change paths

MannLabs · Oct 16, 2024 · 1a46338 · 1a46338
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commit 1a46338
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Showing 3 changed files with 38 additions and 14 deletions.
diff --git a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
@@ -14,7 +14,7 @@
     "directlfq_dir = os.path.dirname(directlfq.__file__)\n",
     "\n",
     "# Navigate up two levels to reach the project root\n",
-    "project_root = os.path.abspath(os.path.join(directlfq_dir, '..', '..'))\n",
+    "project_root = os.path.abspath(os.path.join(directlfq_dir, '..'))\n",
     "\n",
     "output_dir = os.path.join(project_root, 'test_data', 'system_tests')\n",
     "\n",

diff --git a/tests/ratio_tests/systemtest_ratio_mixed_species1.ipynb b/tests/ratio_tests/systemtest_ratio_mixed_species1.ipynb
@@ -17,14 +17,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "INPUT_FILE = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv\"\n",
+    "import os\n",
+    "import directlfq\n",
+    "import alphabase.test_data_downloader\n",
     "\n",
-    "DIRECTLFQ_FILE_PRECURSORS_MS1_MS2 = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursor_ms1_and_ms2.protein_intensities.tsv\"\n",
-    "DIRECTLFQ_FILE_PRECURSORS = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursors.protein_intensities.tsv\"\n",
-    "DIRECTLFQ_FILE_FRAGIONS = \"../../test_data/system_tests/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursor_ms1_and_ms2.protein_intensities.tsv\"\n",
+    "# Get the directory of the directlfq package\n",
+    "directlfq_dir = os.path.dirname(directlfq.__file__)\n",
     "\n",
+    "# Navigate up two levels to reach the project root\n",
+    "project_root = os.path.abspath(os.path.join(directlfq_dir, '..', '..'))\n",
     "\n",
-    "SAMPLEMAP  = \"../../test_data/system_tests/diaPASEF_diann/samplemap.tsv\""
+    "output_dir = os.path.join(project_root, 'test_data', 'system_tests')\n",
+    "\n",
+    "os.makedirs(output_dir, exist_ok=True)\n",
+    "# Now use the absolute path in the DataShareDownloader call\n",
+    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/zjSHOAzKBaF2Z73\", output_dir=output_dir).download()\n"
    ]
   },
   {
@@ -33,9 +40,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import alphabase.test_data_downloader as tdd\n",
+    "INPUT_FILE = f\"{output_dir}/diaPASEF_diann/report.tsv.top3added.tsv\"\n",
+    "\n",
+    "DIRECTLFQ_FILE_PRECURSORS_MS1_MS2 = f\"{output_dir}/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursor_ms1_and_ms2.protein_intensities.tsv\"\n",
+    "DIRECTLFQ_FILE_PRECURSORS = f\"{output_dir}/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursors.protein_intensities.tsv\"\n",
+    "DIRECTLFQ_FILE_FRAGIONS = f\"{output_dir}/diaPASEF_diann/report.tsv.top3added.tsv.diann_precursor_ms1_and_ms2.protein_intensities.tsv\"\n",
+    "\n",
     "\n",
-    "tdd.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/zjSHOAzKBaF2Z73\", output_dir=\"../../test_data/system_tests/\").download()"
+    "SAMPLEMAP  = f\"{output_dir}/diaPASEF_diann/samplemap.tsv\""
    ]
   },
   {

diff --git a/tests/ratio_tests/systemtest_ratio_mixed_species2.ipynb b/tests/ratio_tests/systemtest_ratio_mixed_species2.ipynb
@@ -17,12 +17,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "INPUT_FILE = \"../../test_data/system_tests/Spectronaut_LargeFC/re_run_SN15/20220607_153923_MP-LFC-MS1var-OT-S1-120kMS1_Report.tsv\"\n",
+    "import os\n",
+    "import directlfq\n",
+    "import alphabase.test_data_downloader\n",
     "\n",
-    "DIRECTLFQ_FILE = f\"{INPUT_FILE}.protein_intensities.tsv\"\n",
+    "# Get the directory of the directlfq package\n",
+    "directlfq_dir = os.path.dirname(directlfq.__file__)\n",
+    "\n",
+    "# Navigate up two levels to reach the project root\n",
+    "project_root = os.path.abspath(os.path.join(directlfq_dir, '..'))\n",
+    "\n",
+    "output_dir = os.path.join(project_root, 'test_data', 'system_tests', \"Spectronaut_LargeFC\")\n",
     "\n",
-    "PROTEIN2ORGANISM_FILE = \"../../test_data/system_tests/Spectronaut_LargeFC/re_run_SN15/organism_map.tsv\"\n",
-    "SAMPLEMAP  = \"../../test_data/system_tests/Spectronaut_LargeFC/re_run_SN15/samplemap.tsv\"\n"
+    "os.makedirs(output_dir, exist_ok=True)\n",
+    "# Now use the absolute path in the DataShareDownloader call\n",
+    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/T8sFUGuaQb0d1zP\", output_dir=output_dir).download()\n"
    ]
   },
   {
@@ -31,9 +40,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import alphabase.test_data_downloader as tdd\n",
+    "INPUT_FILE = f\"{output_dir}/re_run_SN15/20220607_153923_MP-LFC-MS1var-OT-S1-120kMS1_Report.tsv\"\n",
+    "\n",
+    "DIRECTLFQ_FILE = f\"{INPUT_FILE}.protein_intensities.tsv\"\n",
     "\n",
-    "tdd.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/T8sFUGuaQb0d1zP\", output_dir=\"../../test_data/system_tests/Spectronaut_LargeFC/\").download()\n"
+    "PROTEIN2ORGANISM_FILE = f\"{output_dir}/re_run_SN15/organism_map.tsv\"\n",
+    "SAMPLEMAP  = f\"{output_dir}/re_run_SN15/samplemap.tsv\"\n"
    ]
   },
   {