I am fumbling around with Pandas (I want to avoid using Excel, I have very basic knowledge of Pandas and a reasonable of Python), trying to add a column based on another column.
Specifically, I have a column with IDs, and I want to enrich my data by making a HTTP query to an API and using a field in the JSON response:
d['m0'] = pd.read_json(f"http://localhost:3000/{d['id']}")['H']['M0']
What I wanted to say in the above was
take the data from a cell in the column id, run the API query, and put the ['H']['M0'] of the JSON response (a string) into the column m0
What I get is
InvalidURL Traceback (most recent call last)
Cell In[5], line 1
----> 1 d['m0'] = pd.read_json(f"http://localhost:3000/{d['id']}")['H']['M0']
I feel that the way th eURI was built is not correct, i.e. the content of the cell for column id was not used, but rather the whole column:
InvalidURL: URL can't contain control characters. '/0 AA13\n1 BB10\n2
AA13, BB10, ...are the ids in the column
If I understand it correctly, you have various ID values and you want to automate it by fetching the JSON corresponding to that ID and use values from JSON to further populate the dataframe.
I have not seen the structure of your JSON or return type of accessed fields; but I feel that you are looking for following:
d['m0'] = d['id'].apply(lambda id: pd.read_json(f"http://localhost:3000/{id}")['H']['M0'])
Related
So, i'm trying to collect data from an API to make a dataframe. The problems is that that when i get the response in JSON some of the values are missing for some rows. That means that one row has all 10 out of 10 values and some only have 8 out of 10.
For e.g. I have such code to fill in the data from the API to then form a DataFrame:
response = r.json()
cols = ['A', 'B', 'C', 'D']
l = []
for entry in response:
l.append([
entry['realizationreport_id'],
entry['suppliercontract_code'],
entry['rid'],
entry['ppvz_inn'],
I get this error because in one of the rows the API didn't give a value in response:
KeyError: 'ppvz_inn'
So i'm tryng to fix it so that the cell of the DataFrame is filled with 0 or Nan if the API doesn't have a value for this specific row
l = []
for entry in response:
l.append([
entry['realizationreport_id'],
entry['suppliercontract_code'],
entry['rid'],
entry['ppvz_inn'],
try:
entry['ppvz_supplier_name'],
except KeyError:
'0',
And now i get this error:
try:
^
SyntaxError: invalid syntax
How to actually make it work and fill those cells with no data?
You cannot have a try-except statement in the middle of your append statement.
You could either work with if statements or first try to fix your JSON data by filling in empty values. You could also maybe use setdefault, see here some info about it.
Use collections.defaultdict. It's a subclass of dict which does not return KeyError, creating a called key instead.
You can cast your existing dict to defaultdict using unpacking.
for entry in response:
entry_defaultdict = defaultdict(list, **entry)
In this case, every call to non-existing object will create an empty list as a value of the key.
I'm working on a personal project and very new (learning as I go) to JSON, NiFi, SQL, etc., so forgive any confusing language used here or a potentially really obvious solution. I can clarify as needed.
I need to take the JSON output from a website's API call and insert it into a table in my MariaDB local server that I've set up. The issue is that the JSON data is nested, and two of the key pieces of data that I need to insert are used as variable key objects rather than values, so I don't know how to extract it and put it in the database table. Essentially, I think I need to identify different pieces of the JSON expression and insert them as values, but I'm clueless how to do so.
I've played around with the EvaluateJSON, SplitJSON, and FlattenJSON processors in particular, but I can't make it work. All I can ever do is get the result of the whole expression, rather than each piece of it.
