removed defusedxml (#424)

* removed defusedxml

* refactor: Add temporary file handling to blast_remote function move `parse_xml`

* add test_blast

* add golden data

* Add pytest-mock to dev dependencies

---------

Co-authored-by: Rodrigo V Honorato <[email protected]>
Co-authored-by: Rodrigo Vargas Honorato <[email protected]>

pyproject.toml

@@ -17,7 +17,6 @@ classifiers = [
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 bio = "1.6.2"
-defusedxml = "0.7.1"
 lxml = "5.2.1"
 mdanalysis = "2.7.0"
 requests = "2.31.0"

src/arctic3d/modules/blast.py

@@ -1,13 +1,15 @@
 """Function to BLAST input sequence and return accession id."""
+
 import logging
 import os
 import shlex
 import shutil
 import subprocess
+import tempfile
 from pathlib import Path
 
 from Bio.Blast import NCBIWWW
-from defusedxml import lxml as ET
+from lxml import etree as ET
 
 log = logging.getLogger("arctic3d.log")
 
@@ -87,7 +89,7 @@ def blast_local(fasta_file, db):
     return uniprot_id
 
 
-def blast_remote(fasta_file):
+def blast_remote(fasta_file: str) -> str:
     """
     Blast sequence.
 
@@ -106,12 +108,22 @@ def blast_remote(fasta_file):
         "blastp", "swissprot", fasta_file, hitlist_size=50
     )
 
-    # temp file for storing results
-    with open("blast_res.xml", "w") as save_output:
+    # TODO: Handle scenario in which the `qblast` call fails
+
+    with tempfile.NamedTemporaryFile(
+        mode="w+", delete=True, suffix=".xml"
+    ) as temp:
         blast_res = blast_res_handle.read()
-        save_output.write(blast_res)
+        temp.write(blast_res)
+        temp.flush()
+        accession_id = parse_xml(temp.name)
+
+    return accession_id
+
 
-    tree = ET.parse("blast_res.xml")
+def parse_xml(xml_file: str) -> str:
+    """Parse the BLAST XML file and return the first (?) accession ID."""
+    tree = ET.parse(source=xml_file, parser=ET.XMLParser(encoding="utf-8"))
     root = tree.getroot()
 
     # root [BlastOutput_iterations] [Iteration] [Iteration_hits] \

tests/golden_data/1crn.fasta

@@ -0,0 +1,2 @@
+>1CRN_1|Chain A|CRAMBIN|Crambe hispanica subsp. abyssinica (3721)
+TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN

tests/golden_data/blast.xml

@@ -0,0 +1,97 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastp</BlastOutput_program>
+  <BlastOutput_version>BLASTP 2.15.0+</BlastOutput_version>
+  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>swissprot</BlastOutput_db>
+  <BlastOutput_query-ID>Query_544091</BlastOutput_query-ID>
+  <BlastOutput_query-def>1CRN_1|Chain A|CRAMBIN|Crambe hispanica subsp. abyssinica (3721)</BlastOutput_query-def>
+  <BlastOutput_query-len>46</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>0.05</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+<BlastOutput_iterations>
+<Iteration>
+  <Iteration_iter-num>1</Iteration_iter-num>
+  <Iteration_query-ID>Query_544091</Iteration_query-ID>
+  <Iteration_query-def>1CRN_1|Chain A|CRAMBIN|Crambe hispanica subsp. abyssinica (3721)</Iteration_query-def>
+  <Iteration_query-len>46</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>sp|P01542.2|</Hit_id>
+  <Hit_def>RecName: Full=Crambin [Crambe hispanica subsp. abyssinica]</Hit_def>
+  <Hit_accession>P01542</Hit_accession>
+  <Hit_len>46</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>92.4337</Hsp_bit-score>
+      <Hsp_score>228</Hsp_score>
+      <Hsp_evalue>2.38732e-26</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>46</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>46</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>45</Hsp_identity>
+      <Hsp_positive>46</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>46</Hsp_align-len>
+      <Hsp_qseq>TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN</Hsp_qseq>
+      <Hsp_hseq>TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN</Hsp_hseq>
+      <Hsp_midline>TTCCPSIVARSNFNVCRLPGTPEA+CATYTGCIIIPGATCPGDYAN</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+<Hit>
+  <Hit_num>2</Hit_num>
+  <Hit_id>sp|P01541.1|</Hit_id>
+  <Hit_def>RecName: Full=Denclatoxin-B [Dendrophthora clavata]</Hit_def>
+  <Hit_accession>P01541</Hit_accession>
+  <Hit_len>46</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>53.9138</Hsp_bit-score>
+      <Hsp_score>128</Hsp_score>
+      <Hsp_evalue>3.34186e-11</Hsp_evalue>
+      <Hsp_query-from>2</Hsp_query-from>
+      <Hsp_query-to>46</Hsp_query-to>
+      <Hsp_hit-from>2</Hsp_hit-from>
+      <Hsp_hit-to>46</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>23</Hsp_identity>
+      <Hsp_positive>31</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>45</Hsp_align-len>
+      <Hsp_qseq>TCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN</Hsp_qseq>
+      <Hsp_hseq>SCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH</Hsp_hseq>
+      <Hsp_midline>+CCP+  AR+ +N+CRLPGTP  +CA  +GC II G  CP  Y +</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>483204</Statistics_db-num>
+      <Statistics_db-len>183688421</Statistics_db-len>
+      <Statistics_hsp-len>0</Statistics_hsp-len>
+      <Statistics_eff-space>0</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>

tests/test_blast.py

@@ -0,0 +1,43 @@
+from io import StringIO
+from pathlib import Path
+
+import pytest
+
+from arctic3d.modules.blast import blast_remote, parse_xml
+
+from . import golden_data
+
+
+@pytest.fixture
+def fasta_file():
+    return Path(golden_data, "1crn.fasta")
+
+
+@pytest.fixture
+def xml_file():
+    return Path(golden_data, "blast.xml")
+
+
+def test_blast_remote(mocker, fasta_file, xml_file):
+
+    # Mock the remote blast call by passing the xml file as stringIo as return value
+    with open(xml_file, "r") as f:
+        xml = f.read()
+    xml_string_io = StringIO(xml)
+
+    mock_qbplast = mocker.patch("Bio.Blast.NCBIWWW.qblast")
+    mock_qbplast.return_value = xml_string_io
+
+    accession_id = blast_remote(fasta_file)
+
+    assert accession_id == "P01541"
+
+
+@pytest.mark.skip(reason="Not implemented")
+def test_blast_local():
+    pass
+
+
+def test_parse_xml(xml_file):
+    accession_id = parse_xml(xml_file)
+    assert accession_id == "P01541"