Ecollect

ecollect

EDirect query-source normalizer and PubMed SOLR workaround wrapper. It can count matching PubMed records, return a limited eSearchResult subset, or emit a deduplicated UID list from query, history, inline IDs, raw rest data, or input files.

Quick Start

• Command: ecollect
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/ecollect
• Prerequisite: network access to NCBI EUtils for query and history-based modes

When To Use This Tool

• Turn -query, -id, -input, -rest, or history-server state (-web / -key) into a normalized UID list.
• Use PubMed-specific -count or -subset helper modes when working around large-result SOLR behavior.
• Deduplicate identifiers before sending them to downstream efetch, esummary, or other EDirect stages.
• Preserve an EDirect shell workflow instead of writing your own UID-expansion logic around EUtils.

Common Patterns

# 1) Ask PubMed for just the count of matching records
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
ecollect -db pubmed -count 'BRCA1[Title]'

# 2) Retrieve a small eSearchResult XML subset for inspection
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
ecollect -db pubmed -subset 'BRCA1[Title]' -retmax 3

# 3) Normalize explicit IDs into a deduplicated UID list
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
ecollect -db pubmed -id 7 3 7 1

Recommended Workflow

1. Decide which source mode you are using: PubMed query, explicit IDs, input file, raw rest payload, or history-server coordinates.
2. Always set -db first so the wrapper knows which downstream semantics to apply.
3. Use -count or -subset only when you specifically want PubMed query introspection; use the normal path when you want a final UID list.
4. Inspect a small sample before bulk fetches, especially if you also apply date filters or rely on history-server state.

Guardrails

• -db is mandatory. Bare invocation or incomplete argument sets fail with ERROR: Missing -db argument.
• -help is not a real help switch. The live result is ERROR: Unrecognized argument -help followed by the missing -db complaint.
• The wrapper appends its own bin directory to PATH and sources ecommon.sh, so behavior here is broader than a single network call.
• -count and -subset are specialized PubMed SOLR workaround modes, not generic options for every Entrez database.
• Final UID output is deduplicated through sort -n | uniq, so original order is not preserved.
• -tranquil suppresses the usual No items found warning/retry handling. That is useful for expected-empty searches but easy to misuse if you need loud failures.