{"5381":{"wind_speed":4.0,"tm_st_snp":26.0,"tm_off_snp":74.0,"tm_def_snp":63.0,"temperature":58.0,"st_snp":8.0,"punts":4.0,"punt_yds":178.0,"punt_lng":55.0,"punt_in_20":1.0,"punt_avg":44.5,"humidity":47.0,"gp":1.0,"gms_active":1.0},
"1023":{"wind_speed":4.0,"tm_st_snp":26.0,"tm_off_snp":82.0,"tm_def_snp":56.0,"temperature":74.0,"off_snp":82.0,"humidity":66.0,"gs":1.0,"gp":1.0,"gms_active":1.0},
"5300":{"wind_speed":17.0,"tm_st_snp":27.0,"tm_off_snp":80.0,"tm_def_snp":64.0,"temperature":64.0,"st_snp":21.0,"pts_std":9.0,"pts_ppr":9.0,"pts_half_ppr":9.0,"idp_tkl_solo":4.0,"idp_tkl_loss":1.0,"idp_tkl":4.0,"idp_sack":1.0,"idp_qb_hit":2.0,"humidity":100.0,"gp":1.0,"gms_active":1.0,"def_snp":23.0},
"608":{"wind_speed":6.0,"tm_st_snp":20.0,"tm_off_snp":53.0,"tm_def_snp":79.0,"temperature":88.0,"st_snp":4.0,"pts_std":5.5,"pts_ppr":5.5,"pts_half_ppr":5.5,"idp_tkl_solo":4.0,"idp_tkl_loss":1.0,"idp_tkl_ast":1.0,"idp_tkl":5.0,"humidity":78.0,"gs":1.0,"gp":1.0,"gms_active":1.0,"def_snp":56.0},
"3396":{"wind_speed":6.0,"tm_st_snp":20.0,"tm_off_snp":60.0,"tm_def_snp":70.0,"temperature":63.0,"st_snp":19.0,"off_snp":13.0,"humidity":100.0,"gp":1.0,"gms_active":1.0}}
This is a snapshot of an output with a couple thousand lines. Each of the numeric keys that you see above (5381, 1023, 5300, etc) are player IDs for the following stats. I have a table set up with three columns: Player ID, Stat ID, and Stat Value. For example, I need that first snippet to be inserted into my table as such:
Player ID Stat ID Stat Value
5381 wind_speed 4.0
5381 tm_st_snp 26.0
5381 tm_off_snp 74.0
And so on, for each piece of data. But I don't know how to have NiFi select the right pieces of data to insert in the right columns.
I believe that it's possible to use jolt to transform your json into a format:
[
{"playerId":"5381", "statId":"wind_speed", "statValue": 0.123},
{"playerId":"5381", "statId":"tm_st_snp", "statValue": 0.456},
...
]
then use PutDatabaseRecord with json reader.
Another approach is to use ExecuteGroovyScript processor.
Add new parameter to it with name SQL.mydb and link it to your DBCP controller service
And use the following script as Script Body parameter:
import groovy.json.JsonSlurper
import groovy.json.JsonBuilder
def ff=session.get()
if(!ff)return
//read flow file content and parse it
def body = ff.read().withReader("UTF-8"){reader->
new JsonSlurper().parse(reader)
}
def results = []
//use defined sql connection to create a batch
SQL.mydb.withTransaction{
def cmd = 'insert into mytable(playerId, statId, statValue) values(?,?,?)'
results = SQL.mydb.withBatch(100, cmd){statement->
//run through all keys/subkeys in flow file body
body.each{pid,keys->
keys.each{k,v->
statement.addBatch(pid,k,v)
}
}
}
}
//write results as a new flow file content
ff.write("UTF-8"){writer->
new JsonBuilder(results).writeTo(writer)
}
//transfer to success
REL_SUCCESS << ff
I have an Excel file in which are given more then 2000 organisms, where each one of them has a Bioproject ID associated (like PRJNA12997). The idea is to use these IDs to get the sequence for a later multiple alignment with other five sequences that I have in a text file.
Can anyone help me understand how I can do this using biopython? At least the part with the bioproject ID.
You can first get the info using Bio.Entrez:
from Bio import Entrez
Entrez.email = "Your.Name.Here#example.org"
# This call to efetch fails sometimes with a 400 error.
handle = Entrez.efetch(db="bioproject", id="PRJNA12997")
I've been trying, and Entrez.read(handle) doesn't seems to work. But if you do record_xml = handle.read() you'll get the XML entry for this record. In this XML you can get the ID for the organism, in this case 12997.
handle = Entrez.esearch(db="nuccore", term="12997[BioProject]")
search_results = Entrez.read(handle)
Now you can efecth from your search results. At this point you should use Biopython to parse whatever you will get in the efetch step, playing with the rettype http://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/
for result in search_results["IdList"]:
entry = Entrez.efetch(db="nuccore", id=result, rettype="fasta")
this_seq_in_fasta = entry.read()
I have a CSV file with 3 columns: tweetid , tweet, and Userid. However within the tweet column there are comma separated values.
i.e. of 1 row of data:
`396124437168537600`,"I really wish I didn't give up everything I did for you, I'm so mad at my self for even letting it get as far as it did.",savava143
I want to extract all 3 fields individually, but REGEX_EXTRACT is giving me an error with this code:
a = LOAD tweets USING PigStorage(',') AS (f1,f2,f3);
b = FILTER a BY REGEX_EXTRACT(f1,'(.*)\\"(.*)',1);
The error is:
error: Filter's condition must evaluate to boolean.
In the use case shared, reading the data using PigStrorage(',') will result in missing savava143 (last field value)
A = LOAD '/Users/muralirao/learning/pig/a.csv' USING PigStorage(',') AS (f1,f2,f3);
DUMP A;
Output : A : Observe that the last field value is missing.
