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Use `Prism.plugins.fileHighlight.highlight` instead."),e=!0),Prism.plugins.fileHighlight.highlight.apply(this,arguments)})}(); \ No newline at end of file diff --git a/rnacentral/sequence_search/static/rnacentral/sequence-search/search.py b/rnacentral/sequence_search/static/rnacentral/sequence-search/search.py new file mode 100644 index 000000000..689cdb98e --- /dev/null +++ b/rnacentral/sequence_search/static/rnacentral/sequence-search/search.py @@ -0,0 +1,128 @@ +""" +Copyright [2009-present] EMBL-European Bioinformatics Institute +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +Usage: python search.py [file] [database] +Examples: +python search.py file.fasta # search in all databases +python search.py file.fasta mirbase # search in miRBase only +""" + +import json +import requests +import sys +import time +from Bio import SeqIO +from pathlib import Path + +SERVER = "https://sequence-search.rnacentral.org/" + +def get_sequence_search_result(description, sequence, job_id): + """Poll job status then retrieve all paginated sequence search results.""" + job_status = "pending" + while True: + try: + data = requests.get(SERVER + "api/job-status/" + job_id, timeout=30).json() + job_status = data["status"] + progress = data.get("progress", 0) + except requests.exceptions.RequestException as e: + print("Error checking job status, retrying: {}".format(e)) + time.sleep(10) + continue + + if job_status == "finished": + break + elif job_status in ("error", "not_found"): + print("Search failed for record: {}".format(description)) + return {"job_id": job_id, "status": job_status, "description": description, "sequence": str(sequence)} + else: + print(" {:.0f}% complete...".format(progress)) + time.sleep(10) + + # Fetch results page by page + results = [] + page = 1 + page_size = 100 + hit_count = None + + while True: + try: + url = "{}api/job-results/{}?page={}&page_size={}".format(SERVER, job_id, page, page_size) + data = requests.get(url, timeout=30).json() + except requests.exceptions.RequestException as e: + print("Error fetching results page {} for {}: {}".format(page, description, e)) + break + + if hit_count is None: + hit_count = data.get("hit_count", 0) + + entries = data.get("entries", []) + results.extend(entries) + + if not entries or len(results) >= hit_count: + break + + page += 1 + + return { + "job_id": job_id, + "hits": hit_count or 0, + "status": job_status, + "description": description, + "sequence": str(sequence), + "results": results, + } + + +def main(): + if len(sys.argv) == 1: + print("You must specify the FASTA file") + exit() + elif len(sys.argv) == 2: + filename = sys.argv[1] + database = [] + elif len(sys.argv) == 3: + filename = sys.argv[1] + database = [sys.argv[2]] + else: + print("Usage: python search.py file.fasta [database]") + exit() + + Path("results").mkdir(parents=True, exist_ok=True) + + with open(filename, mode="r") as handle: + for record in SeqIO.parse(handle, "fasta"): + description = record.description + sequence = record.seq + + data = {"databases": database, "sequence": str(sequence)} + post_job = requests.post(SERVER + "api/submit-job", json=data) + + job_id = None + if post_job.status_code == 200: + job_id = post_job.json()["job_id"] + else: + print("Failed to submit job for record:\n{}\n{}".format(description, sequence)) + + if job_id: + result = get_sequence_search_result(description, sequence, job_id) + if result: + hits = result.get("hits", 0) + if hits == 0: + print("No results found for {}".format(description)) + else: + print("Saving {} hit(s) for {}".format(hits, description)) + with open("results/" + description + ".json", "w") as f: + json.dump(result, f) + + +if __name__ == "__main__": + main() diff --git a/rnacentral/sequence_search/templates/api.html b/rnacentral/sequence_search/templates/api.html index 15a948b7e..78bf5eb44 100644 --- a/rnacentral/sequence_search/templates/api.html +++ b/rnacentral/sequence_search/templates/api.html @@ -27,7 +27,8 @@

Overview

API Throttling

- The maximum number of requests from the same IP address is limited to 50 requests per minute. + Job submissions (/api/submit-job) are rate limited to 10 requests per minute per IP address. + There is no rate limit on job status or results endpoints.

