feat(*:dependencies): externalisation of the kmd hmdb api client

workflow4metabolomics · Aug 23, 2023 · 92bac50 · 92bac50
1 parent 3bfb9d8
commit 92bac50
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml b/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml
@@ -20,6 +20,7 @@
         <requirement type="package" version="0.24.1">httpx</requirement>
         <requirement type="package" version="2.0.3">pandas</requirement>
         <requirement type="package" version="5.15.0">plotly</requirement>
+        <requirement type="package" version="1.0.1">kmd_hmdb_api_client</requirement>
     </requirements>
     <command detect_errors="exit_code">
 <![CDATA[

diff --git a/tools/kmd_hmdb_data_plot/kmd_hmdb_interrogator.py b/tools/kmd_hmdb_data_plot/kmd_hmdb_interrogator.py
@@ -3,8 +3,8 @@
 import csv
 import operator
 
-import chopin_kmd_hmdb_api_client.client
-from chopin_kmd_hmdb_api_client.api.default import (
+import kmd_hmdb_api_client.client
+from kmd_hmdb_api_client.api.default import (
     api_annotation_get,
     api_compound_find,
     api_taxonomy_get,
@@ -15,7 +15,7 @@
 __version__ = "1.0.0"
 
 
-kmd_hmdb_client = chopin_kmd_hmdb_api_client.client.Client(
+kmd_hmdb_client = kmd_hmdb_api_client.client.Client(
     "https://kmd-hmdb-rest-api.metabolomics-chopin.e-metabohub.fr",
     verify_ssl=False,
     timeout=500,

diff --git a/tools/kmd_hmdb_data_plot/macro.xml b/tools/kmd_hmdb_data_plot/macro.xml
@@ -154,7 +154,14 @@
 
   <xml name="produce_plot_outputs">
     <data name="output" format="html"
-      label="html - ${tool.name} on ${what.tsv_input.name}"
+      label="html - ${tool.name} on ${
+      ' - '
+      + str($what['mz_ratio'])
+      + '±' + str($what['mass_tolerance'])
+      + ' - ' + str($what['database'])
+      if 'get_data' in str($what['to_do'])
+      else ''' ' ''' + $what.csv_input.name + ''' ' '''
+    }"
     >
       <filter>"produce_plot" in str(what['to_do'])</filter>
     </data>