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How to pull metadata from SRA based on Run id?

I have a lot of SRR ids. I got this code line -->

esearch \
  -db sra \
  -query SRR1751234 | \
efetch \
  -format runinfo \
  -mode xml | \
xtract \
  -pattern SraRunInfo \
  -element BioProject BioSample Modelesearch \
  -db sra \
  -query SRR1751234 | \
efetch \
  -format runinfo \
  -mode xml | \
xtract \
  -pattern SraRunInfo \
  -element BioProject BioSample Model

Output like this -->>

PRJNA186035 SAMN02345261 Illumina MiSeq

But I also need collection date,country. Can anyone help me? I need command line which can read my srr ids file and give the summary of that attributes.

metadata sra

Please don't get used to opening multiple questions on the same topic. Keep it focused in a single one: sra data

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