@@ -55,14 +56,140 @@

Example script

|-- ...

- - - - - - - -
+ + + 
"""
+Copyright [2009-present] EMBL-European Bioinformatics Institute
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+Usage: python search.py [file] [database]
+Examples:
+python search.py file.fasta               # search in all databases
+python search.py file.fasta mirbase       # search in miRBase only
+"""
+
+import json
+import requests
+import sys
+import time
+from Bio import SeqIO
+from pathlib import Path
+
+SERVER = "https://sequence-search.rnacentral.org/"
+
+def get_sequence_search_result(description, sequence, job_id):
+    """Poll job status then retrieve all paginated sequence search results."""
+    job_status = "pending"
+    while True:
+        try:
+            data = requests.get(SERVER + "api/job-status/" + job_id, timeout=30).json()
+            job_status = data["status"]
+            progress = data.get("progress", 0)
+        except requests.exceptions.RequestException as e:
+            print("Error checking job status, retrying: {}".format(e))
+            time.sleep(10)
+            continue
+
+        if job_status == "finished":
+            break
+        elif job_status in ("error", "not_found"):
+            print("Search failed for record: {}".format(description))
+            return {"job_id": job_id, "status": job_status, "description": description, "sequence": str(sequence)}
+        else:
+            print("  {:.0f}% complete...".format(progress))
+            time.sleep(10)
+
+    # Fetch results page by page
+    results = []
+    page = 1
+    page_size = 100
+    hit_count = None
+
+    while True:
+        try:
+            url = "{}api/job-results/{}?page={}&page_size={}".format(SERVER, job_id, page, page_size)
+            data = requests.get(url, timeout=30).json()
+        except requests.exceptions.RequestException as e:
+            print("Error fetching results page {} for {}: {}".format(page, description, e))
+            break
+
+        if hit_count is None:
+            hit_count = data.get("hit_count", 0)
+
+        entries = data.get("entries", [])
+        results.extend(entries)
+
+        if not entries or len(results) >= hit_count:
+            break
+
+        page += 1
+
+    return {
+        "job_id": job_id,
+        "hits": hit_count or 0,
+        "status": job_status,
+        "description": description,
+        "sequence": str(sequence),
+        "results": results,
+    }
+
+
+def main():
+    if len(sys.argv) == 1:
+        print("You must specify the FASTA file")
+        exit()
+    elif len(sys.argv) == 2:
+        filename = sys.argv[1]
+        database = []
+    elif len(sys.argv) == 3:
+        filename = sys.argv[1]
+        database = [sys.argv[2]]
+    else:
+        print("Usage: python search.py file.fasta [database]")
+        exit()
+
+    Path("results").mkdir(parents=True, exist_ok=True)
+
+    with open(filename, mode="r") as handle:
+        for record in SeqIO.parse(handle, "fasta"):
+            description = record.description
+            sequence = record.seq
+
+            data = {"databases": database, "sequence": str(sequence)}
+            post_job = requests.post(SERVER + "api/submit-job", json=data)
+
+            job_id = None
+            if post_job.status_code == 200:
+                job_id = post_job.json()["job_id"]
+            else:
+                print("Failed to submit job for record:\n{}\n{}".format(description, sequence))
+
+            if job_id:
+                result = get_sequence_search_result(description, sequence, job_id)
+                if result:
+                    hits = result.get("hits", 0)
+                    if hits == 0:
+                        print("No results found for {}".format(description))
+                    else:
+                        print("Saving {} hit(s) for {}".format(hits, description))
+                        with open("results/" + description + ".json", "w") as f:
+                            json.dump(result, f)
+
+
+if __name__ == "__main__":
+    main()
+
+ + + @@ -75,7 +202,7 @@

Swagger

- +