2-sample-example/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzml-mzqc-example/).
 
 ## Common currency
 With mzQC for archival, quality reports, and as handover format, [mzQC can serve as a common currency](mzQC-common-currency/) for data repositories, journals, and collaborators.

docs/pages/worked-examples/QC2-sample-example.mzQC.md

@@ -53,4 +53,4 @@ Since each column is in turn defined by a cv term, the column can also be assign
 
 
 ### This is the mzQC file once again, in full:
-**[QC2-sample-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/QC2-sample-example.mzQC)**
+**[QC2-sample-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/QC2-sample-example.mzQC)**

docs/pages/worked-examples/USI-example.mzQC.md

@@ -72,4 +72,4 @@ Each row represents one spectrum that can be directly looked up. For USI,
 [even directly from the web](https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09:scan:2).
 
 ### This is the mzQC file once again, in full:
-**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/blob/main/specification_documents/examples/USI-example.mzQC)**
+**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/USI-example.mzQC)**

docs/pages/worked-examples/metabo-batches.mzQC.md

@@ -87,4 +87,4 @@ before | after
 
 
 ### This is the mzQC file once again, in full:
-**[metabo-batches.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/metabo-batches.mzQC)**
+**[metabo-batches.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/metabo-batches.mzQC)**

docs/pages/worked-examples/mzml-mzqc-example.md

@@ -84,4 +84,4 @@ The `<cv>` elements are again very similar to the respective entries in _mzQC_,
 Note that you should also add your software to `<software>` and `<dataProcessing>`.
 
 ### This is the mzQC file once again, in full:
-**[mzml-mzqc-example.mzML](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/mzml-mzqc-example.mzML)**
+**[mzml-mzqc-example.mzML](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/mzml-mzqc-example.mzML)**

docs/pages/worked-examples/set-of-runs.mzQC.md

@@ -456,4 +456,4 @@ On the other hand, ommitting the `healthy`/`diseased` setQualities is not sensib
 }
 ```
 ### This is the mzQC file once again, in full:
-**[sets-of-runs.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/set-of-runs.mzQC)**
+**[sets-of-runs.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/set-of-runs.mzQC)**

meeting_notes/2024/20240626_telco.md

@@ -35,7 +35,7 @@ We will prioritize tools based on use cases for the mzQC manuscript and try to e
 
 ## mzQC manuscript
 
-- Current Status: Manuscript contains ideas and structure but requires substantial work.
+- Current status: Manuscript contains ideas and structure but requires substantial work.
 - We discussed the different use cases. Key next efforts will include getting started on those examples.
 
 ## Other
@@ -46,15 +46,15 @@ We will prioritize tools based on use cases for the mzQC manuscript and try to e
 
 - Wout:
     - Finalize the updates for the individual run and multiple run examples.
-    - Recreate the Quameter to MZ QC conversion script.
+    - Recreate the Quameter to mzQC conversion script.
 - Mathias:
     - Ensure the validation setup runs correctly.
     - Update the QC example, focusing on the metabolomics batch correction and QC sample plots.
 - Nils:
     - Double-check the metabolomics example and ensure it adheres to the final specification.
 - Chris:
-    - Add more metrics to PTX QC.
-    - Reach out to OpenMS developers regarding MZ QC support.
+    - Add more metrics to PTX-QC.
+    - Reach out to OpenMS developers regarding mzQC support.
 - Team:
     - Update the GitHub issue tracker with tasks and responsibilities.
     - Collect and track new QC tools and developers for outreach.

meeting_notes/2024/20240710_telco.md

@@ -0,0 +1,29 @@
+# QC working group teleconference 10 July 2024
+
+- Chris Bielow
+- Wout Bittremieux
+- Eralp Dogu
+- David Tabb
+- Julian Uszkoreit
+- Mathias Walzer
+
+---
+
+## mzQC examples
+
+- We went over the updated mzQC examples and had a discussion on related CV requests.
+- Wout will submit new CV requests to complete the [setQuality](https://github.com/HUPO-PSI/mzQC/pull/219) and [mzML](https://github.com/HUPO-PSI/mzQC/pull/228) examples.
+    - MS:4000177|protein contaminant intensity ratio should use the "ratio" unit instead of "fraction".
+- Additional checks need to be added to the validator: [ensure unit consistency](https://github.com/MS-Quality-Hub/pymzqc/issues/42), [input files to recognize ID-based metrics](https://github.com/MS-Quality-Hub/pymzqc/issues/43), [documentation on how to run locally](https://github.com/MS-Quality-Hub/pymzqc/issues/44).
+- The validator seems to be online again but very slow. Mathias will work on validator documentation and coordinate with Nils for stability issues.
+
+## mzQC manuscript
+
+- Eralp joined us for some fresh perspectives on the manuscript and use cases. We especially discussed the longitudinal QC use case. We can use QCloud data or CPTAC data, which Eralp has used previously with MsStatsQC.
+- Eralp and Mathias will coordinate to decide on the best dataset to use for the longitudinal QC use case.
+- Eralp will look into mzQC support for MsStatsQC through rmzqc. Alternately, a simpler first approach could be to use an external conversion script.
+- Wout will create a Python script to convert between QuaMeter output and mzQC.
+
+## Miscellaneous
+
+- Wout & Dave will be present at HUPO 2024 in Dresden.