[BUG] Failing to parse SRA metadata

[dweemx]

Describe the bug
Problem parsing the XML using pysradb for SRP187520 project. This is probably a bug in pysradb but for tracking purposes we keep this also as an issue here.

To Reproduce
Steps to reproduce the behavior:

1. Configure with these options:

nextflow config vib-singlecell-nf/vsn-pipelines -r develop -entry sra

2. Run using this entry point:

nextflow -C nextflow.config run vib-singlecell-nf/vsn-pipelines -entry sra

3. See error:

Error executing process > 'sra:DOWNLOAD_FROM_SRA:SRA_TO_METADATA (1)'

Caused by:
  Process `sra:DOWNLOAD_FROM_SRA:SRA_TO_METADATA (1)` terminated with an error exit status (1)

Command executed:

  ~/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/src/utils/bin/sra_to_metadata.py             SRP187520                          --sample-filter "Drop-Seq.*"             --output "SRP187520_metadata.tsv"

Command exit status:
  1

Command output:
  Using NCBi's esearch and esummary interface to query...

Command error:
  Traceback (most recent call last):
    File "/opt/venv/lib/python3.6/site-packages/pysradb/sraweb.py", line 91, in xml_to_json
      json = xmltodict.parse(xml)["root"]
    File "/opt/venv/lib/python3.6/site-packages/xmltodict.py", line 327, in parse
      parser.Parse(xml_input, True)
  xml.parsers.expat.ExpatError: not well-formed (invalid token): line 1, column 1761
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
      
    File "~/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/src/utils/bin/sra_to_metadata.py", line 90, in <module>
      
      sample_attribute=True
      
    File "/opt/venv/lib/python3.6/site-packages/pysradb/sraweb.py", line 240, in sra_metadata
      
      exps_json[uid] = self.xml_to_json(exps_xml[uid])
      
    File "/opt/venv/lib/python3.6/site-packages/pysradb/sraweb.py", line 93, in xml_to_json
      
      raise RuntimeError("Unable to parse xml: {}".format(xml))
      
  RuntimeError: Unable to parse xml: <root><Summary><Title>GSM3639563: 10x_wing.disc_rep1; Drosophila melanogaster; RNA-Seq</Title><Platform instrument_model="NextSeq 550">ILLUMINA</Platform><Statistics total_runs="1" total_spots="157920657" total_bases="23688098550" total total_size="10433488343" load_done="true" cluster_name="public"/></Summary><Submitter acc="SRA856056" center_name="GEO" contact_name="Gene Expression Omnibus (GEO), NCBI, NLM, NIH, htt" lab_name=""/><Experiment acc="SRX5464686" ver="1" status="public" name="GSM363950x_wig63: 10x_wing.disc_rep1; Drosophila melanogaster; RNA-Seq"/><Study acc="SRP187520" name="Gene expression atlas of a developing tissue by single cell expression correlation analysis"/><Organism taxid="7227" ScientificName="Drosophila melanogaster"/><Sample acc="SRS4438""/><s562" name=""/><Instrument ILLUMINA="NextSeq 550"/><Library_descriptor><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT>                 <PAIRED/>               </LIBRRARY_SARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Larvae were dissected in Schneider's medium in batches of 5 animals (to prevent hypoxia) and transferred into a tube containing Schneider's medium on ice for a maximum time of 30 minutes. To isolate single cells TrypLE (10x) ssue bwas added and the tissue incubated for 15 minutes in a water bath at 37°C , with gentle mixing every 5 minutes. Schneider's medium was then added to the loosened tissue pellets, followed by gentle mechanical dissociation using a P1000 pipette. The cell suspension was μM ct then passed through a 10 μM cell strainer to remove undigested tissue and cell clumps. 10x libraries were prepared according to 10x Genomica instructions accompanying the Single Cell 3' Library & Gel Bead Kit v2 (CG00052_SingleCell3_ReagentKitv2UserGuide_RevD).</LIBibrarrRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA525603</Bioproject><Biosample>SAMN11054382</Biosample></root>

Work dir:
  ~/work/7f/35f7c4c67b309cfc708133f5fa14bd

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Please complete the following information:

• OS: [e.g. CentOS]
• Nextflow Version: [e.g. 20.10.0]
• vsn-pipelines Version: [e.g. 0.26.1]

Additional context
Add any other context about the problem here.