extract-codebases-from-paper

Extract all tools and approaches from a survey paper, then clone their public codebases for later analysis.

Inputs

The user provides a path to a survey PDF, e.g.:

papers/surveys/Wang2024.pdf

Derive the paper key from the filename (e.g., Wang2024).

Output files

evaluation/papers/<PaperKey>.md — tool inventory (inside the thesis repo)
../extracted-codebases/<tool-name>/ — cloned repositories (outside the thesis repo, to keep it clean)

Never modify my_paper/text.md or any other existing file in the thesis repo.

Procedure

Step 1 — Read the paper

Read the PDF:

Read: <provided path>

If it is a large PDF (>10 pages), read in page ranges of 20 pages at a time until the full paper is covered. Always read the full references section — it contains author names, paper titles, venues, and sometimes artifact URLs that are needed for the search step.

Step 2 — Extract tools

Identify every tool, approach, prototype, or system studied or surveyed in the paper. For each one, record:

Name — exact name as used in the paper
Description — one sentence summary of what it does
Paper title — full title of the paper that introduces or describes the tool (from the reference list)
Authors — author list as it appears in the reference
Venue + Year — conference/journal name and year of publication
Repository URL — any GitHub/GitLab/Bitbucket URL explicitly mentioned in the paper or its references. If none is given, mark as none and proceed to Step 3.5.
Reference — the citation marker as it appears in the paper (e.g., “[42]”)

Step 3 — Ensure the extraction directory exists

mkdir -p ../extracted-codebases

Step 3.5 — Proactive repo search for tools without an explicit URL

For every tool where no repository URL was found in the paper, run the following staged search using curl and python3. Use GIT_ASKPASS=false GIT_TERMINAL_PROMPT=0 for all git operations. Run searches in parallel where possible.

Stage A — GitHub API search

Run all three queries and collect candidates:

Search by tool name:

curl -s "https://api.github.com/search/repositories?q=<ToolName>+microservice&per_page=10"

Search by paper title keywords (3–5 distinctive words from the title):

curl -s "https://api.github.com/search/repositories?q=<title-keywords>+in:name,description&per_page=10"

Search by first author’s GitHub account — try username variations (firstnamelastname, firstname-lastname, flastname) using the users endpoint, then list their public repos:
```
curl -s "https://api.github.com/users/<username-variant>/repos?per_page=50"
```

Parse all results with python3 -c "import sys,json; ...". Filter candidates by: description or name contains tool-related keywords, language matches expected (Java/Python), creation date roughly matches or postdates the paper year.

Stage B — Known research group namespaces

If the paper mentions an author affiliation or lab name, try that as a GitHub org:

curl -s "https://api.github.com/orgs/<org-name>/repos?per_page=50"

Also try common academic/industrial orgs that publish microservice tools (e.g. konveyor, IBM, sosygroup, resess).

Stage C — Fetch artifact/replication pages

If the paper’s reference list contains any URL that is not a direct repo link (e.g., a project page, a GitHub Pages site, or a DOI with supplementary material), fetch it:

curl -s "<url>" | grep -oE 'https://github\.com/[^"' ]+' | sort -u

Extract any GitHub/GitLab URLs found in the page HTML.

Evaluating candidates:

A candidate repo is accepted if at least one of these holds:

Its description or README explicitly mentions the tool name or paper title
It is owned by a confirmed author account and its name/description relates to microservice decomposition
It is linked from the paper’s own artifact page

If a candidate is plausible but unconfirmed, record the URL and mark status as unverified — check manually. If no candidate survives the filter, mark the tool as no public repo found.

Step 4 — Clone available repositories

For each tool that has a confirmed or unverified repository URL:

export GIT_ASKPASS=false GIT_TERMINAL_PROMPT=0
git clone --depth=1 <url> ../extracted-codebases/<tool-name>

Use --depth=1 to avoid downloading full history. If the clone fails (private repo, dead link, etc.), record the failure reason.

After a successful clone, record the commit hash:

git -C ../extracted-codebases/<tool-name> rev-parse HEAD

Step 5 — Write the tool inventory

Write evaluation/papers/<PaperKey>.md with the following structure:

# Tool Inventory — <PaperKey>

Extracted from: <paper path>
Date: <today's date>

## Tools

| Tool | Paper | Authors | Venue | Year | Repo URL | Local Path | Status |
|------|-------|---------|-------|------|----------|------------|--------|
| ToolName | Full paper title | Author1, Author2, ... | ICSE | 2023 | https://... or none found | ../extracted-codebases/tool-name | cloned / failed: <reason> / unverified — check manually / no public repo found |

## Notes

Any relevant notes about the survey scope, exclusions, or ambiguities.

Step 6 — Report to the user

Summarise:

Total tools found
How many were cloned successfully
How many were found but unverified (need manual check)
How many had no public repository despite the search
How many failed (with reasons)
Path to the inventory file and the extraction directory

For tools where no repo was found, list them explicitly with their full reference so the user can search manually:

No repo found for:

HyDec — “Combining Static and Dynamic Analysis to Decompose Monolithic Application into Microservices”, Sellami et al., ICSOC 2022

Log2MS — “Log2MS: …”, Liu et al., ICWS 2022

Reference files

references/feature-model-dimensions.md — the feature model schema (for context on what to look for in tools)