(396124437168537600,"I really wish I didn't give up everything I did for you, I'm so mad at my self for even letting it get as far as it did.")
For the use case shared, to extract all the values from CSV file with field values having ',' we can use either CSVExcelStorage or CSVLoader.
Approach 1 : Using CSVExcelStorage
Ref : http://pig.apache.org/docs/r0.12.0/api/org/apache/pig/piggybank/storage/CSVExcelStorage.html
Input : a.csv
396124437168537600,"I really wish I didn't give up everything I did for you, I'm so mad at my self for even letting it get as far as it did.",savava143
Pig Script :
REGISTER piggybank.jar;
A = LOAD 'a.csv' USING org.apache.pig.piggybank.storage.CSVExcelStorage() AS (f1,f2,f3);
DUMP A;
Output : A
(396124437168537600,I really wish I didn't give up everything I did for you, I'm so mad at my self for even letting it get as far as it did.,savava143)
Approach 2 : Using CSVLoader
Ref : http://pig.apache.org/docs/r0.9.1/api/org/apache/pig/piggybank/storage/CSVLoader.html
Below script makes use of CSVLoader(), DUMP A will result in the same output seen earlier.
A = LOAD 'a.csv' USING org.apache.pig.piggybank.storage.CSVLoader() AS (f1,f2,f3);
The error is that you do not want to FILTER based on a regex but GENERATE new fields based on a regex. To filter, you need to know if the line have to be filtered, hence the boolean requirement.
Therefore, you have to use :
b = FOREACH a GENERATE REGEX_EXTRACT(FIELD, REGEX, HOW_MANY_GROUPS_TO_RETURN);
However, as #Murali Rao said, your values are not just coma separated but CSV (think how you will handle a coma in tweet : it is not a field separator, just some content).
We have a weekly backup process which exports our production Google Appengine Datastore onto Google Cloud Storage, and then into Google BigQuery. Each week, we create a new dataset named like YYYY_MM_DD that contains a copy of the production tables on that day. Over time, we have collected many datasets, like 2014_05_10, 2014_05_17, etc. I want to create a data set Latest_Production_Data that contains a view for each of the tables in the most recent YYYY_MM_DD dataset. This will make it easier for downstream reports to write their query once and always retrieve the most recent data.
To do this, I have code that gets the most recent dataset and the names of all the tables that dataset contains from the BigQuery API. Then, for each of these tables, I fire a tables.insert call to create a view that is a SELECT * from the table I am looking to create a reference to.
This fails for tables that contain a RECORD field, from what looks to be a pretty benign column-naming rule.
For example, I have this table:
For which I issue this API call:
{
'tableReference': {
'projectId': 'redacted',
'tableId': u'AccountDeletionRequest',
'datasetId': 'Latest_Production_Data'
}
'view': {
'query': u'SELECT * FROM [2014_05_17.AccountDeletionRequest]'
},
}
This results in the following error:
HttpError: https://www.googleapis.com/bigquery/v2/projects//datasets/Latest_Production_Data/tables?alt=json returned "Invalid field name "__key__.namespace". Fields must contain only letters, numbers, and underscores, start with a letter or underscore, and be at most 128 characters long.">
When I execute this query in the BigQuery web console, the columns are renamed to translate the . to an _. I kind of expected the same thing to happen when I issued the create view API call.
Is there an easy way I can programmatically create a view for each of the tables in my dataset, regardless of their underlying schema? The problem I'm encountering now is for record columns, but another problem I anticipate is for tables that have repeated fields. Is there some magic alternative to SELECT * that will take care of all these intricacies for me?
Another idea I had was doing a table copy, but I would prefer not to duplicate the data if I can at all avoid it.
Here is the workaround code I wrote to dynamically generate a SELECT statement for each of the tables:
def get_leaf_column_selectors(dataset, table):
schema = table_service.get(
projectId=BQ_PROJECT_ID,
datasetId=dataset,
tableId=table
).execute()['schema']
return ",\n".join([
_get_leaf_selectors("", top_field)
for top_field in schema["fields"]
])
def _get_leaf_selectors(prefix, field):
if prefix:
format = prefix + ".%s"
else:
format = "%s"
if 'fields' not in field:
# Base case
actual_name = format % field["name"]
safe_name = actual_name.replace(".", "_")
return "%s as %s" % (actual_name, safe_name)
else:
# Recursive case
return ",\n".join([
_get_leaf_selectors(format % field["name"], sub_field)
for sub_field in field["fields"]
])
We had a bug where you needed to need to select out the individual fields in the view and use an 'as' to rename the fields to something legal (i.e they don't have '.' in the name).
The bug is now fixed, so you shouldn't see this issue any more. Please ping this thread or start a new question if you see it again.